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build_failure.linux-64.yaml
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recipe_sha: a4575da0b6a8bed7fbc9246e3aced184bc35e545b73847a2be0b0706d3b71c36 # The commit at which this recipe failed to build.
skiplist: true # Set to true to skiplist this recipe so that it will be ignored as long as its latest commit is the one given above.
log: |-
[ 61%] Building CXX object libs/ma/CMakeFiles/libMA.dir/src/module/compare_alignments.cpp.o
cd $SRC_DIR/build/libs/ma && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DDLL_PORT_MA=dllexport -DDLL_PORT_MS=dllimport -DDLL_PORT_util=dllimport -DWITH_PYTHON -DWITH_ZLIB -DlibMA_EXPORTS -I$SRC_DIR/libs/ma/inc -I$SRC_DIR/libs/util/inc -I$SRC_DIR/contrib/./json -I$SRC_DIR/contrib/./intervalTree -I$SRC_DIR/libs/ms/inc -I$SRC_DIR/build/generated -I$SRC_DIR/libs/kswcpp/inc -I$SRC_DIR/libs/minimizerscpp/inc -isystem $SRC_DIR/contrib/pybind11/include -isystem $PREFIX/include/python3.9 -isystem $SRC_DIR/contrib/./pybind11_json/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ma-2.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -std=gnu17 -fPIC -Wall -std=c17 -flto -fno-fat-lto-objects -MD -MT libs/ma/CMakeFiles/libMA.dir/src/module/compare_alignments.cpp.o -MF CMakeFiles/libMA.dir/src/module/compare_alignments.cpp.o.d -o CMakeFiles/libMA.dir/src/module/compare_alignments.cpp.o -c $SRC_DIR/libs/ma/src/module/compare_alignments.cpp
[ 62%] Building CXX object libs/ma/CMakeFiles/libMA.dir/src/module/fileReader.cpp.o
cd $SRC_DIR/build/libs/ma && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DDLL_PORT_MA=dllexport -DDLL_PORT_MS=dllimport -DDLL_PORT_util=dllimport -DWITH_PYTHON -DWITH_ZLIB -DlibMA_EXPORTS -I$SRC_DIR/libs/ma/inc -I$SRC_DIR/libs/util/inc -I$SRC_DIR/contrib/./json -I$SRC_DIR/contrib/./intervalTree -I$SRC_DIR/libs/ms/inc -I$SRC_DIR/build/generated -I$SRC_DIR/libs/kswcpp/inc -I$SRC_DIR/libs/minimizerscpp/inc -isystem $SRC_DIR/contrib/pybind11/include -isystem $PREFIX/include/python3.9 -isystem $SRC_DIR/contrib/./pybind11_json/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ma-2.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -std=gnu17 -fPIC -Wall -std=c17 -flto -fno-fat-lto-objects -MD -MT libs/ma/CMakeFiles/libMA.dir/src/module/fileReader.cpp.o -MF CMakeFiles/libMA.dir/src/module/fileReader.cpp.o.d -o CMakeFiles/libMA.dir/src/module/fileReader.cpp.o -c $SRC_DIR/libs/ma/src/module/fileReader.cpp
[ 64%] Building CXX object libs/ma/CMakeFiles/libMA.dir/src/module/fileWriter.cpp.o
cd $SRC_DIR/build/libs/ma && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DDLL_PORT_MA=dllexport -DDLL_PORT_MS=dllimport -DDLL_PORT_util=dllimport -DWITH_PYTHON -DWITH_ZLIB -DlibMA_EXPORTS -I$SRC_DIR/libs/ma/inc -I$SRC_DIR/libs/util/inc -I$SRC_DIR/contrib/./json -I$SRC_DIR/contrib/./intervalTree -I$SRC_DIR/libs/ms/inc -I$SRC_DIR/build/generated -I$SRC_DIR/libs/kswcpp/inc -I$SRC_DIR/libs/minimizerscpp/inc -isystem $SRC_DIR/contrib/pybind11/include -isystem $PREFIX/include/python3.9 -isystem $SRC_DIR/contrib/./pybind11_json/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ma-2.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -std=gnu17 -fPIC -Wall -std=c17 -flto -fno-fat-lto-objects -MD -MT libs/ma/CMakeFiles/libMA.dir/src/module/fileWriter.cpp.o -MF CMakeFiles/libMA.dir/src/module/fileWriter.cpp.o.d -o CMakeFiles/libMA.dir/src/module/fileWriter.cpp.o -c $SRC_DIR/libs/ma/src/module/fileWriter.cpp
