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build_failure.linux-64.yaml
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build_failure.linux-64.yaml
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recipe_sha: 32b1d7ecdc135748db71cb9fc5c63798223901f27601304e38c20a6c45ea2552 # 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: |-
AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar
AS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-as
CXXFILT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cfilt
ELFEDIT=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-elfedit
GPROF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gprof
LD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld
LD_GOLD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld.gold
NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-nm
OBJCOPY=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objcopy
OBJDUMP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-objdump
RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib
READELF=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-readelf
SIZE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-size
STRINGS=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strings
STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip
INFO: activate-gcc_linux-64.sh made the following environmental changes:
BUILD=x86_64-conda-linux-gnu
CC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc
CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc
CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metamaps-0.1.633d2e0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$PREFIX;$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin
CMAKE_PREFIX_PATH=$PREFIX:$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot/usr
CONDA_BUILD_SYSROOT=$BUILD_PREFIX/x86_64-conda-linux-gnu/sysroot
CONDA_TOOLCHAIN_BUILD=x86_64-conda-linux-gnu
CONDA_TOOLCHAIN_HOST=x86_64-conda-linux-gnu
CPP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cpp
CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include
DEBUG_CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metamaps-0.1.633d2e0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
DEBUG_CPPFLAGS=-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem $PREFIX/include
GCC=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc
GCC_AR=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ar
GCC_NM=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-nm
GCC_RANLIB=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-gcc-ranlib
HOST=x86_64-conda-linux-gnu
LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,$PREFIX/lib -Wl,-rpath-link,$PREFIX/lib -L$PREFIX/lib
MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib
_CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu
build_alias=x86_64-conda-linux-gnu
host_alias=x86_64-conda-linux-gnu
-BUILD=x86_64-conda_cos6-linux-gnu
-CONDA_BUILD_SYSROOT=
INFO: activate-gxx_linux-64.sh made the following environmental changes:
CXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c
CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metamaps-0.1.633d2e0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c
DEBUG_CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metamaps-0.1.633d2e0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c accepts -g... yes
checking for $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c option to enable C11 features... none needed
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking for zlib.h... yes
checking for boost/math/distributions/binomial.hpp... yes
configure: creating ./config.status
config.status: creating Makefile
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -c -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/metamaps-0.1.633d2e0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -O2 -ggdb -fopenmp -std=c11 -Isrc -L $PREFIX/lib -I $PREFIX/include -include src/common/memcpyLink.h -Wl,--wrap=memcpy -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -DUSE_BOOST -o src/map/mash_map.o src/map/mash_map.cpp
In file included from /opt/conda/conda-bld/metamaps_1717782855482/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/math/special_functions/detail/round_fwd.hpp:11,
from /opt/conda/conda-bld/metamaps_1717782855482/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/math/special_functions/math_fwd.hpp:29,
from /opt/conda/conda-bld/metamaps_1717782855482/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/math/special_functions/beta.hpp:13,
from /opt/conda/conda-bld/metamaps_1717782855482/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/math/distributions/binomial.hpp:83,
from src/map/mapWrap.h:23,
from src/map/mash_map.cpp:19:
/opt/conda/conda-bld/metamaps_1717782855482/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include/boost/math/tools/config.hpp:26:6: warning: #warning "Boost.Math requires C14" [-Wcpp]
26 | # warning "Boost.Math requires C14"
| ^~~~~~~
src/map/mapWrap.h: In member function 'void mapWrap::unifyFiles(std::string, const skch::Parameters&, std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >)':
src/map/mapWrap.h:192:44: error: 'wpath' is not a member of 'boost::filesystem'; did you mean 'path'?
192 | boost::filesystem::wpath F(resultsFile);
| ^~~~~
| path
make: *** [Makefile:25: src/map/mash_map.o] Error 1
Traceback (most recent call last):
File "/opt/conda/bin/conda-build", line 11, in <module>
sys.exit(execute())
File "/opt/conda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute
api.build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build
return build_tree(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree
packages_from_this = build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build
utils.check_call_env(
File "/opt/conda/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/conda/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/conda/conda-bld/metamaps_1717782855482/work/conda_build.sh']' returned non-zero exit status 2.
# Last 100 lines of the build log.