From a8e37bb43918e2b608ccdf68be72fea77fc36e5e Mon Sep 17 00:00:00 2001 From: BiocondaBot Date: Thu, 26 Dec 2024 23:09:02 +0000 Subject: [PATCH] [ci skip] add build failure record for recipe recipes/bioconductor-cellbarcode --- .../build_failure.linux-64.yaml | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 recipes/bioconductor-cellbarcode/build_failure.linux-64.yaml diff --git a/recipes/bioconductor-cellbarcode/build_failure.linux-64.yaml b/recipes/bioconductor-cellbarcode/build_failure.linux-64.yaml new file mode 100644 index 0000000000000..b6c039915f659 --- /dev/null +++ b/recipes/bioconductor-cellbarcode/build_failure.linux-64.yaml @@ -0,0 +1,104 @@ +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 + 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.