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build_failure.osx-64.yaml
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build_failure.osx-64.yaml
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recipe_sha: 4e8291e324315102dfd7965b671810693a072508ebc68cbb1d66cbefff5ef4fb # 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: |2-
| ^
/opt/mambaforge/envs/bioconda/conda-bld/epicseg_1717699192253/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/include/R_ext/RS.h:77:22: note: expanded from macro 'F77_CALL'
77 | # define F77_CALL(x) x ## _
| ^
<scratch space>:313:1: note: expanded from here
313 | dgemv_
| ^
2 errors generated.
make: *** [/opt/mambaforge/envs/bioconda/conda-bld/epicseg_1717699192253/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/etc/Makeconf:200: misc.o] Error 1
ERROR: compilation failed for package epicseg
* removing /opt/mambaforge/envs/bioconda/conda-bld/epicseg_1717699192253/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh/lib/R/library/epicseg
Extracting download
source tree in: /opt/mambaforge/envs/bioconda/conda-bld/epicseg_1717699192253/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
export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/epicseg_1717699192253/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh
export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/epicseg_1717699192253/_build_env
export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/epicseg_1717699192253/work
api.build(
INFO: activate-gfortran_osx-64.sh made the following environmental changes:
DEBUG_FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/epicseg-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
return build_tree(
DEBUG_FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/epicseg-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments
F77=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
F90=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran
F95=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran
FC=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran
FC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran
packages_from_this = build(
File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
FFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/epicseg-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
utils.check_call_env(
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)
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/epicseg_1717699192253/work/conda_build.sh']' returned non-zero exit status 1.
FORTRANFLAGS=-march=core2 -mtune=haswell -ftree-vectorize -fPIC -fstack-protector -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/epicseg-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
GFORTRAN=$PREFIX/bin/x86_64-apple-darwin13.4.0-gfortran
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=$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/epicseg-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms
CLANG=x86_64-apple-darwin13.4.0-clang
CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$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 -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/epicseg-1.0 -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=$PREFIX -Dlibdir=lib
NM=x86_64-apple-darwin13.4.0-nm
NMEDIT=x86_64-apple-darwin13.4.0-nmedit
OBJC=x86_64-apple-darwin13.4.0-clang
OBJC_FOR_BUILD=$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/MacOSX10.9.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 -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/epicseg-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CXX_FOR_BUILD=$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/epicseg-1.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
INFO: activate_clang_osx-64.sh made the following environmental changes:
CC_FOR_BUILD=$BUILD_PREFIX/bin/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_15.0.1.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;$PREFIX/bin
OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-CC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang
-CMAKE_ARGS=-DCMAKE_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
-OBJC_FOR_BUILD=$PREFIX/bin/x86_64-apple-darwin13.4.0-clang
x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -fopenmp -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1714471796105/work=/usr/local/src/conda/r-base-4.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o
x86_64-apple-darwin13.4.0-clang -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -fopenmp -I'$PREFIX/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 -I$PREFIX/include -fPIC -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1714471796105/work=/usr/local/src/conda/r-base-4.3.3 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c misc.cpp -o misc.o
# Last 100 lines of the build log.