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build_failure.linux-64.yaml
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build_failure.linux-64.yaml
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recipe_sha: 9ca250dcb0bb92c7fbc8f6d93298df6e822064c3519b9234b23a1ff25b66e86e # 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: |-
[ 0%] Building CXX object ext/bpp/bpp-core/src/CMakeFiles/bpp-core.dir/Bpp/App/ApplicationTools.cpp.o
[ 0%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/compress.c.o
[ 1%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/parse_utree.c.o
[ 1%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/parse_rtree.c.o
[ 2%] Building CXX object ext/bpp/bpp-core/src/CMakeFiles/bpp-core.dir/Bpp/BppString.cpp.o
[ 2%] Building CXX object ext/bpp/bpp-core/src/CMakeFiles/bpp-core.dir/Bpp/Exceptions.cpp.o
[ 3%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/lex_utree.c.o
[ 4%] Building CXX object ext/bpp/bpp-core/src/CMakeFiles/bpp-core.dir/Bpp/Graph/GlobalGraph.cpp.o
/home/benoit/github/libpll-2/src/lex_utree.l: In function 'pll_utree_lex':
/home/benoit/github/libpll-2/src/lex_utree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 2 bytes from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_utree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 1 byte from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_utree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 2 bytes from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_utree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 2 bytes from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_utree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 1 byte from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_utree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 2 bytes from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_utree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 1 byte from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_utree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 2 bytes from a string of the same length [-Wstringop-truncation]
[ 4%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/lex_rtree.c.o
/opt/conda/conda-bld/treerecs_1685351442525/work/ext/bpp/bpp-core/src/Bpp/Graph/GlobalGraph.cpp: In member function 'virtual void bpp::GlobalGraph::orientate()':
/opt/conda/conda-bld/treerecs_1685351442525/work/ext/bpp/bpp-core/src/Bpp/Graph/GlobalGraph.cpp:776:20: error: 'numeric_limits' was not declared in this scope
776 | size_t nbF = numeric_limits<size_t>::infinity();
| ^~~~~~~~~~~~~~
/opt/conda/conda-bld/treerecs_1685351442525/work/ext/bpp/bpp-core/src/Bpp/Graph/GlobalGraph.cpp:776:41: error: expected primary-expression before '>' token
776 | size_t nbF = numeric_limits<size_t>::infinity();
| ^
/opt/conda/conda-bld/treerecs_1685351442525/work/ext/bpp/bpp-core/src/Bpp/Graph/GlobalGraph.cpp:776:44: error: '::infinity' has not been declared
776 | size_t nbF = numeric_limits<size_t>::infinity();
| ^~~~~~~~
make[2]: *** [ext/bpp/bpp-core/src/CMakeFiles/bpp-core.dir/build.make:118: ext/bpp/bpp-core/src/CMakeFiles/bpp-core.dir/Bpp/Graph/GlobalGraph.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:600: ext/bpp/bpp-core/src/CMakeFiles/bpp-core.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 6%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_derivatives.c.o
/home/benoit/github/libpll-2/src/lex_rtree.l: In function 'pll_rtree_lex':
/home/benoit/github/libpll-2/src/lex_rtree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 2 bytes from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_rtree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 1 byte from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_rtree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 2 bytes from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_rtree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 2 bytes from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_rtree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 1 byte from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_rtree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 2 bytes from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_rtree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 1 byte from a string of the same length [-Wstringop-truncation]
/home/benoit/github/libpll-2/src/lex_rtree.l:62:3: warning: '__builtin_strncpy' output truncated before terminating nul copying 2 bytes from a string of the same length [-Wstringop-truncation]
[ 6%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_likelihood.c.o
[ 7%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_partials.c.o
[ 7%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_pmatrix.c.o
[ 8%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/derivatives.c.o
[ 8%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/fasta.c.o
[ 9%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/fast_parsimony.c.o
[ 9%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/gamma.c.o
[ 11%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/hardware.c.o
[ 11%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/likelihood.c.o
[ 12%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/list.c.o
[ 12%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/maps.c.o
[ 13%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/models.c.o
[ 13%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/output.c.o
[ 14%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/parsimony.c.o
[ 14%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/partials.c.o
[ 16%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/phylip.c.o
[ 16%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/pll.c.o
[ 17%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/random.c.o
[ 17%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/repeats.c.o
[ 18%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/rtree.c.o
[ 18%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/stepwise.c.o
[ 19%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/utree.c.o
[ 19%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/utree_moves.c.o
[ 20%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/utree_svg.c.o
[ 20%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_derivatives_sse.c.o
[ 22%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_likelihood_sse.c.o
[ 22%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_partials_sse.c.o
[ 23%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_pmatrix_sse.c.o
[ 23%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/fast_parsimony_sse.c.o
[ 23%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_derivatives_avx.c.o
[ 24%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_likelihood_avx.c.o
[ 24%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_partials_avx.c.o
[ 25%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_pmatrix_avx.c.o
[ 25%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/fast_parsimony_avx.c.o
[ 27%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_derivatives_avx2.c.o
[ 27%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_likelihood_avx2.c.o
[ 28%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_partials_avx2.c.o
[ 28%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/core_pmatrix_avx2.c.o
[ 29%] Building C object ext/pll/libpll-2/src/CMakeFiles/pll_obj.dir/fast_parsimony_avx2.c.o
[ 29%] Built target pll_obj
make: *** [Makefile:146: 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/treerecs_1685351442525/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.