[ 66%] Building CXX object libs/ma/CMakeFiles/libMA.dir/src/module/harmonization.cpp.o
cd $SRC_DIR/build/libs/ma && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DDLL_PORT_MA=dllexport -DDLL_PORT_MS=dllimport -DDLL_PORT_util=dllimport -DWITH_PYTHON -DWITH_ZLIB -DlibMA_EXPORTS -I$SRC_DIR/libs/ma/inc -I$SRC_DIR/libs/util/inc -I$SRC_DIR/contrib/./json -I$SRC_DIR/contrib/./intervalTree -I$SRC_DIR/libs/ms/inc -I$SRC_DIR/build/generated -I$SRC_DIR/libs/kswcpp/inc -I$SRC_DIR/libs/minimizerscpp/inc -isystem $SRC_DIR/contrib/pybind11/include -isystem $PREFIX/include/python3.9 -isystem $SRC_DIR/contrib/./pybind11_json/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ma-2.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -std=gnu17 -fPIC -Wall -std=c17 -flto -fno-fat-lto-objects -MD -MT libs/ma/CMakeFiles/libMA.dir/src/module/harmonization.cpp.o -MF CMakeFiles/libMA.dir/src/module/harmonization.cpp.o.d -o CMakeFiles/libMA.dir/src/module/harmonization.cpp.o -c $SRC_DIR/libs/ma/src/module/harmonization.cpp
[ 67%] Building CXX object libs/ma/CMakeFiles/libMA.dir/src/module/hashMapSeeding.cpp.o
cd $SRC_DIR/build/libs/ma && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DDLL_PORT_MA=dllexport -DDLL_PORT_MS=dllimport -DDLL_PORT_util=dllimport -DWITH_PYTHON -DWITH_ZLIB -DlibMA_EXPORTS -I$SRC_DIR/libs/ma/inc -I$SRC_DIR/libs/util/inc -I$SRC_DIR/contrib/./json -I$SRC_DIR/contrib/./intervalTree -I$SRC_DIR/libs/ms/inc -I$SRC_DIR/build/generated -I$SRC_DIR/libs/kswcpp/inc -I$SRC_DIR/libs/minimizerscpp/inc -isystem $SRC_DIR/contrib/pybind11/include -isystem $PREFIX/include/python3.9 -isystem $SRC_DIR/contrib/./pybind11_json/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ma-2.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -std=gnu17 -fPIC -Wall -std=c17 -flto -fno-fat-lto-objects -MD -MT libs/ma/CMakeFiles/libMA.dir/src/module/hashMapSeeding.cpp.o -MF CMakeFiles/libMA.dir/src/module/hashMapSeeding.cpp.o.d -o CMakeFiles/libMA.dir/src/module/hashMapSeeding.cpp.o -c $SRC_DIR/libs/ma/src/module/hashMapSeeding.cpp
In file included from /opt/conda/conda-bld/ma_1686045558915/work/libs/ma/inc/ma/module/harmonization.h:9,
from /opt/conda/conda-bld/ma_1686045558915/work/libs/ma/src/module/harmonization.cpp:5:
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h: In member function 'std::pair<_FIter, _FIter> interval_tree::IntervalTree<Scalar, Value>::extentBruitForce() const':
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:277:49: error: 'numeric_limits' is not a member of 'std'
277 | std::pair<Scalar, Scalar> x = {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )};
| ^~~~~~~~~~~~~~
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:277:70: error: expected primary-expression before '>' token
277 | std::pair<Scalar, Scalar> x = {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )};
| ^
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:277:73: error: '::max' has not been declared; did you mean 'std::max'?
