+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/local/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/cgatools-1.8.0.1/work.log
+ su pbulk -c '"$@"' make /opt/local/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/cgatools-1.8.0.1/work.log
WARNING: USE_CMAKE is deprecated; use devel/cmake/build.mk instead.
===> Building for cgatools-1.8.0.1
[ 1%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvSegmentStore.hpp.cpp.o
[ 1%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/CnvDetailStore.hpp.cpp.o
[ 1%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/CnvDetailStore.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RangeAnnotationStore.hpp:26,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/CnvSegmentStore.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/CnvSegmentStore.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::getMaxDepth() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::doGetDepth(const Node*, size_t&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RangeAnnotationStore.hpp:26,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/CnvDetailStore.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/CnvDetailStore.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RangeAnnotationStore.hpp:26,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/CnvDetailStore.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:20:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::getMaxDepth() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::doGetDepth(const Node*, size_t&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::getMaxDepth() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::doGetDepth(const Node*, size_t&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp: In member function 'void cgatools::cgdata::CnvDetailStore::bindColumns(cgatools::util::DelimitedFile&, cgatools::reference::Range&, cgatools::cgdata::CnvDetailData&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:37:9: note: in expansion of macro 'CGA_ASSERT'
37 | CGA_ASSERT(df.getMetadata().hasKey("WINDOW_WIDTH"));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:37:9: note: in expansion of macro 'CGA_ASSERT'
37 | CGA_ASSERT(df.getMetadata().hasKey("WINDOW_WIDTH"));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp: In member function 'void cgatools::cgdata::CnvDetailStore::trimTree()':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:129:13: note: in expansion of macro 'CGA_ASSERT'
129 | CGA_ASSERT(r.first.begin_ >= contig.begin_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:129:13: note: in expansion of macro 'CGA_ASSERT'
129 | CGA_ASSERT(r.first.begin_ >= contig.begin_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:132:13: note: in expansion of macro 'CGA_ASSERT'
132 | CGA_ASSERT(r.first.end_<=contig.end_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:132:13: note: in expansion of macro 'CGA_ASSERT'
132 | CGA_ASSERT(r.first.end_<=contig.end_);
| ^~~~~~~~~~
[ 1%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/Dnb.hpp.cpp.o
[ 2%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/EvidenceReader.hpp.cpp.o
[ 2%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/GenomeMetadata.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<double>]':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::reference::RangeAnnotationStore<cgatools::cgdata::CnvDetailStore, cgatools::cgdata::CnvDetailData>::MidpointField<unsigned int>]':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::StringField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::reference::ChromosomeIdField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::reference::ChromosomeIdField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::reference::ChromosomeIdField]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<unsigned int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned int>]':
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp: In member function 'void cgatools::cgdata::CnvDetailStore::bindColumns(cgatools::util::DelimitedFile&, cgatools::reference::Range&, cgatools::cgdata::CnvDetailData&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:37:9: note: in expansion of macro 'CGA_ASSERT'
37 | CGA_ASSERT(df.getMetadata().hasKey("WINDOW_WIDTH"));
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/EvidenceReader.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(std::size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const',
inlined from 'const cgatools::cgdata::CnvDetailData* cgatools::cgdata::CnvDetailStore::getBestOverlappingDetail(const cgatools::reference::Range&) const' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:96:39:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In member function 'const cgatools::cgdata::CnvDetailData* cgatools::cgdata::CnvDetailStore::getBestOverlappingDetail(const cgatools::reference::Range&) const':
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp: In member function 'void cgatools::cgdata::CnvDetailStore::trimTree()':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:132:13: note: in expansion of macro 'CGA_ASSERT'
132 | CGA_ASSERT(r.first.end_<=contig.end_);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvDetailStore.cpp:129:13: note: in expansion of macro 'CGA_ASSERT'
129 | CGA_ASSERT(r.first.begin_ >= contig.begin_);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
[ 3%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/CnvSegmentStore.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
[ 4%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/LibraryReader.hpp.cpp.o
[ 4%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/cgdata/ReferenceSupportReader.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RangeAnnotationStore.hpp:26,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/CnvSegmentStore.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvSegmentStore.cpp:19:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::getMaxDepth() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::doGetDepth(const Node*, size_t&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 5%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/CallDiff.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/ReferenceSupportReader.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/cgdata/ReferenceSupportReader.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<double>]':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::reference::ChromosomeIdField]':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::StringField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<unsigned int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned int>]':
cc1plus: note: source object is likely at address zero
[ 6%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Command.hpp.cpp.o
In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const',
inlined from 'const cgatools::cgdata::CnvSegmentData* cgatools::cgdata::CnvSegmentStore::getBestOverlappingSegment(const cgatools::reference::Range&) const' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/CnvSegmentStore.cpp:86:39:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In member function 'const cgatools::cgdata::CnvSegmentData* cgatools::cgdata::CnvSegmentStore::getBestOverlappingSegment(const cgatools::reference::Range&) const':
cc1plus: note: source object is likely at address zero
[ 6%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/Dnb.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Locus.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/CallDiff.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/CallDiff.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
[ 6%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Crr2Fasta.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/Dnb.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:16:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(std::size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 7%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/DecodeCrr.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp: In member function 'void cgatools::cgdata::LibRecord::initParser(cgatools::util::DelimitedFile&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:34:9: note: in expansion of macro 'CGA_ASSERT'
34 | CGA_ASSERT(delimitedFile.getDelimitedLineParser().getFields().size()==7);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:34:9: note: in expansion of macro 'CGA_ASSERT'
34 | CGA_ASSERT(delimitedFile.getDelimitedLineParser().getFields().size()==7);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:42:9: note: in expansion of macro 'CGA_ASSERT'
42 | CGA_ASSERT(delimitedFile.getDelimitedLineParser().getFields().size()==7);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:42:9: note: in expansion of macro 'CGA_ASSERT'
42 | CGA_ASSERT(delimitedFile.getDelimitedLineParser().getFields().size()==7);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp: In member function 'void cgatools::cgdata::DnbStructure::init(cgatools::util::DelimitedFile&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:68:17: note: in expansion of macro 'CGA_ASSERT_MSG'
68 | CGA_ASSERT_MSG(record.objInArm_<4, CGA_VOUT(record.objInArm_));
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:68:17: note: in expansion of macro 'CGA_ASSERT_MSG'
68 | CGA_ASSERT_MSG(record.objInArm_<4, CGA_VOUT(record.objInArm_));
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:71:17: note: in expansion of macro 'CGA_ASSERT_MSG'
71 | CGA_ASSERT_MSG(record.maxSize_==record.minSize_,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:71:17: note: in expansion of macro 'CGA_ASSERT_MSG'
71 | CGA_ASSERT_MSG(record.maxSize_==record.minSize_,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:76:17: note: in expansion of macro 'CGA_ASSERT_MSG'
76 | CGA_ASSERT_MSG(record.objInArm_<4, CGA_VOUT(record.objInArm_));
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:76:17: note: in expansion of macro 'CGA_ASSERT_MSG'
76 | CGA_ASSERT_MSG(record.objInArm_<4, CGA_VOUT(record.objInArm_));
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:81:17: note: in expansion of macro 'CGA_ASSERT_MSG'
81 | CGA_ASSERT_MSG(record.minSize_<=record.maxSize_,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:81:17: note: in expansion of macro 'CGA_ASSERT_MSG'
81 | CGA_ASSERT_MSG(record.minSize_<=record.maxSize_,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:87:13: note: in expansion of macro 'CGA_ASSERT_EQ'
87 | CGA_ASSERT_EQ(h.gaps_.size()+1,h.reads_.size());
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:87:13: note: in expansion of macro 'CGA_ASSERT_EQ'
87 | CGA_ASSERT_EQ(h.gaps_.size()+1,h.reads_.size());
| ^~~~~~~~~~~~~
[ 7%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Cache.hpp.cpp.o
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<long unsigned int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<long unsigned int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<long unsigned int>]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<int>]':
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp: In member function 'void cgatools::cgdata::LibRecord::initParser(cgatools::util::DelimitedFile&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:42:9: note: in expansion of macro 'CGA_ASSERT'
42 | CGA_ASSERT(delimitedFile.getDelimitedLineParser().getFields().size()==7);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::StringField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'void cgatools::cgdata::LibRecord::initParser(cgatools::util::DelimitedFile&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:36:31:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::cgdata::LibRecord::initParser(cgatools::util::DelimitedFile&)':
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:34:9: note: in expansion of macro 'CGA_ASSERT'
34 | CGA_ASSERT(delimitedFile.getDelimitedLineParser().getFields().size()==7);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp: In member function 'void cgatools::cgdata::DnbStructure::init(cgatools::util::DelimitedFile&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:87:13: note: in expansion of macro 'CGA_ASSERT_EQ'
87 | CGA_ASSERT_EQ(h.gaps_.size()+1,h.reads_.size());
| ^~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:71:17: note: in expansion of macro 'CGA_ASSERT_MSG'
71 | CGA_ASSERT_MSG(record.maxSize_==record.minSize_,
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:68:17: note: in expansion of macro 'CGA_ASSERT_MSG'
68 | CGA_ASSERT_MSG(record.objInArm_<4, CGA_VOUT(record.objInArm_));
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:81:17: note: in expansion of macro 'CGA_ASSERT_MSG'
81 | CGA_ASSERT_MSG(record.minSize_<=record.maxSize_,
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/Dnb.cpp:76:17: note: in expansion of macro 'CGA_ASSERT_MSG'
76 | CGA_ASSERT_MSG(record.objInArm_<4, CGA_VOUT(record.objInArm_));
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/DecodeCrr.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/DecodeCrr.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 8%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/EvidenceReader.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/Evidence2Cache.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Evidence2Cache.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 9%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Evidence2Sam.hpp.cpp.o
[ 9%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Fasta2Crr.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:16:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 10%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Join.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp: In member function 'bool cgatools::cgdata::EvidenceReader::IntervalRecord::isCompatible(cgatools::uint16_t, const cgatools::reference::Range&, const std::string&, bool) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:148:13: note: in expansion of macro 'CGA_ASSERT'
148 | CGA_ASSERT(alignOffset < alignment.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:148:13: note: in expansion of macro 'CGA_ASSERT'
