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build_failure.linux-64.yaml
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recipe_sha: 8be299be68f592196300b378692635c3fb3b08802fa1691c037aa51f26ab0a53 # 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: |2-
libgcc-ng: 13.1.0-he5830b7_0 conda-forge
libgomp: 13.1.0-he5830b7_0 conda-forge
libsanitizer: 12.3.0-h0f45ef3_0 conda-forge
libstdcxx-devel_linux-64: 12.3.0-h8bca6fd_0 conda-forge
libstdcxx-ng: 13.1.0-hfd8a6a1_0 conda-forge
make: 4.3-hd18ef5c_1 conda-forge
sysroot_linux-64: 2.12-he073ed8_16 conda-forge
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Source cache directory is: /opt/conda/conda-bld/src_cache
INFO:conda_build.source:Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: ncbi-magicblast-1.7.0-src_e57cd7940d.tar.gz
INFO:conda_build.source:Downloading source to cache: ncbi-magicblast-1.7.0-src_e57cd7940d.tar.gz
Downloading ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.7.0/ncbi-magicblast-1.7.0-src.tar.gz
INFO:conda_build.source:Downloading ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.7.0/ncbi-magicblast-1.7.0-src.tar.gz
Success
INFO:conda_build.source:Success
Extracting download
source tree in: /opt/conda/conda-bld/magicblast_1689511740328/work
export PREFIX=/opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl
export BUILD_PREFIX=/opt/conda/conda-bld/magicblast_1689511740328/_build_env
export SRC_DIR=/opt/conda/conda-bld/magicblast_1689511740328/work
INFO: activate-binutils_linux-64.sh made the following environmental changes:
ADDR2LINE=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-addr2line
AR=$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/magicblast-1.7.0 -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=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$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/magicblast-1.7.0 -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/magicblast-1.7.0 -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/magicblast-1.7.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix
GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g
VDB=/opt/conda/conda-bld/magicblast_1689511740328/work/vdb
mkdir /opt/conda/conda-bld/magicblast_1689511740328/work/vdb
uname
[[ Linux = Linux ]]
mkdir -p /opt/conda/conda-bld/magicblast_1689511740328/work/vdb/linux/release/x86_64/lib
cp -R /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libkapp-static.a /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libkapp.a /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libkapp.a.3 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libkapp.a.3.0.6 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libktst-static.a /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libktst.a /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libktst.a.3 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libktst.a.3.0.6 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-vdb-static.a /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-vdb.a /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-vdb.a.3 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-vdb.a.3.0.6 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-vdb.so /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-vdb.so.3 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-vdb.so.3.0.6 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-wvdb-static.a /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-wvdb.a /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-wvdb.a.3 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-wvdb.a.3.0.6 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-wvdb.so /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-wvdb.so.3 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libncbi-wvdb.so.3.0.6 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libsam-extract-static.a /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libsam-extract.a /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libsam-extract.a.3 /opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib64/libsam-extract.a.3.0.6 /opt/conda/conda-bld/magicblast_1689511740328/work/vdb/linux/release/x86_64/lib
mkdir /opt/conda/conda-bld/magicblast_1689511740328/work/vdb/interfaces
cp -R '/opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/ncbi-vdb/*' /opt/conda/conda-bld/magicblast_1689511740328/work/vdb/interfaces
cp: cannot stat '/opt/conda/conda-bld/magicblast_1689511740328/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/include/ncbi-vdb/*': No such file or directory
Traceback (most recent call last):
File "/opt/conda/bin/conda-mambabuild", line 10, in <module>
sys.exit(main())
File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 256, in main
call_conda_build(action, config)
File "/opt/conda/lib/python3.8/site-packages/boa/cli/mambabuild.py", line 228, in call_conda_build
result = api.build(
File "/opt/conda/lib/python3.8/site-packages/conda_build/api.py", line 180, in build
return build_tree(
File "/opt/conda/lib/python3.8/site-packages/conda_build/build.py", line 3078, in build_tree
packages_from_this = build(metadata, stats,
File "/opt/conda/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/conda/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/conda/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/conda/conda-bld/magicblast_1689511740328/work/conda_build.sh']' returned non-zero exit status 1.
# Last 100 lines of the build log.