277 | std::pair<Scalar, Scalar> x = {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )};
| ^~~
| std::max
In file included from /opt/conda/conda-bld/ma_1686045558915/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/algorithm:61,
from /opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:6:
/opt/conda/conda-bld/ma_1686045558915/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/bits/stl_algo.h:5756:5: note: 'std::max' declared here
5756 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:277:86: error: 'numeric_limits' is not a member of 'std'
277 | std::pair<Scalar, Scalar> x = {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )};
| ^~~~~~~~~~~~~~
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:277:107: error: expected primary-expression before '>' token
277 | std::pair<Scalar, Scalar> x = {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )};
| ^
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:277:110: error: '::min' has not been declared; did you mean 'std::min'?
277 | std::pair<Scalar, Scalar> x = {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )};
| ^~~
| std::min
/opt/conda/conda-bld/ma_1686045558915/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/bits/stl_algo.h:5736:5: note: 'std::min' declared here
5736 | min(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h: In member function 'std::pair<bool, std::pair<_FIter, _FIter> > interval_tree::IntervalTree<Scalar, Value>::is_valid() const':
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:298:25: error: 'numeric_limits' is not a member of 'std'
298 | true, {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )}};
| ^~~~~~~~~~~~~~
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:298:46: error: expected primary-expression before '>' token
298 | true, {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )}};
| ^
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:298:49: error: '::max' has not been declared; did you mean 'std::max'?
298 | true, {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )}};
| ^~~
| std::max
/opt/conda/conda-bld/ma_1686045558915/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/bits/stl_algo.h:5756:5: note: 'std::max' declared here
5756 | max(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:298:62: error: 'numeric_limits' is not a member of 'std'
298 | true, {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )}};
| ^~~~~~~~~~~~~~
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:298:83: error: expected primary-expression before '>' token
298 | true, {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )}};
| ^
/opt/conda/conda-bld/ma_1686045558915/work/contrib/./intervalTree/IntervalTree.h:298:86: error: '::min' has not been declared; did you mean 'std::min'?
298 | true, {std::numeric_limits<Scalar>::max( ), std::numeric_limits<Scalar>::min( )}};
| ^~~
| std::min
/opt/conda/conda-bld/ma_1686045558915/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/bits/stl_algo.h:5736:5: note: 'std::min' declared here
5736 | min(initializer_list<_Tp> __l, _Compare __comp)
| ^~~
[ 69%] Building CXX object libs/ma/CMakeFiles/libMA.dir/src/module/mappingQuality.cpp.o
cd $SRC_DIR/build/libs/ma && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DDLL_PORT_MA=dllexport -DDLL_PORT_MS=dllimport -DDLL_PORT_util=dllimport -DWITH_PYTHON -DWITH_ZLIB -DlibMA_EXPORTS -I$SRC_DIR/libs/ma/inc -I$SRC_DIR/libs/util/inc -I$SRC_DIR/contrib/./json -I$SRC_DIR/contrib/./intervalTree -I$SRC_DIR/libs/ms/inc -I$SRC_DIR/build/generated -I$SRC_DIR/libs/kswcpp/inc -I$SRC_DIR/libs/minimizerscpp/inc -isystem $SRC_DIR/contrib/pybind11/include -isystem $PREFIX/include/python3.9 -isystem $SRC_DIR/contrib/./pybind11_json/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ma-2.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -std=gnu17 -fPIC -Wall -std=c17 -flto -fno-fat-lto-objects -MD -MT libs/ma/CMakeFiles/libMA.dir/src/module/mappingQuality.cpp.o -MF CMakeFiles/libMA.dir/src/module/mappingQuality.cpp.o.d -o CMakeFiles/libMA.dir/src/module/mappingQuality.cpp.o -c $SRC_DIR/libs/ma/src/module/mappingQuality.cpp