148 | CGA_ASSERT(alignOffset < alignment.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:162:17: note: in expansion of macro 'CGA_ASSERT'
162 | CGA_ASSERT(false);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:162:17: note: in expansion of macro 'CGA_ASSERT'
162 | CGA_ASSERT(false);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:198:17: note: in expansion of macro 'CGA_ASSERT'
198 | CGA_ASSERT(false);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:198:17: note: in expansion of macro 'CGA_ASSERT'
198 | CGA_ASSERT(false);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp: In member function 'std::string cgatools::cgdata::EvidenceReader::IntervalRecord::getAlignment(size_t) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:210:9: note: in expansion of macro 'CGA_ASSERT'
210 | CGA_ASSERT(alleleIndex <= alleleAlignments_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:210:9: note: in expansion of macro 'CGA_ASSERT'
210 | CGA_ASSERT(alleleIndex <= alleleAlignments_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp: In member function 'cgatools::uint32_t cgatools::cgdata::EvidenceReader::countSupportingDnbs(cgatools::uint16_t, cgatools::int32_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:441:9: note: in expansion of macro 'CGA_ASSERT'
441 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:441:9: note: in expansion of macro 'CGA_ASSERT'
441 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp: In member function 'void cgatools::cgdata::EvidenceReader::openDnbs()':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:484:9: note: in expansion of macro 'CGA_ASSERT'
484 | CGA_ASSERT(inInterval());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:484:9: note: in expansion of macro 'CGA_ASSERT'
484 | CGA_ASSERT(inInterval());
| ^~~~~~~~~~
[ 10%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Junction2Vcf.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/Join.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Join.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 11%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionCmp.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp: In function 'std::string cgatools::cgdata::EvidenceReader::IntervalRecord::getAlignment(size_t) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:210:9: note: in expansion of macro 'CGA_ASSERT'
210 | CGA_ASSERT(alleleIndex <= alleleAlignments_.size());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<short unsigned int>]':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::reference::ChromosomeIdField]':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<int>]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<unsigned int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned int>]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::StringField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::cgdata::EvidenceScoreField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::cgdata::EvidenceScoreField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'static void cgatools::cgdata::EvidenceReader::IntervalRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::IntervalRecord&, const cgatools::reference::CrrFile&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:252:28:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In static member function 'static void cgatools::cgdata::EvidenceReader::IntervalRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::IntervalRecord&, const cgatools::reference::CrrFile&)':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::cgdata::AlleleIndexesField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::cgdata::AlleleIndexesField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'static void cgatools::cgdata::EvidenceReader::IntervalRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::IntervalRecord&, const cgatools::reference::CrrFile&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:260:24:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In static member function 'static void cgatools::cgdata::EvidenceReader::IntervalRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::IntervalRecord&, const cgatools::reference::CrrFile&)':
cc1plus: note: source object is likely at address zero
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/Junction2Vcf.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/Junction2Vcf.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp: In member function 'bool cgatools::cgdata::EvidenceReader::IntervalRecord::isCompatible(cgatools::uint16_t, const cgatools::reference::Range&, const std::string&, bool) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:198:17: note: in expansion of macro 'CGA_ASSERT'
198 | CGA_ASSERT(false);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:162:17: note: in expansion of macro 'CGA_ASSERT'
162 | CGA_ASSERT(false);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:148:13: note: in expansion of macro 'CGA_ASSERT'
148 | CGA_ASSERT(alignOffset < alignment.size());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp: In constructor 'cgatools::junctions::CompareJunctionsBySide::CompareJunctionsBySide(int)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::CharField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::CharField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'static void cgatools::cgdata::EvidenceReader::DnbRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::DnbRecord&, const cgatools::reference::CrrFile&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:355:24:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In static member function 'static void cgatools::cgdata::EvidenceReader::DnbRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::DnbRecord&, const cgatools::reference::CrrFile&)':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::StrandField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StrandField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'static void cgatools::cgdata::EvidenceReader::DnbRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::DnbRecord&, const cgatools::reference::CrrFile&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:341:24:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In static member function 'static void cgatools::cgdata::EvidenceReader::DnbRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::DnbRecord&, const cgatools::reference::CrrFile&)':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::SideField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::SideField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'static void cgatools::cgdata::EvidenceReader::DnbRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::DnbRecord&, const cgatools::reference::CrrFile&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:340:24:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In static member function 'static void cgatools::cgdata::EvidenceReader::DnbRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::DnbRecord&, const cgatools::reference::CrrFile&)':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<unsigned char>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned char>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'static void cgatools::cgdata::EvidenceReader::DnbRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::DnbRecord&, const cgatools::reference::CrrFile&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:338:24:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In static member function 'static void cgatools::cgdata::EvidenceReader::DnbRecord::bindToParser(cgatools::util::DelimitedFile&, cgatools::cgdata::EvidenceReader::DnbRecord&, const cgatools::reference::CrrFile&)':
cc1plus: note: source object is likely at address zero
[ 12%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionDiff.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp: In member function 'void cgatools::cgdata::EvidenceReader::openDnbs()':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:484:9: note: in expansion of macro 'CGA_ASSERT'
484 | CGA_ASSERT(inInterval());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
[ 12%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/JunctionType.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp: In member function 'cgatools::uint32_t cgatools::cgdata::EvidenceReader::countSupportingDnbs(cgatools::uint16_t, cgatools::int32_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/EvidenceReader.cpp:441:9: note: in expansion of macro 'CGA_ASSERT'
441 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
[ 12%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/GenomeMetadata.cpp.o
[ 13%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListCrr.hpp.cpp.o
[ 13%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/ListVariants.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/GenomeMetadata.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 14%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Map2Sam.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/ListVariants.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/ListVariants.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 14%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MergedMap2Sam.hpp.cpp.o
[ 15%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/MkVcf.hpp.cpp.o
[ 16%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/Sam2Reads.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/MkVcf.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/MkVcf.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 16%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/SnpDiff.hpp.cpp.o
[ 17%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/TestVariants.hpp.cpp.o
[ 17%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFileCombine.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/VariantFileIterator.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/TestVariants.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/TestVariants.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/VarFileCombine.hpp:25,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/command/VarFileCombine.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 18%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/command/VarFilter.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 19%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/LibraryReader.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
[ 19%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/conv/VcfRecordSource.hpp.cpp.o
[ 20%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/copynumber/CnvFileVcfSource.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/LibraryReader.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/conv/VcfRecordSource.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/conv/VcfRecordSource.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/conv/VcfRecordSource.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/copynumber/CnvFileVcfSource.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/copynumber/CnvFileVcfSource.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 20%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/core.hpp.cpp.o
[ 21%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/Junction.hpp.cpp.o
[ 22%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionCompare.hpp.cpp.o
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<double>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<double>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<double>]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'void cgatools::cgdata::GapTable<T>::load(const std::string&) [with T = int]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/LibraryReader.cpp:54:20:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::cgdata::GapTable<T>::load(const std::string&) [with T = int]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::DelimitedField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::DelimitedField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'void cgatools::cgdata::GapTable<T>::load(const std::string&) [with T = boost::array<signed char, 3>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/LibraryReader.cpp:38:20:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::cgdata::GapTable<T>::load(const std::string&) [with T = boost::array<signed char, 3>]':
cc1plus: note: source object is likely at address zero
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:30,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/Junction.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 22%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/ReferenceSupportReader.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:30,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionCompare.hpp:24,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionCompare.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp: In constructor 'cgatools::junctions::CompareJunctionsBySide::CompareJunctionsBySide(int)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp: In constructor 'cgatools::junctions::CompareJunctionsBySide::CompareJunctionsBySide(int)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
[ 22%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionStat.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::addRange(const Index&, const Index&, const Index&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::merge(const my_type&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::SimpleHistogram::operator+=(const cgatools::util::SimpleHistogram&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/ReferenceSupportReader.cpp:16:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 23%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfRecord.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:30,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionStat.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionStat.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp: In constructor 'cgatools::junctions::CompareJunctionsBySide::CompareJunctionsBySide(int)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::addRange(const Index&, const Index&, const Index&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::merge(const my_type&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::SimpleHistogram::operator+=(const cgatools::util::SimpleHistogram&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionStat.hpp: In member function 'Type& cgatools::junctions::CounterSet<Fields, Type>::operator[](size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:89:37: note: in expansion of macro 'CGA_ASSERT_MSG'
