+ 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 => Bootstrap dependency digest>=20211023: found digest-20220214 ===> Building for cgatools-1.8.0.1 [ 0%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/CnvDetailStore.cpp.o [ 1%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/CnvSegmentStore.cpp.o [ 1%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/Dnb.cpp.o [ 2%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/EvidenceReader.cpp.o [ 2%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/GenomeMetadata.cpp.o [ 3%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/LibraryReader.cpp.o [ 3%] Building CXX object CMakeFiles/cgatools.dir/cgatools/cgdata/ReferenceSupportReader.cpp.o [ 4%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/CallDiff.cpp.o [ 5%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Command.cpp.o [ 5%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Crr2Fasta.cpp.o [ 6%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/DecodeCrr.cpp.o [ 6%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Evidence2Cache.cpp.o [ 7%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Evidence2Sam.cpp.o [ 7%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Fasta2Crr.cpp.o [ 8%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/Join.cpp.o [ 8%] 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/junctions/JunctionVcfWriter.hpp:25, from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/Junction2Vcf.cpp:17: /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:40:11: warning: '.cgatools::junctions::JunctionRef::sourceId_' may be used uninitialized in this function [-Wmaybe-uninitialized] 40 | class JunctionRef | ^~~~~~~~~~~ [ 9%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/JunctionCmp.cpp.o [ 10%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/JunctionDiff.cpp.o [ 10%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/JunctionType.cpp.o /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&)' defined but not used [-Wunused-function] 540 | bool pairedToSameJunction(const vector& 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) | ^~~~~~~~~~~ [ 11%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/ListCrr.cpp.o [ 11%] Building CXX object CMakeFiles/cgatools.dir/cgatools/command/ListVariants.cpp.o /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 >, 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 vl(new VariantFileVariantLister(crr_, variantFileName)); | ^~~~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/shared_ptr.h:52, from /opt/local/gcc10/include/c++/10.3.0/memory:84, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function_base.hpp:16, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/detail/prologue.hpp:17, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function_template.hpp:13, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/detail/maybe_include.hpp:22, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function1.hpp:11, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/program_options/value_semantic.hpp:13, 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, from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:16: /opt/local/gcc10/include/c++/10.3.0/bits/shared_ptr_base.h:351:11: note: candidates are: 'template class std::shared_ptr' 351 | class shared_ptr; | ^~~~~~~~~~ In file included from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/throw_exception.hpp:23, 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.hpp:20, 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, from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:16: /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/exception/exception.hpp:16:44: note: 'template class boost::shared_ptr' 16 | namespace boost { template 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 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 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 vl(new SuperlocusVariantLister(crr_, variantFileName)); | ^~~~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/shared_ptr.h:52, from /opt/local/gcc10/include/c++/10.3.0/memory:84, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function_base.hpp:16, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/detail/prologue.hpp:17, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function_template.hpp:13, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/detail/maybe_include.hpp:22, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function1.hpp:11, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/program_options/value_semantic.hpp:13, 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, from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:16: /opt/local/gcc10/include/c++/10.3.0/bits/shared_ptr_base.h:351:11: note: candidates are: 'template class std::shared_ptr' 351 | class shared_ptr; | ^~~~~~~~~~ In file included from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/throw_exception.hpp:23, 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.hpp:20, 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, from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:16: /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/exception/exception.hpp:16:44: note: 'template class boost::shared_ptr' 16 | namespace boost { template 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 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 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 vl(new VariantListingFileVariantLister(crr_, variantListingFileName)); | ^~~~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/shared_ptr.h:52, from /opt/local/gcc10/include/c++/10.3.0/memory:84, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function_base.hpp:16, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/detail/prologue.hpp:17, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function_template.hpp:13, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/detail/maybe_include.hpp:22, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function1.hpp:11, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/program_options/value_semantic.hpp:13, 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, from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:16: /opt/local/gcc10/include/c++/10.3.0/bits/shared_ptr_base.h:351:11: note: candidates are: 'template class std::shared_ptr' 351 | class shared_ptr; | ^~~~~~~~~~ In file included from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/throw_exception.hpp:23, 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.hpp:20, 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, from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:16: /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/exception/exception.hpp:16:44: note: 'template class boost::shared_ptr' 16 | namespace boost { template 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 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 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 vl = pq.top(); | ^~~~~~~~~~ In file included from /opt/local/gcc10/include/c++/10.3.0/bits/shared_ptr.h:52, from /opt/local/gcc10/include/c++/10.3.0/memory:84, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function_base.hpp:16, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/detail/prologue.hpp:17, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function_template.hpp:13, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/detail/maybe_include.hpp:22, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/function/function1.hpp:11, from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/program_options/value_semantic.hpp:13, 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, from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:16: /opt/local/gcc10/include/c++/10.3.0/bits/shared_ptr_base.h:351:11: note: candidates are: 'template class std::shared_ptr' 351 | class shared_ptr; | ^~~~~~~~~~ In file included from /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/throw_exception.hpp:23, 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.hpp:20, 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, from /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/cgatools/command/ListVariants.cpp:16: /home/pbulk/build/joyent/cgatools/work/.buildlink/include/boost/exception/exception.hpp:16:44: note: 'template class boost::shared_ptr' 16 | namespace boost { template 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 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 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 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); | ^~~~ *** [CMakeFiles/cgatools.dir/cgatools/command/ListVariants.cpp.o] Error code 1 bmake[2]: stopped in /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build 1 error bmake[2]: stopped in /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build *** [CMakeFiles/cgatools.dir/all] Error code 2 bmake[1]: stopped in /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build 1 error bmake[1]: stopped in /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build *** [all] Error code 2 bmake: stopped in /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build 1 error bmake: stopped in /home/pbulk/build/joyent/cgatools/work/cgatools-1.8.0.1-source/_build *** Error code 2 Stop. bmake[1]: stopped in /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools *** Error code 1 Stop. bmake: stopped in /data/jenkins/workspace/pkgsrc-trunk-x86_64/joyent/cgatools