[ 71%] Building CXX object libs/ma/CMakeFiles/libMA.dir/src/module/minimizerSeeding.cpp.o
cd $SRC_DIR/build/libs/ma && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DDLL_PORT_MA=dllexport -DDLL_PORT_MS=dllimport -DDLL_PORT_util=dllimport -DWITH_PYTHON -DWITH_ZLIB -DlibMA_EXPORTS -I$SRC_DIR/libs/ma/inc -I$SRC_DIR/libs/util/inc -I$SRC_DIR/contrib/./json -I$SRC_DIR/contrib/./intervalTree -I$SRC_DIR/libs/ms/inc -I$SRC_DIR/build/generated -I$SRC_DIR/libs/kswcpp/inc -I$SRC_DIR/libs/minimizerscpp/inc -isystem $SRC_DIR/contrib/pybind11/include -isystem $PREFIX/include/python3.9 -isystem $SRC_DIR/contrib/./pybind11_json/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ma-2.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -std=gnu17 -fPIC -Wall -std=c17 -flto -fno-fat-lto-objects -MD -MT libs/ma/CMakeFiles/libMA.dir/src/module/minimizerSeeding.cpp.o -MF CMakeFiles/libMA.dir/src/module/minimizerSeeding.cpp.o.d -o CMakeFiles/libMA.dir/src/module/minimizerSeeding.cpp.o -c $SRC_DIR/libs/ma/src/module/minimizerSeeding.cpp
[ 72%] Building CXX object libs/ma/CMakeFiles/libMA.dir/src/module/needlemanWunsch.cpp.o
cd $SRC_DIR/build/libs/ma && $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DDLL_PORT_MA=dllexport -DDLL_PORT_MS=dllimport -DDLL_PORT_util=dllimport -DWITH_PYTHON -DWITH_ZLIB -DlibMA_EXPORTS -I$SRC_DIR/libs/ma/inc -I$SRC_DIR/libs/util/inc -I$SRC_DIR/contrib/./json -I$SRC_DIR/contrib/./intervalTree -I$SRC_DIR/libs/ms/inc -I$SRC_DIR/build/generated -I$SRC_DIR/libs/kswcpp/inc -I$SRC_DIR/libs/minimizerscpp/inc -isystem $SRC_DIR/contrib/pybind11/include -isystem $PREFIX/include/python3.9 -isystem $SRC_DIR/contrib/./pybind11_json/include -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/ma-2.0.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -std=gnu17 -fPIC -Wall -std=c17 -flto -fno-fat-lto-objects -MD -MT libs/ma/CMakeFiles/libMA.dir/src/module/needlemanWunsch.cpp.o -MF CMakeFiles/libMA.dir/src/module/needlemanWunsch.cpp.o.d -o CMakeFiles/libMA.dir/src/module/needlemanWunsch.cpp.o -c $SRC_DIR/libs/ma/src/module/needlemanWunsch.cpp
make[3]: *** [libs/ma/CMakeFiles/libMA.dir/build.make:286: libs/ma/CMakeFiles/libMA.dir/src/module/harmonization.cpp.o] Error 1
make[3]: *** Waiting for unfinished jobs....
make[3]: Leaving directory '$SRC_DIR/build'
make[2]: *** [CMakeFiles/Makefile2:1231: libs/ma/CMakeFiles/libMA.dir/all] Error 2
make[2]: Leaving directory '$SRC_DIR/build'
make[1]: *** [CMakeFiles/Makefile2:1053: CMakeFiles/maCMD.dir/rule] Error 2
make[1]: Leaving directory '$SRC_DIR/build'
make: *** [Makefile:543: maCMD] Error 2
Traceback (most recent call last):
File "/opt/conda/bin/conda-mambabuild", line 10, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
call_conda_build(action, config)
File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
result = api.build(
File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
return build_tree(
File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
packages_from_this = build(metadata, stats,
File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 2198, in build
utils.check_call_env(cmd, env=env, rewrite_stdout_env=rewrite_env,
File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 451, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/conda/lib/python3.8/site-packages/conda_build/utils.py", line 427, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/ma_1686045558915/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.