89 | #define CGA_ASSERT_L(var1,var2) CGA_ASSERT_MSG((var1)<(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionStat.hpp:78:38: note: in expansion of macro 'CGA_ASSERT_L'
78 | Type &operator[] (size_t i) {CGA_ASSERT_L(i,values_.size()); return values_[i];}
| ^~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:89:37: note: in expansion of macro 'CGA_ASSERT_MSG'
89 | #define CGA_ASSERT_L(var1,var2) CGA_ASSERT_MSG((var1)<(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionStat.hpp:78:38: note: in expansion of macro 'CGA_ASSERT_L'
78 | Type &operator[] (size_t i) {CGA_ASSERT_L(i,values_.size()); return values_[i];}
| ^~~~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:30,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionVcfRecord.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionVcfRecord.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<int>]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<unsigned int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'cgatools::cgdata::ReferenceSupportReader::File::File(const std::string&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/cgdata/ReferenceSupportReader.cpp:36:25:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In constructor 'cgatools::cgdata::ReferenceSupportReader::File::File(const std::string&)':
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp: In constructor 'cgatools::junctions::CompareJunctionsBySide::CompareJunctionsBySide(int)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
[ 24%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/CallDiff.cpp.o
[ 24%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/junctions/JunctionVcfWriter.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::addRange(const Index&, const Index&, const Index&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::merge(const my_type&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::SimpleHistogram::operator+=(const cgatools::util::SimpleHistogram&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
[ 25%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mainpage.hpp.cpp.o
[ 25%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/AlleleAlignment.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:30,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionVcfWriter.hpp:24,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/junctions/JunctionVcfWriter.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp: In constructor 'cgatools::junctions::CompareJunctionsBySide::CompareJunctionsBySide(int)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::addRange(const Index&, const Index&, const Index&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::merge(const my_type&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::SimpleHistogram::operator+=(const cgatools::util::SimpleHistogram&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/AlleleAlignment.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'void cgatools::command::ScoreToCumulative::finishInit(bool)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:296:17: note: in expansion of macro 'CGA_ASSERT'
296 | CGA_ASSERT(data_.begin()->second > .999);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:296:17: note: in expansion of macro 'CGA_ASSERT'
296 | CGA_ASSERT(data_.begin()->second > .999);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:297:17: note: in expansion of macro 'CGA_ASSERT'
297 | CGA_ASSERT(data_.begin()->second < 1.001);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:297:17: note: in expansion of macro 'CGA_ASSERT'
297 | CGA_ASSERT(data_.begin()->second < 1.001);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'double cgatools::command::RecalibratedSomaticScoreCalc::CalibratedScoreHist::getSomaticScore(cgatools::int32_t, cgatools::int32_t, cgatools::int32_t, cgatools::int32_t) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:465:17: note: in expansion of macro 'CGA_ASSERT'
465 | CGA_ASSERT(0 != rs_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:465:17: note: in expansion of macro 'CGA_ASSERT'
465 | CGA_ASSERT(0 != rs_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In constructor 'cgatools::command::RecalibratedSomaticScoreCalc::RecalibratedSomaticScoreCalc(const std::string&, const std::string&, const std::string&, bool, const cgatools::command::ScoreHist&, const cgatools::command::ScoreHist&, const cgatools::reference::CrrFile&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:573:17: note: in expansion of macro 'CGA_ASSERT'
573 | CGA_ASSERT(false);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:573:17: note: in expansion of macro 'CGA_ASSERT'
573 | CGA_ASSERT(false);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'void cgatools::command::SomaticScoreCalc::processLocus(cgatools::uint32_t, const cgatools::variants::Locus&, const cgatools::variants::VariantFileIterator&, const std::string&, const std::vector<cgatools::variants::cdmt::MatchType>&, size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:868:13: note: in expansion of macro 'CGA_ASSERT'
868 | CGA_ASSERT(0 != call);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:868:13: note: in expansion of macro 'CGA_ASSERT'
868 | CGA_ASSERT(0 != call);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 26%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Cigar.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'void cgatools::command::MafReport::annotateByGeneFile(std::string)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:1375:25: note: in expansion of macro 'CGA_ASSERT'
1375 | CGA_ASSERT(itGid != rec.entrezGeneId_.end());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:1375:25: note: in expansion of macro 'CGA_ASSERT'
1375 | CGA_ASSERT(itGid != rec.entrezGeneId_.end());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'const char* cgatools::command::MafReport::vcToString(VariantClassification) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:1525:17: note: in expansion of macro 'CGA_ASSERT'
1525 | CGA_ASSERT(false);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:1525:17: note: in expansion of macro 'CGA_ASSERT'
1525 | CGA_ASSERT(false);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'void cgatools::command::MafReport::orderRangesForMaf(std::vector<cgatools::reference::Range>&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:1591:17: note: in expansion of macro 'CGA_ASSERT'
1591 | CGA_ASSERT(ranges[to].chromosome_ == ranges[from].chromosome_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:1591:17: note: in expansion of macro 'CGA_ASSERT'
1591 | CGA_ASSERT(ranges[to].chromosome_ == ranges[from].chromosome_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'bool cgatools::command::MafReport::addAlleleCountAnnotation(const cgatools::variants::Call&, MafRecord&, size_t, size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:1821:29: note: in expansion of macro 'CGA_ASSERT'
1821 | CGA_ASSERT(!aiIsRef[2]);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:1821:29: note: in expansion of macro 'CGA_ASSERT'
1821 | CGA_ASSERT(!aiIsRef[2]);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:1827:29: note: in expansion of macro 'CGA_ASSERT'
1827 | CGA_ASSERT(aiIsRef[2]);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:1827:29: note: in expansion of macro 'CGA_ASSERT'
1827 | CGA_ASSERT(aiIsRef[2]);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'virtual int cgatools::command::CallDiff::run(boost::program_options::variables_map&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:2257:13: note: in expansion of macro 'CGA_ASSERT'
2257 | CGA_ASSERT(hypotheses.size() == 2);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:2257:13: note: in expansion of macro 'CGA_ASSERT'
2257 | CGA_ASSERT(hypotheses.size() == 2);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'void cgatools::command::CallDiff::dumpSuperlocusStats(std::ostream&, SuperlocusStats&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:2633:13: note: in expansion of macro 'CGA_ASSERT'
2633 | CGA_ASSERT(std::find(simpleCategories.begin(), simpleCategories.end(), cat) !=
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:2633:13: note: in expansion of macro 'CGA_ASSERT'
2633 | CGA_ASSERT(std::find(simpleCategories.begin(), simpleCategories.end(), cat) !=
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp: In constructor 'cgatools::mapping::DnbSequenceIterator::DnbSequenceIterator(const std::string&, size_t, int, bool)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:90:38: note: in expansion of macro 'CGA_ASSERT_MSG'
90 | #define CGA_ASSERT_LE(var1,var2) CGA_ASSERT_MSG((var1)<=(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp:88:9: note: in expansion of macro 'CGA_ASSERT_LE'
88 | CGA_ASSERT_LE(0,position_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:90:38: note: in expansion of macro 'CGA_ASSERT_MSG'
90 | #define CGA_ASSERT_LE(var1,var2) CGA_ASSERT_MSG((var1)<=(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp:88:9: note: in expansion of macro 'CGA_ASSERT_LE'
88 | CGA_ASSERT_LE(0,position_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:89:37: note: in expansion of macro 'CGA_ASSERT_MSG'
89 | #define CGA_ASSERT_L(var1,var2) CGA_ASSERT_MSG((var1)<(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp:89:9: note: in expansion of macro 'CGA_ASSERT_L'
89 | CGA_ASSERT_L(position_,sequence_.size());
| ^~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:89:37: note: in expansion of macro 'CGA_ASSERT_MSG'
89 | #define CGA_ASSERT_L(var1,var2) CGA_ASSERT_MSG((var1)<(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp:89:9: note: in expansion of macro 'CGA_ASSERT_L'
89 | CGA_ASSERT_L(position_,sequence_.size());
| ^~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp: In member function 'char cgatools::mapping::DnbSequenceIterator::operator*() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:90:38: note: in expansion of macro 'CGA_ASSERT_MSG'
90 | #define CGA_ASSERT_LE(var1,var2) CGA_ASSERT_MSG((var1)<=(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp:100:9: note: in expansion of macro 'CGA_ASSERT_LE'
100 | CGA_ASSERT_LE(0,position_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:90:38: note: in expansion of macro 'CGA_ASSERT_MSG'
90 | #define CGA_ASSERT_LE(var1,var2) CGA_ASSERT_MSG((var1)<=(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp:100:9: note: in expansion of macro 'CGA_ASSERT_LE'
100 | CGA_ASSERT_LE(0,position_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:89:37: note: in expansion of macro 'CGA_ASSERT_MSG'
89 | #define CGA_ASSERT_L(var1,var2) CGA_ASSERT_MSG((var1)<(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp:101:9: note: in expansion of macro 'CGA_ASSERT_L'
101 | CGA_ASSERT_L(position_,sequence_.size());
| ^~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:89:37: note: in expansion of macro 'CGA_ASSERT_MSG'
89 | #define CGA_ASSERT_L(var1,var2) CGA_ASSERT_MSG((var1)<(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/AlleleAlignment.hpp:101:9: note: in expansion of macro 'CGA_ASSERT_L'
101 | CGA_ASSERT_L(position_,sequence_.size());
| ^~~~~~~~~~~~
[ 27%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceCache.hpp.cpp.o
[ 27%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/EvidenceSamUtil.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/EvidenceCache.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/EvidenceCache.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(std::size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/EvidenceSamUtil.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/EvidenceSamUtil.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(std::size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
[ 28%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/GapsEstimator.hpp.cpp.o
[ 28%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LaneBatchCache.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/GapsEstimator.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/GapsEstimator.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'void cgatools::command::ScoreToCumulative::finishInit(bool)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:297:17: note: in expansion of macro 'CGA_ASSERT'
297 | CGA_ASSERT(data_.begin()->second < 1.001);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:296:17: note: in expansion of macro 'CGA_ASSERT'
296 | CGA_ASSERT(data_.begin()->second > .999);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'double cgatools::command::RecalibratedSomaticScoreCalc::CalibratedScoreHist::getSomaticScore(cgatools::int32_t, cgatools::int32_t, cgatools::int32_t, cgatools::int32_t) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:465:17: note: in expansion of macro 'CGA_ASSERT'
465 | CGA_ASSERT(0 != rs_);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::StringField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<int>]':
cc1plus: note: source object is likely at address zero
[ 29%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/LibraryData.hpp.cpp.o
[ 29%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/Map2SamConverter.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'void cgatools::command::SomaticScoreCalc::processLocus(cgatools::uint32_t, const cgatools::variants::Locus&, const cgatools::variants::VariantFileIterator&, const std::string&, const std::vector<cgatools::variants::cdmt::MatchType>&, size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:868:13: note: in expansion of macro 'CGA_ASSERT'
