+ case "${usergroup_phase}" in + local run_cmd + run_cmd=run_su + shift + run_su /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/kallisto-0.51.1/work.log + su pbulk -c '"$@"' make /opt/pkg/bin/bmake all BATCH=1 DEPENDS_TARGET=/nonexistent WRKLOG=/tmp/bulklog/kallisto-0.51.1/work.log WARNING: USE_CMAKE is deprecated; use devel/cmake/build.mk instead. ===> Building for kallisto-0.51.1 /opt/pkg/bin/cmake -S/home/pbulk/build/biology/kallisto/work/kallisto-0.51.1 -B/home/pbulk/build/biology/kallisto/work/kallisto-0.51.1 --check-build-system CMakeFiles/Makefile.cmake 0 /opt/pkg/bin/cmake -E cmake_progress_start /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/CMakeFiles /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1//CMakeFiles/progress.marks /opt/pkg/bin/gmake -f CMakeFiles/Makefile2 all gmake[1]: Entering directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.51.1' /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-0.51.1' cd /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1 && /opt/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1 /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1 /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1 /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1 /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/CMakeFiles/bifrost.dir/DependInfo.cmake "--color=" gmake[2]: Leaving directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.51.1' /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-0.51.1' [ 3%] Creating directories for 'bifrost' /opt/pkg/bin/cmake -Dcfgdir= -P /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/tmp/bifrost-mkdirs.cmake /opt/pkg/bin/cmake -E touch /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/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-0.51.1/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-0.51.1/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-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-patch [ 19%] Performing configure step for 'bifrost' cd /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost && mkdir -p build && cd build && cmake .. -DMAX_KMER_SIZE=32 -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 < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- The C compiler identification is GNU 13.3.0 -- The CXX compiler identification is GNU 13.3.0 -- 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 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 (5.7s) -- Generating done (0.1s) -- Build files have been written to: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build cd /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost && /opt/pkg/bin/cmake -E touch /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/bifrost-stamp/bifrost-configure [ 23%] Performing build step for 'bifrost' cd /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost && cd build && gmake gmake[3]: Entering directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build' /opt/pkg/bin/cmake -S/home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost -B/home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/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-0.51.1/ext/bifrost/build/CMakeFiles /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build//CMakeFiles/progress.marks gmake -f CMakeFiles/Makefile2 all gmake[4]: Entering directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/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-0.51.1/ext/bifrost/build' cd /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build && /opt/pkg/bin/cmake -E cmake_depends "Unix Makefiles" /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build/src /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color=" gmake[5]: Leaving directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/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-0.51.1/ext/bifrost/build' [ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o cd /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/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-0.51.1/ext/bifrost/src -I/opt/pkg/include -Wno-subobject-linkage -Wno-return-type -std=c++11 -O3 -DNDEBUG -O3 -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-0.51.1/ext/bifrost/src/Bifrost.cpp In file included from /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/roaring.hh:1, from /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/BitContainer.hpp:4, from /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/KmerCovIndex.hpp:7, from /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:34, from /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:1: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/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++/13.3.0/cmath:47, from /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:6: /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-0.51.1/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-0.51.1/ext/bifrost/src/ColoredCDBG.hpp:369, from /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/Bifrost.cpp:2: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'bool ColoredCDBG::loadColors(const std::string&, const std::string&, std::size_t, bool)': /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/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++/13.3.0/mutex:45, from /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/CompactedDBG.hpp:26: /opt/tools/gcc13/include/c++/13.3.0/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-0.51.1/ext/bifrost/src/getRSS.h:29, from /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/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-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:532:46: error: template argument 1 is invalid 532 | unique_lock lock(mutex_file); | ^ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:532:53: error: 'mutex_file' was not declared in this scope 532 | unique_lock lock(mutex_file); | ^~~~~~~~~~ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'void ColoredCDBG::initUnitigColors(const CCDBG_Build_opt&, std::size_t)': /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:737:5: error: reference to 'mutex' is ambiguous 737 | mutex mutex_it; | ^~~~~ /opt/tools/gcc13/include/c++/13.3.0/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-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:750:42: error: template argument 1 is invalid 750 | unique_lock lock(mutex_it); | ^ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:750:49: error: 'mutex_it' was not declared in this scope; did you mean 'kmutex_t'? 750 | unique_lock lock(mutex_it); | ^~~~~~~~ | kmutex_t /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'void ColoredCDBG::resizeDataUC(std::size_t, std::size_t, std::size_t)': /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:790:5: error: reference to 'mutex' is ambiguous 790 | mutex mutex_it; | ^~~~~ /opt/tools/gcc13/include/c++/13.3.0/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-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:803:42: error: template argument 1 is invalid 803 | unique_lock lock(mutex_it); | ^ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:803:49: error: 'mutex_it' was not declared in this scope; did you mean 'kmutex_t'? 803 | unique_lock lock(mutex_it); | ^~~~~~~~ | kmutex_t /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'void ColoredCDBG::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-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:856:5: error: reference to 'mutex' is ambiguous 856 | mutex mutex_it; | ^~~~~ /opt/tools/gcc13/include/c++/13.3.0/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-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:869:42: error: template argument 1 is invalid 869 | unique_lock lock(mutex_it); | ^ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:869:49: error: 'mutex_it' was not declared in this scope; did you mean 'kmutex_t'? 869 | unique_lock lock(mutex_it); | ^~~~~~~~ | kmutex_t /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'void ColoredCDBG::buildUnitigColors(std::size_t)': /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1060:9: error: reference to 'mutex' is ambiguous 1060 | mutex mutex_file; | ^~~~~ /opt/tools/gcc13/include/c++/13.3.0/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-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1082:50: error: template argument 1 is invalid 1082 | unique_lock lock(mutex_file); | ^ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1082:57: error: 'mutex_file' was not declared in this scope 1082 | unique_lock lock(mutex_file); | ^~~~~~~~~~ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'void ColoredCDBG::buildUnitigColors(std::size_t)': /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1117:17: error: reference to 'mutex' is ambiguous 1117 | mutex mutex_it; | ^~~~~ /opt/tools/gcc13/include/c++/13.3.0/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-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1130:54: error: template argument 1 is invalid 1130 | unique_lock lock(mutex_it); | ^ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1130:61: error: 'mutex_it' was not declared in this scope; did you mean 'kmutex_t'? 1130 | unique_lock lock(mutex_it); | ^~~~~~~~ | kmutex_t /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In member function 'bool ColoredCDBG::search(const std::vector >&, const std::string&, double, bool, std::size_t, bool) const': /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/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++/13.3.0/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-0.51.1/ext/bifrost/src/ColoredCDBG.tcc: In lambda function: /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1740:46: error: template argument 1 is invalid 1740 | unique_lock lock(mutex_files_in); | ^ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1740:53: error: 'mutex_files_in' was not declared in this scope 1740 | unique_lock lock(mutex_files_in); | ^~~~~~~~~~~~~~ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1783:50: error: template argument 1 is invalid 1783 | unique_lock lock(mutex_file_out); | ^ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1783:57: error: 'mutex_file_out' was not declared in this scope 1783 | unique_lock lock(mutex_file_out); | ^~~~~~~~~~~~~~ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1801:46: error: template argument 1 is invalid 1801 | unique_lock lock(mutex_file_out); | ^ /home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/src/ColoredCDBG.tcc:1801:53: error: 'mutex_file_out' was not declared in this scope 1801 | unique_lock lock(mutex_file_out); | ^~~~~~~~~~~~~~ gmake[5]: *** [src/CMakeFiles/bifrost_static.dir/build.make:82: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1 gmake[5]: Leaving directory '/home/pbulk/build/biology/kallisto/work/kallisto-0.51.1/ext/bifrost/build' gmake[4]: *** [CMakeFiles/Makefile2:115: src/CMakeFiles/bifrost_static.dir/all] Error 2 gmake[4]: Leaving directory 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