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build_failure.linux-64.yaml
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recipe_sha: 5d19fabaadfaf7687d740f9e2d47033957403db41a3836624b1d7f73766e540c # The hash of the recipe's meta.yaml 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.
category: compiler error
log: |-
checking pkg-config is at least version 0.9.0... yes
checking for DEPS... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for memset... yes
checking for libintl.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for strings.h... (cached) yes
checking for unistd.h... (cached) yes
checking for wchar.h... yes
checking for GNU libc compatible malloc... yes
checking for _Bool... yes
checking for stdbool.h that conforms to C99... yes
checking for size_t... yes
checking how to run the C preprocessor... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp
checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc needs -traditional... no
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/config.h
config.status: executing depfiles commands
Making all in src
make[1]: Entering directory '$SRC_DIR/src'
make all-am
make[2]: Entering directory '$SRC_DIR/src'
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -DHAVE_CONFIG_H -I. -I$PREFIX/include/libMems-1.6 -I$PREFIX/include/libGenome-1.3 -I$PREFIX/include/libMUSCLE-3.7 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -Ofast -DCOMMAND_LINE -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/mauvealigner-1.2.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -MT mauveAligner.o -MD -MP -MF .deps/mauveAligner.Tpo -c -o mauveAligner.o mauveAligner.cpp
In file included from /opt/conda/conda-bld/mauvealigner_1718134884435/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/ext/hash_map:60,
from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/dptables.h:43,
from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/homology.h:27,
from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/Islands.h:25,
from mauveAligner.cpp:29:
/opt/conda/conda-bld/mauvealigner_1718134884435/_build_env/x86_64-conda-linux-gnu/include/c/12.3.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated. [-Wcpp]
32 | #warning \
| ^~~~~~~
mauveAligner.cpp:47: warning: "NELEMS" redefined
47 | #define NELEMS(a) ( sizeof( a ) / sizeof( *a ) )
|
In file included from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/SlotAllocator.h:20,
from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/AbstractMatch.h:23,
from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/UngappedLocalAlignment.h:18,
from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/Match.h:19,
from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/MatchFinder.h:17,
from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/MemHash.h:20,
from mauveAligner.cpp:21:
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMUSCLE-3.7/libMUSCLE/threadstorage.h:22: note: this is the location of the previous definition
22 | #define NELEMS(o) sizeof(o)/sizeof(o[0])
|
In file included from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/MatchList.h:25,
from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/MatchFinder.h:18:
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/Files.h: In function 'std::string CreateTempFileName(const std::string&)':
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/Files.h:82:20: error: 'class boost::filesystem::path' has no member named 'branch_path'
82 | dir = path.branch_path().string();
| ^~~~~~~~~~~
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/Files.h:86:21: error: 'class boost::filesystem::path' has no member named 'leaf'
86 | name = path.leaf().string();
| ^~~~
In file included from /opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/homology.h:28:
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/algebras.h: In function 'BFloat double2bfloat(double)':
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/algebras.h:190:21: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister]
190 | register BFloat a( 0.0, 0 );
| ^
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_product(const BFloat&, const BFloat&)':
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/algebras.h:209:19: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister]
209 | register BFloat sf(a.f*b.f,a.eb.e);
| ^~
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_double_product(const BFloat&, double)':
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/algebras.h:216:19: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister]
216 | register double mantisse = a.f*b;
| ^~~~~~~~
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/algebras.h: In function 'void bfloat_pr_double_product_accum(BFloat&, double)':
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/algebras.h:229:19: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister]
229 | register double mantisse = a.f*b;
| ^~~~~~~~
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/algebras.h: In function 'BFloat bfloat_pr_quotient(const BFloat&, const BFloat&)':
/opt/conda/conda-bld/mauvealigner_1718134884435/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/include/libMems-1.6/libMems/HomologyHMM/algebras.h:236:19: warning: ISO C17 does not allow 'register' storage class specifier [-Wregister]
236 | register BFloat sf(a.f/b.f, a.e-b.e);
| ^~
make[2]: *** [Makefile:1084: mauveAligner.o] Error 1
make[2]: Leaving directory '$SRC_DIR/src'
make[1]: *** [Makefile:716: all] Error 2
make[1]: Leaving directory '$SRC_DIR/src'
make: *** [Makefile:392: all-recursive] Error 1
Traceback (most recent call last):
File "/opt/conda/bin/conda-build", line 11, in <module>
sys.exit(execute())
File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
api.build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
return build_tree(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
packages_from_this = build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
utils.check_call_env(
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env
return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs)
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/mauvealigner_1718134884435/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.