868 | CGA_ASSERT(0 != call);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<unsigned int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'void cgatools::command::SomaticScoreCalc::loadVarData(const std::string&, const cgatools::reference::CrrFile&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:714:24:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::command::SomaticScoreCalc::loadVarData(const std::string&, const cgatools::reference::CrrFile&)':
cc1plus: note: source object is likely at address zero
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/Map2SamConverter.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/Map2SamConverter.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In constructor 'cgatools::command::RecalibratedSomaticScoreCalc::RecalibratedSomaticScoreCalc(const std::string&, const std::string&, const std::string&, bool, const cgatools::command::ScoreHist&, const cgatools::command::ScoreHist&, const cgatools::reference::CrrFile&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:573:17: note: in expansion of macro 'CGA_ASSERT'
573 | CGA_ASSERT(false);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp: In member function 'void cgatools::mapping::MappingsFlagParser::setSide(size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:68:39: note: in expansion of macro 'CGA_ASSERT'
68 | void setSide(size_t side) {CGA_ASSERT(side<2); flags_ |= side<<1;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:68:39: note: in expansion of macro 'CGA_ASSERT'
68 | void setSide(size_t side) {CGA_ASSERT(side<2); flags_ |= side<<1;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp: In member function 'void cgatools::mapping::MappingsFlagParser::setStrand(size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:70:43: note: in expansion of macro 'CGA_ASSERT'
70 | void setStrand(size_t strand) {CGA_ASSERT(strand<2); flags_ |= strand<<2;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:70:43: note: in expansion of macro 'CGA_ASSERT'
70 | void setStrand(size_t strand) {CGA_ASSERT(strand<2); flags_ |= strand<<2;}
| ^~~~~~~~~~
[ 30%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MapSamUtils.hpp.cpp.o
[ 30%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/MergeMap2SamConverter.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/MapSamUtils.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp: In member function 'void cgatools::mapping::MappingsFlagParser::setSide(std::size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:68:39: note: in expansion of macro 'CGA_ASSERT'
68 | void setSide(size_t side) {CGA_ASSERT(side<2); flags_ |= side<<1;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:68:39: note: in expansion of macro 'CGA_ASSERT'
68 | void setSide(size_t side) {CGA_ASSERT(side<2); flags_ |= side<<1;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp: In member function 'void cgatools::mapping::MappingsFlagParser::setStrand(std::size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:70:43: note: in expansion of macro 'CGA_ASSERT'
70 | void setStrand(size_t strand) {CGA_ASSERT(strand<2); flags_ |= strand<<2;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:70:43: note: in expansion of macro 'CGA_ASSERT'
70 | void setStrand(size_t strand) {CGA_ASSERT(strand<2); flags_ |= strand<<2;}
| ^~~~~~~~~~
[ 31%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamOptions.hpp.cpp.o
[ 32%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamReader.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'void cgatools::command::CallDiff::dumpSuperlocusStats(std::ostream&, SuperlocusStats&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:2633:13: note: in expansion of macro 'CGA_ASSERT'
2633 | CGA_ASSERT(std::find(simpleCategories.begin(), simpleCategories.end(), cat) !=
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp: In member function 'virtual int cgatools::command::CallDiff::run(boost::program_options::variables_map&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/CallDiff.cpp:2257:13: note: in expansion of macro 'CGA_ASSERT'
2257 | CGA_ASSERT(hypotheses.size() == 2);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/Map2SamConverter.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MergeMap2SamConverter.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/MergeMap2SamConverter.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/SamReader.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mapping/SamReader.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(std::size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/SamReader.hpp: In member function 'const SamTag& cgatools::mapping::SamTags<SamTag>::getTag(const std::string&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/SamReader.hpp:63:9: note: in expansion of macro 'CGA_ASSERT_MSG'
63 | CGA_ASSERT_MSG(it!=samTags_.end(), "The tag '" << t << "' not found.");
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/SamReader.hpp:63:9: note: in expansion of macro 'CGA_ASSERT_MSG'
63 | CGA_ASSERT_MSG(it!=samTags_.end(), "The tag '" << t << "' not found.");
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/SamReader.hpp: In member function 'void cgatools::mapping::SamTagField<SamTag>::parse(const char*, const char*)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/SamReader.hpp:103:9: note: in expansion of macro 'CGA_ASSERT_MSG'
103 | CGA_ASSERT_MSG((!isFirst_) || samTags_.samTags_.empty(), "samTags map was not cleaned");
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/SamReader.hpp:103:9: note: in expansion of macro 'CGA_ASSERT_MSG'
103 | CGA_ASSERT_MSG((!isFirst_) || samTags_.samTags_.empty(), "samTags map was not cleaned");
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/SamReader.hpp: In member function 'const cgatools::mapping::SamFileHeader::Records& cgatools::mapping::SamFileHeader::getRecords(const std::string&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/SamReader.hpp:200:9: note: in expansion of macro 'CGA_ASSERT_MSG'
200 | CGA_ASSERT_MSG(it!=recordMap_.end(), "Section is missing: " << section);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/SamReader.hpp:200:9: note: in expansion of macro 'CGA_ASSERT_MSG'
200 | CGA_ASSERT_MSG(it!=recordMap_.end(), "Section is missing: " << section);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp: In member function 'void cgatools::mapping::MappingsFlagParser::setSide(size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:68:39: note: in expansion of macro 'CGA_ASSERT'
68 | void setSide(size_t side) {CGA_ASSERT(side<2); flags_ |= side<<1;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:68:39: note: in expansion of macro 'CGA_ASSERT'
68 | void setSide(size_t side) {CGA_ASSERT(side<2); flags_ |= side<<1;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp: In member function 'void cgatools::mapping::MappingsFlagParser::setStrand(size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:70:43: note: in expansion of macro 'CGA_ASSERT'
70 | void setStrand(size_t strand) {CGA_ASSERT(strand<2); flags_ |= strand<<2;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:70:43: note: in expansion of macro 'CGA_ASSERT'
70 | void setStrand(size_t strand) {CGA_ASSERT(strand<2); flags_ |= strand<<2;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 32%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mapping/SamRecord.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
[ 33%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Command.cpp.o
[ 34%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/mobileelement/MeiFileVcfSource.hpp.cpp.o
[ 34%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/ChromosomeIdField.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/ChromosomeIdField.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/ChromosomeIdField.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(std::size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/conv/VcfRecordSource.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mobileelement/MeiFileVcfSource.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/mobileelement/MeiFileVcfSource.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 35%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CompactDnaSequence.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp: In constructor 'cgatools::command::DocToken::DocToken(const std::string&, bool)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:230:13: note: in expansion of macro 'CGA_ASSERT'
230 | CGA_ASSERT( (0 == html_.size()) == tab_ );
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:230:13: note: in expansion of macro 'CGA_ASSERT'
230 | CGA_ASSERT( (0 == html_.size()) == tab_ );
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp: In member function 'std::string cgatools::command::DocToken::getText() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:283:17: note: in expansion of macro 'CGA_ASSERT'
283 | CGA_ASSERT(!inTag);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:283:17: note: in expansion of macro 'CGA_ASSERT'
283 | CGA_ASSERT(!inTag);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:287:17: note: in expansion of macro 'CGA_ASSERT'
287 | CGA_ASSERT(inTag);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:287:17: note: in expansion of macro 'CGA_ASSERT'
287 | CGA_ASSERT(inTag);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp: In static member function 'static size_t cgatools::command::DocToken::readEntity(const std::string&, size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:392:9: note: in expansion of macro 'CGA_ASSERT'
392 | CGA_ASSERT(pos < line.size() && '&' == line[pos]);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:392:9: note: in expansion of macro 'CGA_ASSERT'
392 | CGA_ASSERT(pos < line.size() && '&' == line[pos]);
| ^~~~~~~~~~
[ 35%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFile.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/CrrFile.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In constructor 'cgatools::command::DocToken::DocToken(const std::string&, bool)',
inlined from 'cgatools::command::DocToken::DocToken(const std::string&, bool)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:225:9:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:230:13: note: in expansion of macro 'CGA_ASSERT'
230 | CGA_ASSERT( (0 == html_.size()) == tab_ );
| ^~~~~~~~~~
In constructor 'cgatools::command::DocToken::DocToken(const std::string&, bool)':
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp: In static member function 'static size_t cgatools::command::DocToken::readEntity(const std::string&, size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:392:9: note: in expansion of macro 'CGA_ASSERT'
392 | CGA_ASSERT(pos < line.size() && '&' == line[pos]);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp: In member function 'std::string cgatools::command::DocToken::getText() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:287:17: note: in expansion of macro 'CGA_ASSERT'
287 | CGA_ASSERT(inTag);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Command.cpp:283:17: note: in expansion of macro 'CGA_ASSERT'
283 | CGA_ASSERT(!inTag);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
[ 36%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/CrrFileWriter.hpp.cpp.o
[ 37%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/GeneDataStore.hpp.cpp.o
[ 37%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Crr2Fasta.cpp.o
[ 37%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RangeAnnotationStore.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/GeneDataStore.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/GeneDataStore.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'std::size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::getMaxDepth() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'std::size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::doGetDepth(const Node*, std::size_t&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(std::size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 38%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/RepeatMaskerStore.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Crr2Fasta.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RangeAnnotationStore.hpp:26,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/RangeAnnotationStore.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::getMaxDepth() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::doGetDepth(const Node*, size_t&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 38%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/reference/range.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RangeAnnotationStore.hpp:26,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RepeatMaskerStore.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/RepeatMaskerStore.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/reference/range.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::getMaxDepth() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::doGetDepth(const Node*, size_t&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 39%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/BaseUtil.hpp.cpp.o
[ 39%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedFile.hpp.cpp.o
[ 40%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/DelimitedLineParser.hpp.cpp.o
[ 41%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/DecodeCrr.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/DelimitedFile.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(std::size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/DelimitedLineParser.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(std::size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 41%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Exception.hpp.cpp.o
[ 42%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Files.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/DecodeCrr.cpp:16:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 43%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/GenericHistogram.hpp.cpp.o
[ 43%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/IndirectComparator.hpp.cpp.o
