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build_failure.osx-64.yaml
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recipe_sha: 451a18d20c15fd6308d14d27734b055a3c87b5a2b3f72fd3f016961c6b035670 # 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.
log: |-
STRIP=x86_64-apple-darwin13.4.0-strip
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0
ac_cv_func_malloc_0_nonnull=yes
ac_cv_func_realloc_0_nonnull=yes
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/assembly-stats-1.0.1 -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/assembly-stats-1.0.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
-- The C compiler identification is Clang 18.1.8
-- The CXX compiler identification is Clang 18.1.8
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: $BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PythonInterp: /opt/mambaforge/envs/bioconda/bin/python (found version "3.10.16")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Configuring done (2.3s)
-- Generating done (0.1s)
-- Build files have been written to: $SRC_DIR/build
[ 5%] Building CXX object gtest-1.7.0/CMakeFiles/gtest.dir/src/gtest-all.cc.o
[ 10%] Linking CXX static library libgtest.a
[ 10%] Built target gtest
[ 15%] Building CXX object gtest-1.7.0/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[ 21%] Linking CXX static library libgtest_main.a
[ 21%] Built target gtest_main
[ 26%] Building CXX object CMakeFiles/fasta.dir/fasta.cpp.o
[ 31%] Linking CXX static library libfasta.a
[ 31%] Built target fasta
[ 36%] Building CXX object CMakeFiles/fastq.dir/fastq.cpp.o
[ 42%] Linking CXX static library libfastq.a
[ 42%] Built target fastq
[ 47%] Building CXX object CMakeFiles/filetype.dir/filetype.cpp.o
[ 52%] Linking CXX static library libfiletype.a
[ 52%] Built target filetype
[ 57%] Building CXX object CMakeFiles/stats.dir/stats.cpp.o
[ 63%] Linking CXX static library libstats.a
[ 63%] Built target stats
[ 68%] Building CXX object CMakeFiles/runUnitTests.dir/fasta_unittest.cpp.o
[ 73%] Building CXX object CMakeFiles/runUnitTests.dir/fastq_unittest.cpp.o
[ 78%] Building CXX object CMakeFiles/runUnitTests.dir/filetype_unittest.cpp.o
[ 84%] Building CXX object CMakeFiles/runUnitTests.dir/stats_unittest.cpp.o
[ 89%] Linking CXX executable runUnitTests
[ 89%] Built target runUnitTests
[ 94%] Building CXX object CMakeFiles/assembly-stats.dir/assembly-stats.cpp.o
[100%] Linking CXX executable assembly-stats
[100%] Built target assembly-stats
Resource usage statistics from building assembly-stats:
Process count: 8
CPU time: Sys=0:00:01.0, User=0:00:10.1
Memory: 140.3M
Disk usage: 18.3K
Time elapsed: 0:00:31.9
Packaging assembly-stats
Packaging assembly-stats-1.0.1-h5fa12a8_9
number of files: 1
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 589, in execute
api.build(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build
return build_tree(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree
packages_from_this = build(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2765, in build
newly_built_packages = bundlers[pkg_type](
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 1874, 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 1653, 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 1759, 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 1635, 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 488, in mk_relative_osx
existing_rpaths = macho.get_rpaths(path, build_prefix=prefix)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 252, in get_rpaths
dylib_loads = otool(path, build_prefix, is_rpath)
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/os_utils/macho.py", line 221, in otool
lines = check_output([otool, "-l", path], stderr=STDOUT).decode("utf-8")
File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 421, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/opt/mambaforge/envs/bioconda/lib/python3.10/subprocess.py", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['/opt/mambaforge/envs/bioconda/conda-bld/assembly-stats_1734455441579/_build_env/bin/llvm-otool', '-l', '/opt/mambaforge/envs/bioconda/conda-bld/assembly-stats_1734455441579/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold/bin/assembly-stats']' died with <Signals.SIGABRT: 6>.
# Last 100 lines of the build log.
reason: |-
see https://github.com/conda/conda-build/issues/5429
category: |-
conda/mamba bug