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build_failure.osx-64.yaml
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build_failure.osx-64.yaml
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recipe_sha: d374fd7f3d0e1029da2f87970da29699ccc64d43ccb4c288aec82cbe51d2e934 # 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: |-
INFO:conda_build.source:Downloading source to cache: 2.1.4_a67bd7b5bb.tar.gz
Downloading https://github.com/cbg-ethz/PredictHaplo/archive/2.1.4.tar.gz
INFO:conda_build.source:Downloading https://github.com/cbg-ethz/PredictHaplo/archive/2.1.4.tar.gz
Success
INFO:conda_build.source:Success
Extracting download
source tree in: /opt/mambaforge/envs/bioconda/conda-bld/predicthaplo_1685353899145/work
export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/predicthaplo_1685353899145/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p
export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/predicthaplo_1685353899145/_build_env
export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/predicthaplo_1685353899145/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 -fPIE -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/predicthaplo-2.1.4 -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=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$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=10.9
DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/predicthaplo-2.1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
HOST=x86_64-apple-darwin13.4.0
INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool
LD=x86_64-apple-darwin13.4.0-ld
LDFLAGS=-Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib
LDFLAGS_LD=-pie -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_14.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.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
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 -fPIE -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/predicthaplo-2.1.4 -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 -fPIE -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/predicthaplo-2.1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -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/predicthaplo-2.1.4 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O3 -fPIC -std=c11 -Werror -stdlib=libc -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -DSCYTHE_LAPACK -DSCYTHE_DEBUG=0 -DHAVE_TRUNC -ISCYTHE/include/ -c -o PredictHaplo_externAlign.o PredictHaplo_externAlign.cpp
In file included from PredictHaplo_externAlign.cpp:22:
In file included from SCYTHE/include/scythestat/distributions.h:101:
In file included from SCYTHE/include/scythestat/matrix.h:72:
SCYTHE/include/scythestat/algorithm.h:86:27: error: 'binary_function<double, double, double>' is deprecated [-Werror,-Wdeprecated-declarations]
struct ax_plus_b : std::binary_function<T,T,T>
^
SCYTHE/include/scythestat/la.h:732:24: note: in instantiation of template class 'scythe::ax_plus_b<double>' requested here
ax_plus_b<T>(constant));
^
SCYTHE/include/scythestat/la.h:936:7: note: in instantiation of function template specialization 'scythe::(anonymous namespace)::gaxpy_alg<scythe::Col, double, scythe::Col, scythe::Concrete, scythe::Col, scythe::Concrete>' requested here
gaxpy_alg(res, B, C, A[0]);
^
/opt/mambaforge/envs/bioconda/conda-bld/predicthaplo_1685353899145/_build_env/bin/../include/c/v1/__functional/binary_function.h:24:29: note: 'binary_function<double, double, double>' has been explicitly marked deprecated here
struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function
^
/opt/mambaforge/envs/bioconda/conda-bld/predicthaplo_1685353899145/_build_env/bin/../include/c/v1/__config:862:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11'
# define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED
^
/opt/mambaforge/envs/bioconda/conda-bld/predicthaplo_1685353899145/_build_env/bin/../include/c/v1/__config:847:49: note: expanded from macro '_LIBCPP_DEPRECATED'
# define _LIBCPP_DEPRECATED __attribute__((deprecated))
^
1 error generated.
make: *** [<builtin>: PredictHaplo_externAlign.o] Error 1
Traceback (most recent call last):
File "/opt/mambaforge/envs/bioconda/bin/conda-mambabuild", line 10, in <module>
sys.exit(main())
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
call_conda_build(action, config)
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
result = api.build(
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
return build_tree(
File "/opt/mambaforge/envs/bioconda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
packages_from_this = build(metadata, stats,
File "/opt/mambaforge/envs/bioconda/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/mambaforge/envs/bioconda/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/mambaforge/envs/bioconda/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/mambaforge/envs/bioconda/conda-bld/predicthaplo_1685353899145/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.