[ 44%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Md5.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/GenericHistogram.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::addRange(const Index&, const Index&, const Index&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::merge(const my_type&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::SimpleHistogram::operator+=(const cgatools::util::SimpleHistogram&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
[ 44%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeIntersector.hpp.cpp.o
[ 45%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/RangeSet.hpp.cpp.o
[ 45%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Evidence2Cache.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/util/RangeIntersector.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'std::size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::getMaxDepth() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'std::size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::doGetDepth(const Node*, std::size_t&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
[ 45%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/Streams.hpp.cpp.o
[ 46%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/StringSet.hpp.cpp.o
[ 47%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/util/parse.hpp.cpp.o
[ 47%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Allele.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/Evidence2Cache.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Cache.cpp:16:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 48%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/AlleleDiffSegment.hpp.cpp.o
[ 48%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Call.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Allele.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Allele.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Cache.cpp: In member function 'void cgatools::command::Evidence2CacheConfig::init()':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Cache.cpp:78:9: note: in expansion of macro 'CGA_ASSERT'
78 | CGA_ASSERT(!referenceFileName_.empty());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Cache.cpp:78:9: note: in expansion of macro 'CGA_ASSERT'
78 | CGA_ASSERT(!referenceFileName_.empty());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Call.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 49%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffMatchType.hpp.cpp.o
[ 49%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/CallDiffResult.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 50%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Locus.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/CallDiffResult.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/CallDiffResult.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Cache.cpp:78:9: note: in expansion of macro 'CGA_ASSERT'
78 | CGA_ASSERT(!referenceFileName_.empty());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Locus.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Locus.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
[ 51%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Evidence2Sam.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
[ 51%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedAllele.hpp.cpp.o
[ 52%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/PhasedHypothesis.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/PhasedAllele.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/PhasedAllele.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/EvidenceSamUtil.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/PhasedAllele.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/PhasedHypothesis.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/PhasedHypothesis.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'void cgatools::command::EvidenceDnbBuffer::removeLastInterval(cgatools::int32_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:114:13: note: in expansion of macro 'CGA_ASSERT'
114 | CGA_ASSERT(!intervals_.empty());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:114:13: note: in expansion of macro 'CGA_ASSERT'
114 | CGA_ASSERT(!intervals_.empty());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:115:13: note: in expansion of macro 'CGA_ASSERT_EQ'
115 | CGA_ASSERT_EQ(intervals_.front().id_,intervalId);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:115:13: note: in expansion of macro 'CGA_ASSERT_EQ'
115 | CGA_ASSERT_EQ(intervals_.front().id_,intervalId);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'std::__cxx11::list<cgatools::mapping::EvidenceDnbRecord>::iterator cgatools::command::EvidenceDnbBuffer::removeMappingRecord(std::__cxx11::list<cgatools::mapping::EvidenceDnbRecord>::iterator)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:127:13: note: in expansion of macro 'CGA_ASSERT_MSG'
127 | CGA_ASSERT_MSG(it!=evidenceDnbIndex_.end(),"corrupted evidenceDnbIndex_");
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:127:13: note: in expansion of macro 'CGA_ASSERT_MSG'
127 | CGA_ASSERT_MSG(it!=evidenceDnbIndex_.end(),"corrupted evidenceDnbIndex_");
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:129:17: note: in expansion of macro 'CGA_ASSERT_MSG'
129 | CGA_ASSERT_MSG(it!=evidenceDnbIndex_.end() && it->first == dnbId,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:129:17: note: in expansion of macro 'CGA_ASSERT_MSG'
129 | CGA_ASSERT_MSG(it!=evidenceDnbIndex_.end() && it->first == dnbId,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'void cgatools::command::EvidenceDnbBuffer::findDnbRecordsOfTheSameDnb(std::__cxx11::list<cgatools::mapping::EvidenceDnbRecord>::iterator&, EvidenceDnbSet&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:140:13: note: in expansion of macro 'CGA_ASSERT_MSG'
140 | CGA_ASSERT_MSG(it!=evidenceDnbIndex_.end(),"corrupted evidenceDnbIndex_");
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:140:13: note: in expansion of macro 'CGA_ASSERT_MSG'
140 | CGA_ASSERT_MSG(it!=evidenceDnbIndex_.end(),"corrupted evidenceDnbIndex_");
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'bool cgatools::command::EvidenceDnbBuffer::empty() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:147:13: note: in expansion of macro 'CGA_ASSERT_EQ'
147 | CGA_ASSERT_EQ(evidenceDnbs_.empty(),evidenceDnbIndex_.empty());
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:147:13: note: in expansion of macro 'CGA_ASSERT_EQ'
147 | CGA_ASSERT_EQ(evidenceDnbs_.empty(),evidenceDnbIndex_.empty());
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In constructor 'cgatools::command::FullMappingRange::FullMappingRange(cgatools::mapping::EvidenceDnbRecord&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:179:13: note: in expansion of macro 'CGA_ASSERT_MSG'
179 | CGA_ASSERT_MSG(armRanges_[0]<=armRanges_[1],
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:179:13: note: in expansion of macro 'CGA_ASSERT_MSG'
179 | CGA_ASSERT_MSG(armRanges_[0]<=armRanges_[1],
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:181:13: note: in expansion of macro 'CGA_ASSERT_MSG'
181 | CGA_ASSERT_MSG(armRanges_[2]<=armRanges_[3],
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:181:13: note: in expansion of macro 'CGA_ASSERT_MSG'
181 | CGA_ASSERT_MSG(armRanges_[2]<=armRanges_[3],
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'void cgatools::command::Evidence2SamConverter::processIntervals(cgatools::mapping::EvidenceDnbRecord&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:333:17: note: in expansion of macro 'CGA_ASSERT_MSG'
333 | CGA_ASSERT_MSG(it->intervalId_ >= interval.id_,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:333:17: note: in expansion of macro 'CGA_ASSERT_MSG'
333 | CGA_ASSERT_MSG(it->intervalId_ >= interval.id_,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:338:21: note: in expansion of macro 'CGA_ASSERT'
338 | CGA_ASSERT(!dnbSet.empty());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:338:21: note: in expansion of macro 'CGA_ASSERT'
338 | CGA_ASSERT(!dnbSet.empty());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'void cgatools::command::Evidence2SamConverter::init()':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:556:17: note: in expansion of macro 'CGA_ASSERT_MSG'
556 | CGA_ASSERT_MSG(!config_.outputFileName_.empty(),"The output file name must be provided");
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:556:17: note: in expansion of macro 'CGA_ASSERT_MSG'
556 | CGA_ASSERT_MSG(!config_.outputFileName_.empty(),"The output file name must be provided");
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'const cgatools::reference::CompactDnaSequence& cgatools::command::Evidence2SamConverter::getChrSequence(const std::string&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:570:13: note: in expansion of macro 'CGA_ASSERT_EQ'
570 | CGA_ASSERT_EQ(chrSequence_->getName(),chrName);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:570:13: note: in expansion of macro 'CGA_ASSERT_EQ'
570 | CGA_ASSERT_EQ(chrSequence_->getName(),chrName);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
[ 53%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/Superlocus.hpp.cpp.o
[ 53%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/SuperlocusIterator.hpp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/PhasedAllele.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/PhasedHypothesis.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Superlocus.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/Superlocus.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/PhasedAllele.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/PhasedHypothesis.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Superlocus.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/SuperlocusIterator.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/SuperlocusIterator.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
[ 54%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileIterator.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'bool cgatools::command::EvidenceDnbBuffer::empty() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:147:13: note: in expansion of macro 'CGA_ASSERT_EQ'
147 | CGA_ASSERT_EQ(evidenceDnbs_.empty(),evidenceDnbIndex_.empty());
| ^~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In constructor 'cgatools::command::FullMappingRange::FullMappingRange(cgatools::mapping::EvidenceDnbRecord&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:181:13: note: in expansion of macro 'CGA_ASSERT_MSG'
181 | CGA_ASSERT_MSG(armRanges_[2]<=armRanges_[3],
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:179:13: note: in expansion of macro 'CGA_ASSERT_MSG'
179 | CGA_ASSERT_MSG(armRanges_[0]<=armRanges_[1],
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'void cgatools::command::Evidence2SamConverter::init()':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:556:17: note: in expansion of macro 'CGA_ASSERT_MSG'
556 | CGA_ASSERT_MSG(!config_.outputFileName_.empty(),"The output file name must be provided");
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
[ 54%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/VariantFileVcfSource.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'std::__cxx11::list<cgatools::mapping::EvidenceDnbRecord>::iterator cgatools::command::EvidenceDnbBuffer::removeMappingRecord(std::__cxx11::list<cgatools::mapping::EvidenceDnbRecord>::iterator)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:129:17: note: in expansion of macro 'CGA_ASSERT_MSG'
129 | CGA_ASSERT_MSG(it!=evidenceDnbIndex_.end() && it->first == dnbId,
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:127:13: note: in expansion of macro 'CGA_ASSERT_MSG'
127 | CGA_ASSERT_MSG(it!=evidenceDnbIndex_.end(),"corrupted evidenceDnbIndex_");
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'void cgatools::command::EvidenceDnbBuffer::removeLastInterval(cgatools::int32_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:115:13: note: in expansion of macro 'CGA_ASSERT_EQ'
115 | CGA_ASSERT_EQ(intervals_.front().id_,intervalId);
| ^~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:114:13: note: in expansion of macro 'CGA_ASSERT'
114 | CGA_ASSERT(!intervals_.empty());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp: In member function 'void cgatools::command::Evidence2SamConverter::processIntervals(cgatools::mapping::EvidenceDnbRecord&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:338:21: note: in expansion of macro 'CGA_ASSERT'
338 | CGA_ASSERT(!dnbSet.empty());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In member function 'void cgatools::command::EvidenceDnbBuffer::findDnbRecordsOfTheSameDnb(std::__cxx11::list<cgatools::mapping::EvidenceDnbRecord>::iterator&, EvidenceDnbSet&)',
inlined from 'void cgatools::command::Evidence2SamConverter::processIntervals(cgatools::mapping::EvidenceDnbRecord&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:337:60:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:140:13: note: in expansion of macro 'CGA_ASSERT_MSG'
140 | CGA_ASSERT_MSG(it!=evidenceDnbIndex_.end(),"corrupted evidenceDnbIndex_");
| ^~~~~~~~~~~~~~
In member function 'void cgatools::command::Evidence2SamConverter::processIntervals(cgatools::mapping::EvidenceDnbRecord&)':
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Evidence2Sam.cpp:333:17: note: in expansion of macro 'CGA_ASSERT_MSG'
333 | CGA_ASSERT_MSG(it->intervalId_ >= interval.id_,
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/VariantFileIterator.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/VariantFileIterator.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(std::size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/conv/VcfRecordSource.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/VariantFileVcfSource.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build/smoketest/cgatools/variants/VariantFileVcfSource.hpp.cpp:15:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 54%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Fasta2Crr.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
