+ case "${usergroup_phase}" in
+ local run_cmd
+ run_cmd=run_su
+ shift
+ run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/kallisto-0.50.1/work.log
+ su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/kallisto-0.50.1/work.log
=> Bootstrap dependency digest>=20211023: found digest-20220214
===> Building for kallisto-0.50.1
/opt/pkg/bin/cmake -S/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1 -B/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1 --check-build-system CMakeFiles/Makefile.cmake 0
/opt/pkg/bin/cmake -E cmake_progress_start /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/CMakeFiles /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1//CMakeFiles/progress.marks
/opt/pkg/bin/gmake -f CMakeFiles/Makefile2 all
gmake[1]: Entering directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1'
/opt/pkg/bin/gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/depend
gmake[2]: Entering directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1'
cd /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1 && /opt/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1 /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1 /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1 /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1 /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/CMakeFiles/bifrost.dir/DependInfo.cmake "--color="
gmake[2]: Leaving directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1'
/opt/pkg/bin/gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/build
gmake[2]: Entering directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1'
[ 3%] Creating directories for 'bifrost'
/opt/pkg/bin/cmake -Dcfgdir= -P /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/tmp/bifrost-mkdirs.cmake
/opt/pkg/bin/cmake -E touch /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-mkdir
[ 7%] No download step for 'bifrost'
/opt/pkg/bin/cmake -E echo_append
/opt/pkg/bin/cmake -E touch /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-download
[ 11%] No update step for 'bifrost'
/opt/pkg/bin/cmake -E echo_append
/opt/pkg/bin/cmake -E touch /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-update
[ 15%] No patch step for 'bifrost'
/opt/pkg/bin/cmake -E echo_append
/opt/pkg/bin/cmake -E touch /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-patch
[ 19%] Performing configure step for 'bifrost'
cd /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost && mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX= "-DCMAKE_CXX_FLAGS=-Wno-subobject-linkage -Wno-return-type"
CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
-- The C compiler identification is GNU 13.2.0
-- The CXX compiler identification is GNU 13.2.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /home/pbulk/build/biology/kallisto/work/.cwrapper/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/pbulk/build/biology/kallisto/work/.cwrapper/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
Compilation architecture:
Build type: Release
Maximum k-mer size: 31
Maximum g-mer size: 31
-- Found ZLIB: /opt/pkg/lib/libz.so (found version "1.3.1")
-- Configuring done (5.5s)
-- Generating done (0.0s)
-- Build files have been written to: /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build
cd /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost && /opt/pkg/bin/cmake -E touch /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/bifrost-stamp/bifrost-configure
[ 23%] Performing build step for 'bifrost'
cd /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost && cd build && gmake
gmake[3]: Entering directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build'
/opt/pkg/bin/cmake -S/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost -B/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build --check-build-system CMakeFiles/Makefile.cmake 0
/opt/pkg/bin/cmake -E cmake_progress_start /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/CMakeFiles /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build//CMakeFiles/progress.marks
gmake -f CMakeFiles/Makefile2 all
gmake[4]: Entering directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build'
gmake -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/depend
gmake[5]: Entering directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build'
cd /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build && /opt/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color="
gmake[5]: Leaving directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build'
gmake -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/build
gmake[5]: Entering directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build'
[ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
cd /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/build/src && /home/pbulk/build/biology/kallisto/work/.cwrapper/bin/g++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src -I/opt/pkg/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -O3 -DNDEBUG -O2 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp
In file included from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/roaring.hh:1,
from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/BitContainer.hpp:4,
