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build_failure.osx-64.yaml
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build_failure.osx-64.yaml
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recipe_sha: 8f26375d8b5482a572de19471f95b0c74d50dea5df302d8ab63ff1f5fd6927b9 # 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: |2-
Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-711-ha20a434_0/bin/../lib/libtapi.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-711-ha20a434_0/bin/../lib/libtapi.dylib' (no such file), '/usr/local/lib/libtapi.dylib' (no such file), '/usr/lib/libtapi.dylib' (no such file, not in dyld cache)
clang-16: error: unable to execute command: Abort trap: 6
clang-16: error: linker command failed due to signal (use -v to see invocation)
error: command '/opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/_build_env/bin/x86_64-apple-darwin13.4.0-clang' failed with exit code 1
Extracting download
source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/work
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 2506, in build
utils.check_call_env(
export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
File "/opt/mambaforge/envs/bioconda/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)
export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/_build_env
File "/opt/mambaforge/envs/bioconda/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/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/work/conda_build.sh']' returned non-zero exit status 1.
export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bamread_1718324170755/work
INFO: activate_clang_osx-64.sh made the following environmental changes:
AR=x86_64-apple-darwin13.4.0-ar
AS=x86_64-apple-darwin13.4.0-as
CC=x86_64-apple-darwin13.4.0-clang
CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamread-0.0.16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms
CLANG=x86_64-apple-darwin13.4.0-clang
CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.13 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
CMAKE_PREFIX_PATH=:$PREFIX
CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0
CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0
CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13
DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamread-0.0.16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
HOST=x86_64-apple-darwin13.4.0
INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool
LD=x86_64-apple-darwin13.4.0-ld
LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib
LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib
LIBTOOL=x86_64-apple-darwin13.4.0-libtool
LIPO=x86_64-apple-darwin13.4.0-lipo
MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib
NM=x86_64-apple-darwin13.4.0-nm
NMEDIT=x86_64-apple-darwin13.4.0-nmedit
OBJC=x86_64-apple-darwin13.4.0-clang
OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
OTOOL=x86_64-apple-darwin13.4.0-otool
PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff
RANLIB=x86_64-apple-darwin13.4.0-ranlib
REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding
SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk
SEGEDIT=x86_64-apple-darwin13.4.0-segedit
SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table
SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack
SIZE=x86_64-apple-darwin13.4.0-size
STRINGS=x86_64-apple-darwin13.4.0-strings
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
Compiling bamread/src/bamread.pyx because it changed.
[1/1] Cythonizing bamread/src/bamread.pyx
running install
running build
running build_py
creating build
creating build/lib.macosx-10.9-x86_64-cpython-312
creating build/lib.macosx-10.9-x86_64-cpython-312/bamread
copying bamread/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-312/bamread
copying bamread/read.py -> build/lib.macosx-10.9-x86_64-cpython-312/bamread
creating build/lib.macosx-10.9-x86_64-cpython-312/bamread/src
copying bamread/src/__init__.py -> build/lib.macosx-10.9-x86_64-cpython-312/bamread/src
running egg_info
writing bamread.egg-info/PKG-INFO
writing dependency_links to bamread.egg-info/dependency_links.txt
writing requirements to bamread.egg-info/requires.txt
writing top-level names to bamread.egg-info/top_level.txt
reading manifest file 'bamread.egg-info/SOURCES.txt'
writing manifest file 'bamread.egg-info/SOURCES.txt'
creating build/lib.macosx-10.9-x86_64-cpython-312/bin
copying bin/bamread -> build/lib.macosx-10.9-x86_64-cpython-312/bin
creating build/lib.macosx-10.9-x86_64-cpython-312/tests
copying tests/control.bam -> build/lib.macosx-10.9-x86_64-cpython-312/tests
copying bamread/src/bamread.c -> build/lib.macosx-10.9-x86_64-cpython-312/bamread/src
copying bamread/src/bamread.pyx -> build/lib.macosx-10.9-x86_64-cpython-312/bamread/src
copying bamread/src/bamwrite.pyx -> build/lib.macosx-10.9-x86_64-cpython-312/bamread/src
running build_ext
building 'bamread.src.bamread' extension
creating build/temp.macosx-10.9-x86_64-cpython-312
creating build/temp.macosx-10.9-x86_64-cpython-312/bamread
creating build/temp.macosx-10.9-x86_64-cpython-312/bamread/src
x86_64-apple-darwin13.4.0-clang -fno-strict-overflow -DNDEBUG -O2 -Wall -fPIC -O2 -isystem $PREFIX/include -fPIC -O2 -isystem $PREFIX/include -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamread-0.0.16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 -I$PREFIX/include/python3.12 -c bamread/src/bamread.c -o build/temp.macosx-10.9-x86_64-cpython-312/bamread/src/bamread.o
x86_64-apple-darwin13.4.0-clang -bundle -undefined dynamic_lookup -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bamread-0.0.16 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.13 build/temp.macosx-10.9-x86_64-cpython-312/bamread/src/bamread.o -o build/lib.macosx-10.9-x86_64-cpython-312/bamread/src/bamread.cpython-312-darwin.so
# Last 100 lines of the build log.