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build_failure.osx-64.yaml
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build_failure.osx-64.yaml
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recipe_sha: eadeb5962e3754b3c69828174d7d5f7e483e79ed9304eae11626f173217335b7 # 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: |-
build_alias=x86_64-apple-darwin13.4.0
host_alias=x86_64-apple-darwin13.4.0
INFO: activate_clangxx_osx-64.sh made the following environmental changes:
CLANGXX=x86_64-apple-darwin13.4.0-clang
CXX=x86_64-apple-darwin13.4.0-clang
CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/glimmerhmm-3.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/glimmerhmm-3.0.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
make: Entering directory '$SRC_DIR/sources'
x86_64-apple-darwin13.4.0-clang -g -c glimmerhmm.c
x86_64-apple-darwin13.4.0-clang -g -c graph.c
x86_64-apple-darwin13.4.0-clang -g -c sites.c
x86_64-apple-darwin13.4.0-clang -g -c tree_util_prob.c
x86_64-apple-darwin13.4.0-clang -g -c util.c
x86_64-apple-darwin13.4.0-clang -g -o glimmerhmm glimmerhmm.o graph.o sites.o tree_util_prob.o util.o -lm
make: Leaving directory '$SRC_DIR/sources'
make: Entering directory '$SRC_DIR/train'
/bin/rm -f core* splicescore *.o score build? build-icm \
build-icm-noframe erfapp falsecomp findsites karlin score2 scoreATG \
scoreATG2 scoreSTOP scoreSTOP2
make: Leaving directory '$SRC_DIR/train'
make: Entering directory '$SRC_DIR/train'
x86_64-apple-darwin13.4.0-clang -Wall -g -c misc.c
x86_64-apple-darwin13.4.0-clang -Wall -g -c build-icm.c
x86_64-apple-darwin13.4.0-clang -Wall -g -c build-icm-noframe.c
x86_64-apple-darwin13.4.0-clang -Wall -g -o build-icm build-icm.o misc.o -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -o build-icm-noframe build-icm-noframe.o misc.o -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o build1.o build1.c
x86_64-apple-darwin13.4.0-clang -Wall -g build1.c -o build1 -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o build2.o build2.c
x86_64-apple-darwin13.4.0-clang -Wall -g build2.c -o build2 -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o falsecomp.o falsecomp.c
x86_64-apple-darwin13.4.0-clang -Wall -g falsecomp.c -o falsecomp -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o findsites.o findsites.c
x86_64-apple-darwin13.4.0-clang -Wall -g findsites.c -o findsites -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o karlin.o karlin.c
x86_64-apple-darwin13.4.0-clang -Wall -g karlin.c -o karlin -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o score.o score.c
x86_64-apple-darwin13.4.0-clang -Wall -g score.c -o score -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o score2.o score2.c
x86_64-apple-darwin13.4.0-clang -Wall -g score2.c -o score2 -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o scoreATG.o scoreATG.c
x86_64-apple-darwin13.4.0-clang -Wall -g scoreATG.c -o scoreATG -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o scoreATG2.o scoreATG2.c
x86_64-apple-darwin13.4.0-clang -Wall -g scoreATG2.c -o scoreATG2 -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o scoreSTOP.o scoreSTOP.c
x86_64-apple-darwin13.4.0-clang -Wall -g scoreSTOP.c -o scoreSTOP -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o scoreSTOP2.o scoreSTOP2.c
x86_64-apple-darwin13.4.0-clang -Wall -g scoreSTOP2.c -o scoreSTOP2 -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -c -o erfapp.o erfapp.c
x86_64-apple-darwin13.4.0-clang -Wall -g erfapp.c -o erfapp -lm
x86_64-apple-darwin13.4.0-clang -Wall -g -c splicescore.c
x86_64-apple-darwin13.4.0-clang -Wall -g -c sites.c
x86_64-apple-darwin13.4.0-clang -Wall -g -c utils.c
x86_64-apple-darwin13.4.0-clang splicescore.o sites.o utils.o -o splicescore -lm
make: Leaving directory '$SRC_DIR/train'
Resource usage statistics from building glimmerhmm:
Process count: 5
CPU time: Sys=0:00:00.2, User=0:00:00.7
Memory: 54.8M
Disk usage: 276.9K
Time elapsed: 0:00:12.4
Packaging glimmerhmm
Packaging glimmerhmm-3.0.4-pl5321h4a92bd6_8
error: /opt/mambaforge/envs/bioconda/conda-bld/glimmerhmm_1718142227412/_build_env/bin/x86_64-apple-darwin13.4.0-install_name_tool: changing install names or rpaths can't be redone for: /opt/mambaforge/envs/bioconda/conda-bld/glimmerhmm_1718142227412/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/share/glimmerhmm/train/splicescore (for architecture x86_64) because larger updated load commands do not fit (the program must be relinked, and you may need to use -headerpad or -headerpad_max_install_names)
number of files: 491
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in <module>
sys.exit(execute())
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
api.build(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
return build_tree(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
packages_from_this = build(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2711, in build
newly_built_packages = bundlers[pkg_type](output_d, m, env, stats)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1850, in bundle_conda
files = post_process_files(metadata, initial_files)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1664, in post_process_files
post_build(m, new_files, build_python=python)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1727, in post_build
post_process_shared_lib(m, f, prefix_files, host_prefix)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 1603, in post_process_shared_lib
mk_relative_osx(path, host_prefix, m, files=files, rpaths=rpaths)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/post.py", line 491, in mk_relative_osx
macho.add_rpath(path, rpath_new, build_prefix=prefix, verbose=True)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 297, in add_rpath
raise RuntimeError("install_name_tool failed with exit status %d" % code)
RuntimeError: install_name_tool failed with exit status 1
# Last 100 lines of the build log.