from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/KmerCovIndex.hpp:7,
from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:32,
from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:1:
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/roaring.h:27: warning: "_POSIX_C_SOURCE" redefined
27 | #define _POSIX_C_SOURCE 200809L
|
In file included from /usr/include/iso/math_iso.h:32,
from /usr/include/math.h:35,
from /opt/tools/gcc13/include/c++/13.2.0/cmath:47,
from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:4:
/usr/include/sys/feature_tests.h:342: note: this is the location of the previous definition
342 | #define _POSIX_C_SOURCE 200112L
|
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/roaring.h:30: warning: "_XOPEN_SOURCE" redefined
30 | #define _XOPEN_SOURCE 700
|
/usr/include/sys/feature_tests.h:344: note: this is the location of the previous definition
344 | #define _XOPEN_SOURCE 600
|
In file included from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.hpp:369,
from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/Bifrost.cpp:2:
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'bool ColoredCDBG<Unitig_data_t>::loadColors(const std::string&, const std::string&, std::size_t, bool)':
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:517:9: error: reference to 'mutex' is ambiguous
517 | mutex mutex_file;
| ^~~~~
In file included from /opt/tools/gcc13/include/c++/13.2.0/mutex:45,
from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/CompactedDBG.hpp:24:
/opt/tools/gcc13/include/c++/13.2.0/bits/std_mutex.h:96:9: note: candidates are: 'class std::mutex'
96 | class mutex : private __mutex_base
| ^~~~~
In file included from /usr/include/sys/t_lock.h:39,
from /usr/include/sys/thread.h:36,
from /usr/include/sys/procfs.h:70,
from /usr/include/procfs.h:45,
from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/getRSS.h:29,
from /home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.hpp:12:
/usr/include/sys/mutex.h:63:16: note: 'struct mutex'
63 | typedef struct mutex {
| ^~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function:
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:532:46: error: template argument 1 is invalid
532 | unique_lock<mutex> lock(mutex_file);
| ^
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:532:53: error: 'mutex_file' was not declared in this scope
532 | unique_lock<mutex> lock(mutex_file);
| ^~~~~~~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'void ColoredCDBG<Unitig_data_t>::initUnitigColors(const CCDBG_Build_opt&, std::size_t)':
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:737:5: error: reference to 'mutex' is ambiguous
737 | mutex mutex_it;
| ^~~~~
/opt/tools/gcc13/include/c++/13.2.0/bits/std_mutex.h:96:9: note: candidates are: 'class std::mutex'
96 | class mutex : private __mutex_base
| ^~~~~
/usr/include/sys/mutex.h:63:16: note: 'struct mutex'
63 | typedef struct mutex {
| ^~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function:
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:750:42: error: template argument 1 is invalid
750 | unique_lock<mutex> lock(mutex_it);
| ^
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:750:49: error: 'mutex_it' was not declared in this scope; did you mean 'kmutex_t'?
750 | unique_lock<mutex> lock(mutex_it);
| ^~~~~~~~
| kmutex_t
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'void ColoredCDBG<Unitig_data_t>::resizeDataUC(std::size_t, std::size_t, std::size_t)':
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:790:5: error: reference to 'mutex' is ambiguous
790 | mutex mutex_it;
| ^~~~~
/opt/tools/gcc13/include/c++/13.2.0/bits/std_mutex.h:96:9: note: candidates are: 'class std::mutex'
96 | class mutex : private __mutex_base
| ^~~~~
/usr/include/sys/mutex.h:63:16: note: 'struct mutex'
63 | typedef struct mutex {
| ^~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function:
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:803:42: error: template argument 1 is invalid
803 | unique_lock<mutex> lock(mutex_it);
| ^
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:803:49: error: 'mutex_it' was not declared in this scope; did you mean 'kmutex_t'?
803 | unique_lock<mutex> lock(mutex_it);
| ^~~~~~~~
| kmutex_t
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'void ColoredCDBG<Unitig_data_t>::resizeDataUC(std::size_t, std::size_t, std::size_t) [with Unitig_data_t = void; std::size_t = long unsigned int]':
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:856:5: error: reference to 'mutex' is ambiguous
856 | mutex mutex_it;
| ^~~~~
/opt/tools/gcc13/include/c++/13.2.0/bits/std_mutex.h:96:9: note: candidates are: 'class std::mutex'
96 | class mutex : private __mutex_base
| ^~~~~
/usr/include/sys/mutex.h:63:16: note: 'struct mutex'
63 | typedef struct mutex {
| ^~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function:
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:869:42: error: template argument 1 is invalid
869 | unique_lock<mutex> lock(mutex_it);
| ^
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:869:49: error: 'mutex_it' was not declared in this scope; did you mean 'kmutex_t'?
