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build_failure.linux-64.yaml
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build_failure.linux-64.yaml
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recipe_sha: e012ba21d33790d74fa3bd1b6883d0278e83a96dc5f265d468abf3d43927b632 # 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-
sysroot_linux-64: 2.17-h4a8ded7_16 conda-forge
tzdata: 2024a-h8827d51_1 conda-forge
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Source cache directory is: /opt/conda/conda-bld/src_cache
Downloading source to cache: userApps.v469.src_3f95b26ccc.tgz
Downloading http://hgdownload.cse.ucsc.edu/admin/exe/userApps.archive/userApps.v469.src.tgz
Success
Extracting download
Applying patch: /opt/recipe/include.patch
Applying patch: /opt/recipe/include.patch with args:
['-Np0', '-i', '/tmp/tmpj88djt1f/include.patch.native', '--binary']
checking file kent/src/inc/common.mk
Hunk #1 succeeded at 21 (offset 4 lines).
checking file kent/src/utils/bedJoinTabOffset.py
checking file kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
patching file kent/src/inc/common.mk
Hunk #1 succeeded at 21 (offset 4 lines).
patching file kent/src/utils/bedJoinTabOffset.py
patching file kent/src/utils/expMatrixToBarchartBed/expMatrixToBarchartBed
Patch analysis gives:
[[ RA--D0L-VE ]] - [[ include.patch ]]
Key:
R :: Reversible A :: Applicable
Y :: Build-prefix patch in use M :: Minimal, non-amalgamated
D :: Dry-runnable N :: Patch level (1 is preferred)
L :: Patch level not-ambiguous O :: Patch applies without offsets
V :: Patch applies without fuzz E :: Patch applies without emitting to stderr
source tree in: /opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/work
export PREFIX=/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p
export BUILD_PREFIX=/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/_build_env
export SRC_DIR=/opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/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
DWP=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-dwp
ELFEDIT=$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/ucsc-bedjointaboffset-469 -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/ucsc-bedjointaboffset-469 -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=-Dbuildtype=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=
mkdir -p /opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin
cp kent/src/utils/bedJoinTabOffset /opt/conda/conda-bld/ucsc-bedjointaboffset_1724792239783/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_p/bin
cp: omitting directory 'kent/src/utils/bedJoinTabOffset'
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/ucsc-bedjointaboffset_1724792239783/work/conda_build.sh']' returned non-zero exit status 1.
# Last 100 lines of the build log.