[ 55%] Building CXX object smoketest/CMakeFiles/cgatoolscompileheader.dir/cgatools/variants/calib/CalibratedScorer.hpp.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
[ 56%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Join.cpp.o
[ 56%] Linking CXX static library libcgatoolscompileheader.a
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Fasta2Crr.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
[ 56%] Built target cgatoolscompileheader
[ 56%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Junction2Vcf.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/Join.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:16:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::getMaxDepth() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::doGetDepth(const Node*, size_t&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp: In member function 'std::string cgatools::command::CompactPctJoinOutputStream::getPctOverlapString(const std::pair<long int, long int>&, std::vector<std::pair<long int, long int> >&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:357:17: note: in expansion of macro 'CGA_ASSERT'
357 | CGA_ASSERT(rangeB.first <= rangeA.second);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:357:17: note: in expansion of macro 'CGA_ASSERT'
357 | CGA_ASSERT(rangeB.first <= rangeA.second);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:358:17: note: in expansion of macro 'CGA_ASSERT'
358 | CGA_ASSERT(rangeA.first <= rangeB.second);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:358:17: note: in expansion of macro 'CGA_ASSERT'
358 | CGA_ASSERT(rangeA.first <= rangeB.second);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp: In member function 'virtual int cgatools::command::Join::run(boost::program_options::variables_map&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:536:17: note: in expansion of macro 'CGA_ASSERT'
536 | CGA_ASSERT(overlap >= 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:536:17: note: in expansion of macro 'CGA_ASSERT'
536 | CGA_ASSERT(overlap >= 0);
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/Junction2Vcf.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Junction2Vcf.cpp:16:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp: In constructor 'cgatools::junctions::CompareJunctionsBySide::CompareJunctionsBySide(int)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::addRange(const Index&, const Index&, const Index&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::merge(const my_type&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::SimpleHistogram::operator+=(const cgatools::util::SimpleHistogram&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
[ 57%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/JunctionCmp.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionCmp.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp: In constructor 'cgatools::junctions::CompareJunctionsBySide::CompareJunctionsBySide(int)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionVcfWriter.hpp:25,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Junction2Vcf.cpp:17:
In constructor 'cgatools::junctions::JunctionRef::JunctionRef(cgatools::junctions::JunctionRef&&)',
inlined from 'void std::__new_allocator<_Tp>::construct(_Up*, _Args&& ...) [with _Up = cgatools::junctions::JunctionRef; _Args = {cgatools::junctions::JunctionRef}; _Tp = cgatools::junctions::JunctionRef]' at /opt/local/gcc13/include/c++/13.3.0/bits/new_allocator.h:191:4,
inlined from 'static void std::allocator_traits<std::allocator<_CharT> >::construct(allocator_type&, _Up*, _Args&& ...) [with _Up = cgatools::junctions::JunctionRef; _Args = {cgatools::junctions::JunctionRef}; _Tp = cgatools::junctions::JunctionRef]' at /opt/local/gcc13/include/c++/13.3.0/bits/alloc_traits.h:538:17,
inlined from 'std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::emplace_back(_Args&& ...) [with _Args = {cgatools::junctions::JunctionRef}; _Tp = cgatools::junctions::JunctionRef; _Alloc = std::allocator<cgatools::junctions::JunctionRef>]' at /opt/local/gcc13/include/c++/13.3.0/bits/vector.tcc:117:30,
inlined from 'void std::vector<_Tp, _Alloc>::push_back(value_type&&) [with _Tp = cgatools::junctions::JunctionRef; _Alloc = std::allocator<cgatools::junctions::JunctionRef>]' at /opt/local/gcc13/include/c++/13.3.0/bits/stl_vector.h:1299:21,
inlined from 'void cgatools::junctions::JunctionRefs::addJunctions(const cgatools::junctions::Junctions&, cgatools::uint32_t)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionCompare.hpp:110:26,
inlined from 'cgatools::junctions::JunctionRefs::JunctionRefs(const cgatools::junctions::Junctions&, cgatools::uint32_t)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionCompare.hpp:104:25,
inlined from 'void cgatools::command::Junction2Vcf::saveVcf(std::ostream&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Junction2Vcf.cpp:92:71:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionCompare.hpp:40:11: warning: '<unnamed>.cgatools::junctions::JunctionRef::sourceId_' may be used uninitialized [-Wmaybe-uninitialized]
40 | class JunctionRef
| ^~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionCompare.hpp: In member function 'void cgatools::command::Junction2Vcf::saveVcf(std::ostream&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionCompare.hpp:110:26: note: '<anonymous>' declared here
110 | push_back(it);
| ~~~~~~~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::addRange(const Index&, const Index&, const Index&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::merge(const my_type&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::SimpleHistogram::operator+=(const cgatools::util::SimpleHistogram&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionStat.hpp: In member function 'Type& cgatools::junctions::CounterSet<Fields, Type>::operator[](size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:89:37: note: in expansion of macro 'CGA_ASSERT_MSG'
89 | #define CGA_ASSERT_L(var1,var2) CGA_ASSERT_MSG((var1)<(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionStat.hpp:78:38: note: in expansion of macro 'CGA_ASSERT_L'
78 | Type &operator[] (size_t i) {CGA_ASSERT_L(i,values_.size()); return values_[i];}
| ^~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:89:37: note: in expansion of macro 'CGA_ASSERT_MSG'
89 | #define CGA_ASSERT_L(var1,var2) CGA_ASSERT_MSG((var1)<(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionStat.hpp:78:38: note: in expansion of macro 'CGA_ASSERT_L'
78 | Type &operator[] (size_t i) {CGA_ASSERT_L(i,values_.size()); return values_[i];}
| ^~~~~~~~~~~~
In member function 'std::string cgatools::command::CompactPctJoinOutputStream::getPctOverlapString(const std::pair<long int, long int>&, std::vector<std::pair<long int, long int> >&)',
inlined from 'virtual void cgatools::command::CompactPctJoinOutputStream::finishRecord(const std::vector<std::__cxx11::basic_string<char> >&, const std::pair<long int, long int>&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:330:60:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:358:17: note: in expansion of macro 'CGA_ASSERT'
358 | CGA_ASSERT(rangeA.first <= rangeB.second);
| ^~~~~~~~~~
In member function 'virtual void cgatools::command::CompactPctJoinOutputStream::finishRecord(const std::vector<std::__cxx11::basic_string<char> >&, const std::pair<long int, long int>&)':
cc1plus: note: source object is likely at address zero
In member function 'std::string cgatools::command::CompactPctJoinOutputStream::getPctOverlapString(const std::pair<long int, long int>&, std::vector<std::pair<long int, long int> >&)',
inlined from 'virtual void cgatools::command::CompactPctJoinOutputStream::finishRecord(const std::vector<std::__cxx11::basic_string<char> >&, const std::pair<long int, long int>&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:330:60:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:357:17: note: in expansion of macro 'CGA_ASSERT'
357 | CGA_ASSERT(rangeB.first <= rangeA.second);
| ^~~~~~~~~~
In member function 'virtual void cgatools::command::CompactPctJoinOutputStream::finishRecord(const std::vector<std::__cxx11::basic_string<char> >&, const std::pair<long int, long int>&)':
cc1plus: note: source object is likely at address zero
[ 58%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/JunctionDiff.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp: In member function 'virtual int cgatools::command::Join::run(boost::program_options::variables_map&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Join.cpp:536:17: note: in expansion of macro 'CGA_ASSERT'
536 | CGA_ASSERT(overlap >= 0);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
[ 58%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/JunctionType.cpp.o
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/parse.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionDiff.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp: In constructor 'cgatools::junctions::CompareJunctionsBySide::CompareJunctionsBySide(int)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::addRange(const Index&, const Index&, const Index&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::GenericHistogram<Value, Index>::merge(const my_type&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:98:13: note: in expansion of macro 'CGA_ASSERT_MSG'
98 | CGA_ASSERT_MSG(src.buckets_.size()==buckets_.size(),
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:104:17: note: in expansion of macro 'CGA_ASSERT_MSG'
104 | CGA_ASSERT_MSG(srcObj.first == myObj.first,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In member function 'void cgatools::util::SimpleHistogram::operator+=(const cgatools::util::SimpleHistogram&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:173:13: note: in expansion of macro 'CGA_ASSERT'
173 | CGA_ASSERT(other.count_.size() == count_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionStat.hpp: In member function 'Type& cgatools::junctions::CounterSet<Fields, Type>::operator[](size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:89:37: note: in expansion of macro 'CGA_ASSERT_MSG'
89 | #define CGA_ASSERT_L(var1,var2) CGA_ASSERT_MSG((var1)<(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionStat.hpp:78:38: note: in expansion of macro 'CGA_ASSERT_L'
78 | Type &operator[] (size_t i) {CGA_ASSERT_L(i,values_.size()); return values_[i];}
| ^~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:89:37: note: in expansion of macro 'CGA_ASSERT_MSG'
89 | #define CGA_ASSERT_L(var1,var2) CGA_ASSERT_MSG((var1)<(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/JunctionStat.hpp:78:38: note: in expansion of macro 'CGA_ASSERT_L'
78 | Type &operator[] (size_t i) {CGA_ASSERT_L(i,values_.size()); return values_[i];}
| ^~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp: In function 'void cgatools::util::GenericHistogram<Value, Index>::addRange(const Index&, const Index&, const Index&) [with Value = long unsigned int; Index = long unsigned int]':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/GenericHistogram.hpp:55:13: note: in expansion of macro 'CGA_ASSERT_MSG'
55 | CGA_ASSERT_MSG(bucketSize<bucketSize+bucketSize,"Invalid bucket size:"<<bucketSize);
| ^~~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:25:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::getMaxDepth() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:146:13: note: in expansion of macro 'CGA_ASSERT'
146 | CGA_ASSERT(size_ == sz);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:147:13: note: in expansion of macro 'CGA_ASSERT'
147 | CGA_ASSERT(0 == root_ || depth > 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp: In member function 'size_t cgatools::util::IntervalTree<TRange, TBoundary, TValue, Overlap, GetBoundary, BoundaryLess>::doGetDepth(const Node*, size_t&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:282:13: note: in expansion of macro 'CGA_ASSERT'
282 | CGA_ASSERT(!h->right_ || h->left_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:284:13: note: in expansion of macro 'CGA_ASSERT'
284 | CGA_ASSERT(!boundaryLess_(h->rmax_, getBoundary_(h->key(), 1)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:286:17: note: in expansion of macro 'CGA_ASSERT'
286 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->left_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:288:17: note: in expansion of macro 'CGA_ASSERT'
288 | CGA_ASSERT(!boundaryLess_(h->rmax_, h->right_->rmax_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:290:13: note: in expansion of macro 'CGA_ASSERT'
290 | CGA_ASSERT(!isRed(h->right_));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/RangeIntersector.hpp:291:13: note: in expansion of macro 'CGA_ASSERT'
291 | CGA_ASSERT(!(isRed(h->left_) && isRed(h->left_->left_)));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp: In constructor 'cgatools::junctions::CompareJunctionsBySide::CompareJunctionsBySide(int)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/junctions/Junction.hpp:177:13: note: in expansion of macro 'CGA_ASSERT_MSG'
177 | CGA_ASSERT_MSG(side==JUNCTION_LEFT_SIDE || side>=JUNCTION_RIGHT_SIDE,
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In function 'cgatools::reference::Range cgatools::command::{anonymous}::junctionRange(const cgatools::junctions::Junction&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:119:9: note: in expansion of macro 'CGA_ASSERT'
119 | CGA_ASSERT(r.begin_ <= r.end_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:119:9: note: in expansion of macro 'CGA_ASSERT'
119 | CGA_ASSERT(r.begin_ <= r.end_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In function 'int cgatools::command::{anonymous}::junctionStrandChange(const cgatools::junctions::Junction&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:183:9: note: in expansion of macro 'CGA_ASSERT'
183 | CGA_ASSERT(jj.sideSections_[0].strand_ != JUNCTION_UNKNOWN_STRAND);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:183:9: note: in expansion of macro 'CGA_ASSERT'
