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build_failure.linux-64.yaml
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recipe_sha: 5d9e1fb602de088de623591a9c19295b874c8191aae8f446e60911e3024904ff # 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: |-
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT hts/samrecord.lo -MD -MP -MF hts/.deps/samrecord.Tpo -c hts/samrecord.cc -fPIC -DPIC -o hts/.libs/samrecord.o
x86_64-conda-linux-gnu-c: warning: switch '-ffor-scope' is no longer supported
hts/samrecord.cc: In member function 'void Sequence::samrecord_private::parse_tags()':
hts/samrecord.cc:182:85: warning: 'std::pointer_to_unary_function<_Arg, _Result> std::ptr_fun(_Result (*)(_Arg)) [with _Arg = int; _Result = int]' is deprecated: use 'std::function' instead [-Wdeprecated-declarations]
182 | whitespace_start = find_if( whitespace_end1,tags_end, not1(ptr_fun<int,int>(std::isspace)) );
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
In file included from /opt/conda/conda-bld/libsequence_1685480858268/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/string:48,
from ../Sequence/samrecord.hpp:6,
from hts/samrecord.cc:1:
/opt/conda/conda-bld/libsequence_1685480858268/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/bits/stl_function.h:1126:5: note: declared here
1126 | ptr_fun(_Result (*__x)(_Arg))
| ^~~~~~~
hts/samrecord.cc:182:68: warning: 'constexpr std::unary_negate<_Predicate> std::not1(const _Predicate&) [with _Predicate = pointer_to_unary_function<int, int>]' is deprecated: use 'std::not_fn' instead [-Wdeprecated-declarations]
182 | whitespace_start = find_if( whitespace_end1,tags_end, not1(ptr_fun<int,int>(std::isspace)) );
| ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/opt/conda/conda-bld/libsequence_1685480858268/_build_env/x86_64-conda-linux-gnu/include/c/12.2.0/bits/stl_function.h:1046:5: note: declared here
1046 | not1(const _Predicate& __pred)
| ^~~~
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT hts/samrecord.lo -MD -MP -MF hts/.deps/samrecord.Tpo -c hts/samrecord.cc -o hts/samrecord.o >/dev/null 2>&1
depbase=echo hts/samflag.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\
/bin/sh ../libtool --tag=CXX --mode=compile $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT hts/samflag.lo -MD -MP -MF $depbase.Tpo -c -o hts/samflag.lo hts/samflag.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT hts/samflag.lo -MD -MP -MF hts/.deps/samflag.Tpo -c hts/samflag.cc -fPIC -DPIC -o hts/.libs/samflag.o
x86_64-conda-linux-gnu-c: warning: switch '-ffor-scope' is no longer supported
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT hts/samflag.lo -MD -MP -MF hts/.deps/samflag.Tpo -c hts/samflag.cc -o hts/samflag.o >/dev/null 2>&1
depbase=echo hts/samfunctions.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\
/bin/sh ../libtool --tag=CXX --mode=compile $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT hts/samfunctions.lo -MD -MP -MF $depbase.Tpo -c -o hts/samfunctions.lo hts/samfunctions.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT hts/samfunctions.lo -MD -MP -MF hts/.deps/samfunctions.Tpo -c hts/samfunctions.cc -fPIC -DPIC -o hts/.libs/samfunctions.o
x86_64-conda-linux-gnu-c: warning: switch '-ffor-scope' is no longer supported
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT hts/samfunctions.lo -MD -MP -MF hts/.deps/samfunctions.Tpo -c hts/samfunctions.cc -o hts/samfunctions.o >/dev/null 2>&1
depbase=echo polySiteVector.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\
/bin/sh ../libtool --tag=CXX --mode=compile $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -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.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT polySiteVector.lo -MD -MP -MF .deps/polySiteVector.Tpo -c polySiteVector.cc -fPIC -DPIC -o .libs/polySiteVector.o
