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build_failure.linux-64.yaml
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recipe_sha: a1e9b48f8e4acc8474beadc47e5e81908493eb592a4453e282bd7776d66f98f9 # 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-
copy_test_source_files: true
final: true
source tree in: /opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/work
export PREFIX=/opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/_h_env_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/bioconductor-adacgh2_1736183818755/_build_env
export SRC_DIR=/opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/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/bioconductor-adacgh2-2.46.0 -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=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release -DCMAKE_FIND_ROOT_PATH_MODE_PROGRAM=NEVER -DCMAKE_FIND_ROOT_PATH_MODE_LIBRARY=ONLY -DCMAKE_FIND_ROOT_PATH_MODE_INCLUDE=ONLY -DCMAKE_FIND_ROOT_PATH=$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/bioconductor-adacgh2-2.46.0 -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=-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=
During startup - Warning message:
Setting LC_TIME failed, using "C"
* installing to library /opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library
* installing *source* package ADaCGH2 ...
** package ADaCGH2 successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: x86_64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-1) 13.3.0
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c init.c -o init.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c r_haarseg.c -o r_haarseg.o
$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -shared -L$PREFIX/lib/R/lib -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$PREFIX/lib -o ADaCGH2.so init.o r_haarseg.o -L$PREFIX/lib/R/lib -lR
installing to /opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/00LOCK-work/00new/ADaCGH2/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
During startup - Warning message:
Setting LC_TIME failed, using "C"
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '$PREFIX/lib/R/library/multitaper/libs/multitaper.so':
libopenblas.so.0: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... asNamespace -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ADaCGH2
* removing /opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pl/lib/R/library/ADaCGH2
Traceback (most recent call last):
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2558, in build
utils.check_call_env(
File "/opt/conda/lib/python3.10/site-packages/conda_build/utils.py", line 404, 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 380, in _func_defaulting_env_to_os_environ
raise subprocess.CalledProcessError(proc.returncode, _args)
subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/work/conda_build.sh']' returned non-zero exit status 1.
The above exception was the direct cause of the following exception:
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 589, in execute
api.build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/api.py", line 209, in build
return build_tree(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 3712, in build_tree
packages_from_this = build(
File "/opt/conda/lib/python3.10/site-packages/conda_build/build.py", line 2566, in build
raise BuildScriptException(str(exc), caused_by=exc) from exc
conda_build.exceptions.BuildScriptException: Command '['/bin/bash', '-o', 'errexit', '/opt/conda/conda-bld/bioconductor-adacgh2_1736183818755/work/conda_build.sh']' returned non-zero exit status 1.
# Last 100 lines of the build log.