869 | unique_lock<mutex> lock(mutex_it);
| ^~~~~~~~
| kmutex_t
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'void ColoredCDBG<Unitig_data_t>::buildUnitigColors(std::size_t)':
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1060:9: error: reference to 'mutex' is ambiguous
1060 | mutex mutex_file;
| ^~~~~
/opt/tools/gcc13/include/c++/13.2.0/bits/std_mutex.h:96:9: note: candidates are: 'class std::mutex'
96 | class mutex : private __mutex_base
| ^~~~~
/usr/include/sys/mutex.h:63:16: note: 'struct mutex'
63 | typedef struct mutex {
| ^~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function:
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1082:50: error: template argument 1 is invalid
1082 | unique_lock<mutex> lock(mutex_file);
| ^
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1082:57: error: 'mutex_file' was not declared in this scope
1082 | unique_lock<mutex> lock(mutex_file);
| ^~~~~~~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'void ColoredCDBG<Unitig_data_t>::buildUnitigColors(std::size_t)':
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1117:17: error: reference to 'mutex' is ambiguous
1117 | mutex mutex_it;
| ^~~~~
/opt/tools/gcc13/include/c++/13.2.0/bits/std_mutex.h:96:9: note: candidates are: 'class std::mutex'
96 | class mutex : private __mutex_base
| ^~~~~
/usr/include/sys/mutex.h:63:16: note: 'struct mutex'
63 | typedef struct mutex {
| ^~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function:
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1130:54: error: template argument 1 is invalid
1130 | unique_lock<mutex> lock(mutex_it);
| ^
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1130:61: error: 'mutex_it' was not declared in this scope; did you mean 'kmutex_t'?
1130 | unique_lock<mutex> lock(mutex_it);
| ^~~~~~~~
| kmutex_t
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'bool ColoredCDBG<Unitig_data_t>::search(const std::vector<std::__cxx11::basic_string<char> >&, const std::string&, double, bool, std::size_t, bool) const':
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1718:9: error: reference to 'mutex' is ambiguous
1718 | mutex mutex_files_in, mutex_file_out;
| ^~~~~
/opt/tools/gcc13/include/c++/13.2.0/bits/std_mutex.h:96:9: note: candidates are: 'class std::mutex'
96 | class mutex : private __mutex_base
| ^~~~~
/usr/include/sys/mutex.h:63:16: note: 'struct mutex'
63 | typedef struct mutex {
| ^~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function:
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1740:46: error: template argument 1 is invalid
1740 | unique_lock<mutex> lock(mutex_files_in);
| ^
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1740:53: error: 'mutex_files_in' was not declared in this scope
1740 | unique_lock<mutex> lock(mutex_files_in);
| ^~~~~~~~~~~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1783:50: error: template argument 1 is invalid
1783 | unique_lock<mutex> lock(mutex_file_out);
| ^
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1783:57: error: 'mutex_file_out' was not declared in this scope
1783 | unique_lock<mutex> lock(mutex_file_out);
| ^~~~~~~~~~~~~~
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1801:46: error: template argument 1 is invalid
1801 | unique_lock<mutex> lock(mutex_file_out);
| ^
/home/pbulk/build/biology/kallisto/work/kallisto-0.50.1/ext/bifrost/src/ColoredCDBG.tcc:1801:53: error: 'mutex_file_out' was not declared in this scope
1801 | unique_lock<mutex> lock(mutex_file_out);
| ^~~~~~~~~~~~~~
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