183 | CGA_ASSERT(jj.sideSections_[0].strand_ != JUNCTION_UNKNOWN_STRAND);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:184:9: note: in expansion of macro 'CGA_ASSERT'
184 | CGA_ASSERT(jj.sideSections_[1].strand_ != JUNCTION_UNKNOWN_STRAND);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:184:9: note: in expansion of macro 'CGA_ASSERT'
184 | CGA_ASSERT(jj.sideSections_[1].strand_ != JUNCTION_UNKNOWN_STRAND);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In function 'void cgatools::command::{anonymous}::findPair(const cgatools::junctions::Junction&, int, const LocationJunctionMap&, cgatools::int32_t, cgatools::int32_t, std::vector<ContigCopyEvent>&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:274:9: note: in expansion of macro 'CGA_ASSERT'
274 | CGA_ASSERT(p != others.end()); // we must find at least "start" itself
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:274:9: note: in expansion of macro 'CGA_ASSERT'
274 | CGA_ASSERT(p != others.end()); // we must find at least "start" itself
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In member function 'const cgatools::command::{anonymous}::RelatedJunctionGraph::RelatedJunctions& cgatools::command::{anonymous}::RelatedJunctionGraph::relatedJunctions(const std::string&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:419:13: note: in expansion of macro 'CGA_ASSERT'
419 | CGA_ASSERT(r != related_.end());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:419:13: note: in expansion of macro 'CGA_ASSERT'
419 | CGA_ASSERT(r != related_.end());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In static member function 'static void cgatools::command::{anonymous}::RelatedJunctionGraph::findNeighbors(const cgatools::junctions::Junction&, const cgatools::command::{anonymous}::LocationJunctionMap&, int, RelatedJunctions&, size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:456:17: note: in expansion of macro 'CGA_ASSERT'
456 | CGA_ASSERT(pos != locMap.end());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:456:17: note: in expansion of macro 'CGA_ASSERT'
456 | CGA_ASSERT(pos != locMap.end());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:465:25: note: in expansion of macro 'CGA_ASSERT'
465 | CGA_ASSERT(distance >= 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:465:25: note: in expansion of macro 'CGA_ASSERT'
465 | CGA_ASSERT(distance >= 0);
| ^~~~~~~~~~
[ 59%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/ListCrr.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In function 'bool cgatools::command::{anonymous}::pairedToSameJunction(const std::vector<ContigCopyEvent>&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:542:9: note: in expansion of macro 'CGA_ASSERT'
542 | CGA_ASSERT(!evts.empty());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:542:9: note: in expansion of macro 'CGA_ASSERT'
542 | CGA_ASSERT(!evts.empty());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:546:13: note: in expansion of macro 'CGA_ASSERT'
546 | CGA_ASSERT(evts.front().a_ == evts[ii].a_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:546:13: note: in expansion of macro 'CGA_ASSERT'
546 | CGA_ASSERT(evts.front().a_ == evts[ii].a_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In function 'bool cgatools::command::{anonymous}::isInPlaceInversion(const ContigCopyEvent&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:580:9: note: in expansion of macro 'CGA_ASSERT'
580 | CGA_ASSERT(nonoverlapLen >= 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:580:9: note: in expansion of macro 'CGA_ASSERT'
580 | CGA_ASSERT(nonoverlapLen >= 0);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In member function 'void cgatools::command::{anonymous}::SvEventStore::writeReport(std::ostream&, const cgatools::reference::CrrFile&, const cgatools::command::{anonymous}::IdToJunctionMap&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:864:21: note: in expansion of macro 'CGA_ASSERT'
864 | CGA_ASSERT(jit != byId.end());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:864:21: note: in expansion of macro 'CGA_ASSERT'
864 | CGA_ASSERT(jit != byId.end());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In member function 'void cgatools::command::{anonymous}::SvEventStore::collectAffectedGenes(cgatools::command::{anonymous}::SvEvent&, const cgatools::reference::CrrFile&, const cgatools::command::{anonymous}::IdToJunctionMap&, const cgatools::reference::GeneDataStore&, cgatools::uint32_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:908:17: note: in expansion of macro 'CGA_ASSERT'
908 | CGA_ASSERT(jit != byId.end());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:908:17: note: in expansion of macro 'CGA_ASSERT'
908 | CGA_ASSERT(jit != byId.end());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In member function 'cgatools::command::{anonymous}::SvEventStore::RangeRelationship cgatools::command::{anonymous}::SvEventStore::rangeRelationship(const cgatools::reference::Range&, const cgatools::reference::Location&, bool)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:1077:13: note: in expansion of macro 'CGA_ASSERT'
1077 | CGA_ASSERT(range.chromosome_ == p.chromosome_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:1077:13: note: in expansion of macro 'CGA_ASSERT'
1077 | CGA_ASSERT(range.chromosome_ == p.chromosome_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In member function 'virtual int cgatools::command::JunctionType::run(boost::program_options::variables_map&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:1395:25: note: in expansion of macro 'CGA_ASSERT'
1395 | CGA_ASSERT(!evts.empty());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:1395:25: note: in expansion of macro 'CGA_ASSERT'
1395 | CGA_ASSERT(!evts.empty());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: At global scope:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:540:10: warning: 'bool cgatools::command::{anonymous}::pairedToSameJunction(const std::vector<ContigCopyEvent>&)' defined but not used [-Wunused-function]
540 | bool pairedToSameJunction(const vector<ContigCopyEvent>& evts)
| ^~~~~~~~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:505:12: warning: 'std::string cgatools::command::{anonymous}::formatLocation(const cgatools::reference::CrrFile&, const cgatools::reference::Location&)' defined but not used [-Wunused-function]
505 | string formatLocation(const CrrFile& crr, const Location& loc)
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:498:12: warning: 'std::string cgatools::command::{anonymous}::formatRange(const cgatools::reference::CrrFile&, const cgatools::reference::Range&)' defined but not used [-Wunused-function]
498 | string formatRange(const CrrFile& crr, const Range& r)
| ^~~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Streams.hpp:23,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListCrr.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In function 'int cgatools::command::{anonymous}::junctionStrandChange(const cgatools::junctions::Junction&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:184:9: note: in expansion of macro 'CGA_ASSERT'
184 | CGA_ASSERT(jj.sideSections_[1].strand_ != JUNCTION_UNKNOWN_STRAND);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:183:9: note: in expansion of macro 'CGA_ASSERT'
183 | CGA_ASSERT(jj.sideSections_[0].strand_ != JUNCTION_UNKNOWN_STRAND);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In function 'cgatools::reference::Range cgatools::command::{anonymous}::junctionRange(const cgatools::junctions::Junction&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:119:9: note: in expansion of macro 'CGA_ASSERT'
119 | CGA_ASSERT(r.begin_ <= r.end_);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
[ 59%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/ListVariants.cpp.o
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In function 'void cgatools::command::{anonymous}::findPair(const cgatools::junctions::Junction&, int, const LocationJunctionMap&, cgatools::int32_t, cgatools::int32_t, std::vector<ContigCopyEvent>&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:274:9: note: in expansion of macro 'CGA_ASSERT'
274 | CGA_ASSERT(p != others.end()); // we must find at least "start" itself
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In function 'bool cgatools::command::{anonymous}::isInPlaceInversion(const ContigCopyEvent&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:580:9: note: in expansion of macro 'CGA_ASSERT'
580 | CGA_ASSERT(nonoverlapLen >= 0);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::StringField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StringField]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<unsigned int>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned int>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<unsigned int>]':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::StrandField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::StrandField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'void cgatools::reference::RepeatMaskerStore::bindColumns(cgatools::util::DelimitedFile&, cgatools::reference::Range&, cgatools::reference::RepeatMaskerAnnotation&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RepeatMaskerStore.hpp:52:20:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::reference::RepeatMaskerStore::bindColumns(cgatools::util::DelimitedFile&, cgatools::reference::Range&, cgatools::reference::RepeatMaskerAnnotation&)':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::util::ValueField<double>]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::util::ValueField<double>]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'void cgatools::reference::RepeatMaskerStore::bindColumns(cgatools::util::DelimitedFile&, cgatools::reference::Range&, cgatools::reference::RepeatMaskerAnnotation&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RepeatMaskerStore.hpp:51:20:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::reference::RepeatMaskerStore::bindColumns(cgatools::util::DelimitedFile&, cgatools::reference::Range&, cgatools::reference::RepeatMaskerAnnotation&)':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&) [with Field = cgatools::reference::ChromosomeIdField]',
inlined from 'void cgatools::util::DelimitedFile::addField(const Field&, FieldParserType) [with Field = cgatools::reference::ChromosomeIdField]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedFile.hpp:139:33,
inlined from 'void cgatools::reference::RangeAnnotationStore<Derived, TValue>::bindRangeColumns(cgatools::util::DelimitedFile&, cgatools::reference::Range&, const std::string&, const std::string&, const std::string&) [with Derived = cgatools::reference::RepeatMaskerStore; TValue = cgatools::reference::RepeatMaskerAnnotation]' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RangeAnnotationStore.hpp:113:20,
inlined from 'void cgatools::reference::RepeatMaskerStore::bindColumns(cgatools::util::DelimitedFile&, cgatools::reference::Range&, cgatools::reference::RepeatMaskerAnnotation&)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/RepeatMaskerStore.hpp:48:25:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:50: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ~~~^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
In member function 'void cgatools::reference::RepeatMaskerStore::bindColumns(cgatools::util::DelimitedFile&, cgatools::reference::Range&, cgatools::reference::RepeatMaskerAnnotation&)':
cc1plus: note: source object is likely at address zero
[ 60%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Map2Sam.cpp.o
In member function 'cgatools::command::{anonymous}::SvEventStore::RangeRelationship cgatools::command::{anonymous}::SvEventStore::rangeRelationship(const cgatools::reference::Range&, const cgatools::reference::Location&, bool)',
inlined from 'cgatools::command::{anonymous}::SvEventStore::RangeRelationship cgatools::command::{anonymous}::SvEventStore::rangeRelationship(const cgatools::reference::Range&, const cgatools::reference::Location&, bool)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:1075:27,
inlined from 'void cgatools::command::{anonymous}::SvEventStore::findGeneFusions(cgatools::command::{anonymous}::SvEvent&, const cgatools::junctions::Junction&, const cgatools::reference::CrrFile&, const cgatools::reference::GeneDataStore&, cgatools::uint32_t)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:997:56:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:1077:13: note: in expansion of macro 'CGA_ASSERT'
1077 | CGA_ASSERT(range.chromosome_ == p.chromosome_);
| ^~~~~~~~~~
In function 'void cgatools::command::{anonymous}::SvEventStore::findGeneFusions(cgatools::command::{anonymous}::SvEvent&, const cgatools::junctions::Junction&, const cgatools::reference::CrrFile&, const cgatools::reference::GeneDataStore&, cgatools::uint32_t)':
cc1plus: note: source object is likely at address zero
In member function 'cgatools::command::{anonymous}::SvEventStore::RangeRelationship cgatools::command::{anonymous}::SvEventStore::rangeRelationship(const cgatools::reference::Range&, const cgatools::reference::Location&, bool)',
inlined from 'cgatools::command::{anonymous}::SvEventStore::RangeRelationship cgatools::command::{anonymous}::SvEventStore::rangeRelationship(const cgatools::reference::Range&, const cgatools::reference::Location&, bool)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:1075:27,
inlined from 'void cgatools::command::{anonymous}::SvEventStore::findGeneFusions(cgatools::command::{anonymous}::SvEvent&, const cgatools::junctions::Junction&, const cgatools::reference::CrrFile&, const cgatools::reference::GeneDataStore&, cgatools::uint32_t)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:994:54:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:1077:13: note: in expansion of macro 'CGA_ASSERT'
1077 | CGA_ASSERT(range.chromosome_ == p.chromosome_);
| ^~~~~~~~~~
In function 'void cgatools::command::{anonymous}::SvEventStore::findGeneFusions(cgatools::command::{anonymous}::SvEvent&, const cgatools::junctions::Junction&, const cgatools::reference::CrrFile&, const cgatools::reference::GeneDataStore&, cgatools::uint32_t)':
