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build_failure.linux-64.yaml
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build_failure.linux-64.yaml
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recipe_sha: 950218319b05117f649a224c4689e3993db070bb73859f2668fead45d8dab9e4 # 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: |2-
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../Sequence/SummStatsDeprecated/Snn.hpp:38:10: note: declared here
38 | double Snn_statistic( const unsigned individuals[],
| ^~~~~~~~~~~~~
../Sequence/bits/Snn.tcc: In function 'std::vector<std::vector<double> > Sequence::Snn_test_pairwise_details(const PolyTable&, const unsigned int*, const size_t&, shuffler&, const unsigned int&)':
../Sequence/bits/Snn.tcc:112:50: warning: 'double Sequence::Snn_statistic(const unsigned int*, const std::vector<std::vector<double> >&, const unsigned int*, const size_t&, const unsigned int&)' is deprecated [-Wdeprecated-declarations]
112 | const double observed = Snn_statistic( &individuals[0],dkj,_config,2,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
113 | _config[0]_config[1]);
| ~~~~~~~~~~~~~~~~~~~~~~
../Sequence/SummStatsDeprecated/Snn.hpp:38:10: note: declared here
38 | double Snn_statistic( const unsigned individuals[],
| ^~~~~~~~~~~~~
../Sequence/bits/Snn.tcc:119:44: warning: 'double Sequence::Snn_statistic(const unsigned int*, const std::vector<std::vector<double> >&, const unsigned int*, const size_t&, const unsigned int&)' is deprecated [-Wdeprecated-declarations]
119 | double perm = Snn_statistic( &individuals[0],dkj,_config,2,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
120 | _config[0]_config[1]);
| ~~~~~~~~~~~~~~~~~~~~~~
../Sequence/SummStatsDeprecated/Snn.hpp:38:10: note: declared here
38 | double Snn_statistic( const unsigned individuals[],
| ^~~~~~~~~~~~~
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT summstats_deprecated/Snn.lo -MD -MP -MF summstats_deprecated/.deps/Snn.Tpo -c summstats_deprecated/Snn.cc -o summstats_deprecated/Snn.o >/dev/null 2>&1
depbase=echo polySiteVector.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\
/bin/sh ../libtool --tag=CXX --mode=compile $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT polySiteVector.lo -MD -MP -MF $depbase.Tpo -c -o polySiteVector.lo polySiteVector.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT polySiteVector.lo -MD -MP -MF .deps/polySiteVector.Tpo -c polySiteVector.cc -fPIC -DPIC -o .libs/polySiteVector.o
In file included from polySiteVector.cc:24:
../Sequence/PolyTable.hpp:238:59: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations]
238 | std::istream &operator>>(std::istream &s, PolyTable &c);
| ^
../Sequence/PolyTable.hpp:60:39: note: declared here
60 | class __attribute__((deprecated)) PolyTable
| ^~~~~~~~~
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT polySiteVector.lo -MD -MP -MF .deps/polySiteVector.Tpo -c polySiteVector.cc -o polySiteVector.o >/dev/null 2>&1
depbase=echo summstats_deprecated/SummStats.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\
/bin/sh ../libtool --tag=CXX --mode=compile $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT summstats_deprecated/SummStats.lo -MD -MP -MF $depbase.Tpo -c -o summstats_deprecated/SummStats.lo summstats_deprecated/SummStats.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -I$PREFIX/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -O3 -DNDEBUG -MT summstats_deprecated/SummStats.lo -MD -MP -MF summstats_deprecated/.deps/SummStats.Tpo -c summstats_deprecated/SummStats.cc -fPIC -DPIC -o summstats_deprecated/.libs/SummStats.o
In file included from ../Sequence/SimData.hpp:65,
from summstats_deprecated/SummStats.cc:2:
../Sequence/PolyTable.hpp:238:59: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations]
238 | std::istream &operator>>(std::istream &s, PolyTable &c);
| ^
../Sequence/PolyTable.hpp:60:39: note: declared here
60 | class __attribute__((deprecated)) PolyTable
| ^~~~~~~~~
../Sequence/SimData.hpp:81:56: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations]
81 | const SimData::const_site_iterator &end);
| ^
../Sequence/PolyTable.hpp:60:39: note: declared here
60 | class __attribute__((deprecated)) PolyTable
| ^~~~~~~~~
../Sequence/SimData.hpp:81:56: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations]
81 | const SimData::const_site_iterator &end);
| ^
../Sequence/PolyTable.hpp:60:39: note: declared here
60 | class __attribute__((deprecated)) PolyTable
| ^~~~~~~~~
../Sequence/SimData.hpp:81:56: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations]
81 | const SimData::const_site_iterator &end);
| ^
../Sequence/PolyTable.hpp:60:39: note: declared here
60 | class __attribute__((deprecated)) PolyTable
| ^~~~~~~~~
../Sequence/SimData.hpp:81:56: warning: 'PolyTable' is deprecated [-Wdeprecated-declarations]
81 | const SimData::const_site_iterator &end);
| ^
../Sequence/PolyTable.hpp:60:39: note: declared here
60 | class __attribute__((deprecated)) PolyTable
| ^~~~~~~~~
summstats_deprecated/SummStats.cc: In function 'double Sequence::Gmin(const polySiteVector&, const std::vector<unsigned int>&)':
summstats_deprecated/SummStats.cc:38:21: error: 'numeric_limits' was not declared in this scope
38 | unsigned mdxy = numeric_limits<unsigned>::max();
| ^~~~~~~~~~~~~~
summstats_deprecated/SummStats.cc:38:36: error: expected primary-expression before 'unsigned'
38 | unsigned mdxy = numeric_limits<unsigned>::max();
| ^~~~~~~~
make[2]: *** [Makefile:803: summstats_deprecated/SummStats.lo] Error 1
make[1]: *** [Makefile:407: all-recursive] Error 1
make: *** [Makefile:337: all] Error 2
make[2]: Leaving directory '$SRC_DIR/src'
make[1]: Leaving directory '$SRC_DIR'
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/libsequence_1685480385020/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.