x86_64-conda-linux-gnu-c: warning: switch '-ffor-scope' is no longer supported
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT polySiteVector.lo -MD -MP -MF .deps/polySiteVector.Tpo -c polySiteVector.cc -o polySiteVector.o >/dev/null 2>&1
depbase=echo SummStats/SummStats.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||';\
/bin/sh ../libtool --tag=CXX --mode=compile $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT SummStats/SummStats.lo -MD -MP -MF $depbase.Tpo -c -o SummStats/SummStats.lo SummStats/SummStats.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I.. -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Wall -W -Woverloaded-virtual -Wnon-virtual-dtor -Wcast-qual -Wconversion -Wsign-conversion -Wsign-promo -Wsynth -ffor-scope -DHAVE_HTSLIB -DNDEBUG -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/libsequence-1.8.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -DNDEBUG -MT SummStats/SummStats.lo -MD -MP -MF SummStats/.deps/SummStats.Tpo -c SummStats/SummStats.cc -fPIC -DPIC -o SummStats/.libs/SummStats.o
x86_64-conda-linux-gnu-c: warning: switch '-ffor-scope' is no longer supported
In file included from SummStats/SummStats.cc:2:
../Sequence/SimData.hpp: In member function 'virtual void Sequence::SimData::Binary(const bool&, const unsigned int&, const bool&)':
../Sequence/SimData.hpp:96:33: warning: unused parameter 'haveOutgroup' [-Wunused-parameter]
96 | void Binary (const bool & haveOutgroup = false,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
../Sequence/SimData.hpp:97:37: warning: unused parameter 'outgroup' [-Wunused-parameter]
97 | const unsigned & outgroup = 0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
../Sequence/SimData.hpp:98:33: warning: unused parameter 'strictInfSites' [-Wunused-parameter]
98 | const bool & strictInfSites = true)
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~
SummStats/SummStats.cc: In function 'double Sequence::Gmin(const polySiteVector&, const std::vector<unsigned int>&)':
SummStats/SummStats.cc:42:21: error: 'numeric_limits' was not declared in this scope
42 | unsigned mdxy = numeric_limits<unsigned>::max(),sumdxy=0;
| ^~~~~~~~~~~~~~
SummStats/SummStats.cc:42:36: error: expected primary-expression before 'unsigned'
42 | unsigned mdxy = numeric_limits<unsigned>::max(),sumdxy=0;
| ^~~~~~~~
SummStats/SummStats.cc:42:14: warning: unused variable 'mdxy' [-Wunused-variable]
42 | unsigned mdxy = numeric_limits<unsigned>::max(),sumdxy=0;
| ^~~~
SummStats/SummStats.cc:43:3: warning: no return statement in function returning non-void [-Wreturn-type]
43 | }
| ^
SummStats/SummStats.cc:40:38: warning: unused parameter 'pt' [-Wunused-parameter]
40 | double Gmin(const polySiteVector & pt, const std::vector< unsigned > & config)
| ~~~~~~~~~~~~~~~~~~~~~~~^~
SummStats/SummStats.cc:40:74: warning: unused parameter 'config' [-Wunused-parameter]
40 | double Gmin(const polySiteVector & pt, const std::vector< unsigned > & config)
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~
SummStats/SummStats.cc: At global scope:
SummStats/SummStats.cc:10:10: warning: 'double {anonymous}::__nSLsum(const unsigned int&, const Sequence::SimData&, const std::vector<long unsigned int>&)' declared 'static' but never defined [-Wunused-function]
10 | double __nSLsum(const unsigned & core,
| ^~~~~~~~
make[2]: *** [Makefile:647: SummStats/SummStats.lo] Error 1
make[2]: Leaving directory '$SRC_DIR/src'
make[1]: *** [Makefile:394: all-recursive] Error 1
make[1]: Leaving directory '$SRC_DIR'
make: *** [Makefile:325: all] 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/libsequence_1685480858268/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.