cc1plus: note: source object is likely at address zero
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/variants/Call.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/ListVariants.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:16:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const',
inlined from 'void cgatools::command::{anonymous}::SvEventStore::collectContainedGenes(cgatools::command::{anonymous}::SvEvent&, const cgatools::reference::CrrFile&, const cgatools::reference::GeneDataStore&, int)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:955:50,
inlined from 'void cgatools::command::{anonymous}::SvEventStore::annotateEvents(const cgatools::reference::CrrFile&, const cgatools::command::{anonymous}::IdToJunctionMap&, const cgatools::reference::GeneDataStore&, int, cgatools::uint32_t)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:827:42:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
In function 'void cgatools::command::{anonymous}::SvEventStore::annotateEvents(const cgatools::reference::CrrFile&, const cgatools::command::{anonymous}::IdToJunctionMap&, const cgatools::reference::GeneDataStore&, int, cgatools::uint32_t)':
cc1plus: note: source object is likely at address zero
In member function 'void cgatools::command::{anonymous}::SvEventStore::collectAffectedGenes(cgatools::command::{anonymous}::SvEvent&, const cgatools::reference::CrrFile&, const cgatools::command::{anonymous}::IdToJunctionMap&, const cgatools::reference::GeneDataStore&, cgatools::uint32_t)',
inlined from 'void cgatools::command::{anonymous}::SvEventStore::annotateEvents(const cgatools::reference::CrrFile&, const cgatools::command::{anonymous}::IdToJunctionMap&, const cgatools::reference::GeneDataStore&, int, cgatools::uint32_t)' at /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:826:41:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:908:17: note: in expansion of macro 'CGA_ASSERT'
908 | CGA_ASSERT(jit != byId.end());
| ^~~~~~~~~~
In function 'void cgatools::command::{anonymous}::SvEventStore::annotateEvents(const cgatools::reference::CrrFile&, const cgatools::command::{anonymous}::IdToJunctionMap&, const cgatools::reference::GeneDataStore&, int, cgatools::uint32_t)':
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In function 'static void cgatools::command::{anonymous}::RelatedJunctionGraph::findNeighbors(const cgatools::junctions::Junction&, const cgatools::command::{anonymous}::LocationJunctionMap&, int, RelatedJunctions&, size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:465:25: note: in expansion of macro 'CGA_ASSERT'
465 | CGA_ASSERT(distance >= 0);
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:456:17: note: in expansion of macro 'CGA_ASSERT'
456 | CGA_ASSERT(pos != locMap.end());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp: In member function 'cgatools::util::DelimitedLineParser& cgatools::util::DelimitedLineParser::setField(size_t, const Field&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/DelimitedLineParser.hpp:271:13: note: in expansion of macro 'CGA_ASSERT'
271 | CGA_ASSERT(offset < fields_.size());
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp: In member function 'const cgatools::cgdata::EvidenceReader::IntervalRecord& cgatools::cgdata::EvidenceReader::getInterval() const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/cgdata/EvidenceReader.hpp:130:13: note: in expansion of macro 'CGA_ASSERT'
130 | CGA_ASSERT(inInterval_);
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp: In member function 'void cgatools::command::VariantListingFileVariantLister::buildQueue()':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:341:13: note: in expansion of macro 'CGA_ASSERT'
341 | CGA_ASSERT(bu::isCalledSequence(nextCall_.alleleSeq_) &&
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:341:13: note: in expansion of macro 'CGA_ASSERT'
341 | CGA_ASSERT(bu::isCalledSequence(nextCall_.alleleSeq_) &&
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp: In member function 'virtual int cgatools::command::ListVariants::run(boost::program_options::variables_map&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:429:78: error: template argument 1 is invalid
429 | vector< shared_ptr<VariantLister> >, VariantListerDescByPosition > pq;
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:429:78: error: template argument 2 is invalid
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:429:78: error: template argument 3 is invalid
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:434:17: error: reference to 'shared_ptr' is ambiguous
434 | shared_ptr<VariantLister> vl(new VariantFileVariantLister(crr_, variantFileName));
| ^~~~~~~~~~
In file included from /opt/local/gcc13/include/c++/13.3.0/bits/shared_ptr.h:53,
from /opt/local/gcc13/include/c++/13.3.0/memory:80,
from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/any.hpp:27,
from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/program_options/value_semantic.hpp:12,
from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/program_options/options_description.hpp:13,
from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/program_options.hpp:15,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/Command.hpp:24,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/command/ListVariants.hpp:21:
/opt/local/gcc13/include/c++/13.3.0/bits/shared_ptr_base.h:395:11: note: candidates are: 'template<class _Tp> class std::shared_ptr'
395 | class shared_ptr;
| ^~~~~~~~~~
In file included from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/throw_exception.hpp:21,
from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/type_index/stl_type_index.hpp:33,
from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/type_index.hpp:29,
from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/any/detail/placeholder.hpp:15,
from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/any.hpp:23:
/home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/exception/exception.hpp:17:44: note: 'template<class T> class boost::shared_ptr'
17 | namespace boost { template <class T> class shared_ptr; }
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:434:41: error: expected primary-expression before '>' token
434 | shared_ptr<VariantLister> vl(new VariantFileVariantLister(crr_, variantFileName));
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:434:43: error: 'vl' was not declared in this scope; did you mean 'vm'?
434 | shared_ptr<VariantLister> vl(new VariantFileVariantLister(crr_, variantFileName));
| ^~
| vm
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:436:24: error: request for member 'push' in 'pq', which is of non-class type 'int'
436 | pq.push(vl);
| ^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:440:17: error: reference to 'shared_ptr' is ambiguous
440 | shared_ptr<VariantLister> vl(new SuperlocusVariantLister(crr_, variantFileName));
| ^~~~~~~~~~
/opt/local/gcc13/include/c++/13.3.0/bits/shared_ptr_base.h:395:11: note: candidates are: 'template<class _Tp> class std::shared_ptr'
395 | class shared_ptr;
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/exception/exception.hpp:17:44: note: 'template<class T> class boost::shared_ptr'
17 | namespace boost { template <class T> class shared_ptr; }
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:440:41: error: expected primary-expression before '>' token
440 | shared_ptr<VariantLister> vl(new SuperlocusVariantLister(crr_, variantFileName));
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:440:43: error: 'vl' was not declared in this scope; did you mean 'vm'?
440 | shared_ptr<VariantLister> vl(new SuperlocusVariantLister(crr_, variantFileName));
| ^~
| vm
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:442:24: error: request for member 'push' in 'pq', which is of non-class type 'int'
442 | pq.push(vl);
| ^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:447:13: error: reference to 'shared_ptr' is ambiguous
447 | shared_ptr<VariantLister> vl(new VariantListingFileVariantLister(crr_, variantListingFileName));
| ^~~~~~~~~~
/opt/local/gcc13/include/c++/13.3.0/bits/shared_ptr_base.h:395:11: note: candidates are: 'template<class _Tp> class std::shared_ptr'
395 | class shared_ptr;
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/exception/exception.hpp:17:44: note: 'template<class T> class boost::shared_ptr'
17 | namespace boost { template <class T> class shared_ptr; }
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:447:37: error: expected primary-expression before '>' token
447 | shared_ptr<VariantLister> vl(new VariantListingFileVariantLister(crr_, variantListingFileName));
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:447:39: error: 'vl' was not declared in this scope; did you mean 'vm'?
447 | shared_ptr<VariantLister> vl(new VariantListingFileVariantLister(crr_, variantListingFileName));
| ^~
| vm
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:449:20: error: request for member 'push' in 'pq', which is of non-class type 'int'
449 | pq.push(vl);
| ^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:454:20: error: request for member 'empty' in 'pq', which is of non-class type 'int'
454 | while (!pq.empty())
| ^~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:456:13: error: reference to 'shared_ptr' is ambiguous
456 | shared_ptr<VariantLister> vl = pq.top();
| ^~~~~~~~~~
/opt/local/gcc13/include/c++/13.3.0/bits/shared_ptr_base.h:395:11: note: candidates are: 'template<class _Tp> class std::shared_ptr'
395 | class shared_ptr;
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/exception/exception.hpp:17:44: note: 'template<class T> class boost::shared_ptr'
17 | namespace boost { template <class T> class shared_ptr; }
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:456:37: error: expected primary-expression before '>' token
456 | shared_ptr<VariantLister> vl = pq.top();
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:456:39: error: 'vl' was not declared in this scope; did you mean 'vm'?
456 | shared_ptr<VariantLister> vl = pq.top();
| ^~
| vm
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:456:47: error: request for member 'top' in 'pq', which is of non-class type 'int'
456 | shared_ptr<VariantLister> vl = pq.top();
| ^~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:457:16: error: request for member 'pop' in 'pq', which is of non-class type 'int'
457 | pq.pop();
| ^~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:464:20: error: request for member 'push' in 'pq', which is of non-class type 'int'
464 | pq.push(vl);
| ^~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In member function 'void cgatools::command::{anonymous}::SvEventStore::writeReport(std::ostream&, const cgatools::reference::CrrFile&, const cgatools::command::{anonymous}::IdToJunctionMap&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:864:21: note: in expansion of macro 'CGA_ASSERT'
864 | CGA_ASSERT(jit != byId.end());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp: In member function 'virtual int cgatools::command::JunctionType::run(boost::program_options::variables_map&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:52: warning: array subscript 0 is outside array bounds of 'volatile char [0]' [-Warray-bounds=]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/JunctionType.cpp:1395:25: note: in expansion of macro 'CGA_ASSERT'
1395 | CGA_ASSERT(!evts.empty());
| ^~~~~~~~~~
cc1plus: note: source object is likely at address zero
In file included from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/CrrFile.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/Map2SamConverter.hpp:22,
from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Map2Sam.cpp:17:
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In constructor 'cgatools::reference::Range::Range(const cgatools::reference::Location&, const cgatools::reference::Location&)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:87:38: note: in expansion of macro 'CGA_ASSERT_MSG'
87 | #define CGA_ASSERT_EQ(var1,var2) CGA_ASSERT_MSG((var1)==(var2), CGA_VOUT(var1)<<CGA_VOUT(var2))
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:120:13: note: in expansion of macro 'CGA_ASSERT_EQ'
120 | CGA_ASSERT_EQ(beginLoc.chromosome_, endLoc.chromosome_);
| ^~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp: In member function 'cgatools::reference::Range cgatools::reference::Range::overlappingRange(const cgatools::reference::Range&) const':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/reference/range.hpp:166:13: note: in expansion of macro 'CGA_ASSERT'
166 | CGA_ASSERT(intersects(rr));
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp: In member function 'void cgatools::mapping::MappingsFlagParser::setSide(size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:68:39: note: in expansion of macro 'CGA_ASSERT'
68 | void setSide(size_t side) {CGA_ASSERT(side<2); flags_ |= side<<1;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:68:39: note: in expansion of macro 'CGA_ASSERT'
68 | void setSide(size_t side) {CGA_ASSERT(side<2); flags_ |= side<<1;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp: In member function 'void cgatools::mapping::MappingsFlagParser::setStrand(size_t)':
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:17: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:70:43: note: in expansion of macro 'CGA_ASSERT'
70 | void setStrand(size_t strand) {CGA_ASSERT(strand<2); flags_ |= strand<<2;}
| ^~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:41:42: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
41 | if (ch == '\0') *p = ch; p++; ch = *p; \
| ^
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/util/Exception.hpp:58:30: note: in expansion of macro 'CGA_ASSERT_MSG'
58 | #define CGA_ASSERT(expr) CGA_ASSERT_MSG(expr, "")
| ^~~~~~~~~~~~~~
/home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/./cgatools/mapping/MapSamUtils.hpp:70:43: note: in expansion of macro 'CGA_ASSERT'
70 | void setStrand(size_t strand) {CGA_ASSERT(strand<2); flags_ |= strand<<2;}
| ^~~~~~~~~~
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