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[ci skip] add build failure record for recipe recipes/bioconductor-ce…
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recipes/bioconductor-cellbarcode/build_failure.linux-64.yaml
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| recipe_sha: e826f00d9158344210f0f6ca1aa6b9d857dbec24bc1a4fed4fb0e37daaa4f3c7 # 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- | ||
| summary: Cellular DNA Barcode Analysis toolkit | ||
| extra: | ||
| copy_test_source_files: true | ||
| final: true | ||
| source tree in: /opt/conda/conda-bld/bioconductor-cellbarcode_1735254346691/work | ||
| export PREFIX=/opt/conda/conda-bld/bioconductor-cellbarcode_1735254346691/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol | ||
| export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-cellbarcode_1735254346691/_build_env | ||
| export SRC_DIR=/opt/conda/conda-bld/bioconductor-cellbarcode_1735254346691/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-cellbarcode-1.12.0 -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-cellbarcode-1.12.0 -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=$PREFIX -Dlibdir=lib | ||
| _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_conda_cos6_linux_gnu | ||
| build_alias=x86_64-conda-linux-gnu | ||
| host_alias=x86_64-conda-linux-gnu | ||
| -BUILD=x86_64-conda_cos6-linux-gnu | ||
| -CONDA_BUILD_SYSROOT= | ||
| INFO: activate-gxx_linux-64.sh made the following environmental changes: | ||
| CXX=$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/bioconductor-cellbarcode-1.12.0 -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/bioconductor-cellbarcode-1.12.0 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix | ||
| GXX=$BUILD_PREFIX/bin/x86_64-conda-linux-gnu-g | ||
| During startup - Warning message: | ||
| Setting LC_TIME failed, using "C" | ||
| * installing to library /opt/conda/conda-bld/bioconductor-cellbarcode_1735254346691/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/library | ||
| * installing *source* package CellBarcode ... | ||
| ** package CellBarcode successfully unpacked and MD5 sums checked | ||
| ** using staged installation | ||
| ** libs | ||
| using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 13.3.0-1) 13.3.0 | ||
| $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/BH/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c RcppExports.cpp -o RcppExports.o | ||
| $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/BH/include' -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -fpic -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1734433466103/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c lib_10X_barcode.cpp -o lib_10X_barcode.o | ||
| lib_10X_barcode.cpp:6:10: fatal error: zlib.h: No such file or directory | ||
| 6 | #include "zlib.h" | ||
| | ^~~~~~~~ | ||
| compilation terminated. | ||
| make: *** [/opt/conda/conda-bld/bioconductor-cellbarcode_1735254346691/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/etc/Makeconf:204: lib_10X_barcode.o] Error 1 | ||
| ERROR: compilation failed for package CellBarcode | ||
| * removing /opt/conda/conda-bld/bioconductor-cellbarcode_1735254346691/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/lib/R/library/CellBarcode | ||
| 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-cellbarcode_1735254346691/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-cellbarcode_1735254346691/work/conda_build.sh']' returned non-zero exit status 1. | ||
| # Last 100 lines of the build log. |