-
Notifications
You must be signed in to change notification settings - Fork 3.3k
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
[ci skip] add build failure record for recipe recipes/bioconductor-me…
…thylkit
- Loading branch information
1 parent
3fa5cb4
commit 90d7945
Showing
1 changed file
with
104 additions
and
0 deletions.
There are no files selected for viewing
104 changes: 104 additions & 0 deletions
104
recipes/bioconductor-methylkit/build_failure.linux-64.yaml
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,104 @@ | ||
| recipe_sha: adca17bc7f6da666dc80f84c990193d17e8f0657616b08b6f385fb7b58660cf3 # The hash of the recipe's meta.yaml at which this recipe failed to build. | ||
| skiplist: false # 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- | ||
| source tree in: /opt/conda/conda-bld/bioconductor-methylkit_1735251216058/work | ||
| export PREFIX=/opt/conda/conda-bld/bioconductor-methylkit_1735251216058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_ | ||
| export BUILD_PREFIX=/opt/conda/conda-bld/bioconductor-methylkit_1735251216058/_build_env | ||
| export SRC_DIR=/opt/conda/conda-bld/bioconductor-methylkit_1735251216058/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-methylkit-1.32.0 -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-methylkit-1.32.0 -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-methylkit-1.32.0 -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-methylkit-1.32.0 -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-methylkit_1735251216058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library | ||
| * installing *source* package methylKit ... | ||
| ** package methylKit 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 | ||
| using C11 | ||
| During startup - Warning message: | ||
| Setting LC_TIME failed, using "C" | ||
| $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -I'$PREFIX/lib/R/library/zlibbioc/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 | ||
| During startup - Warning message: | ||
| Setting LC_TIME failed, using "C" | ||
| $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -std=gnu11 -I"$PREFIX/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'$PREFIX/lib/R/library/Rcpp/include' -I'$PREFIX/lib/R/library/Rhtslib/include' -I'$PREFIX/lib/R/library/zlibbioc/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 methCall.cpp -o methCall.o | ||
| methCall.cpp:17:10: fatal error: zlib.h: No such file or directory | ||
| 17 | #include "zlib.h" | ||
| | ^~~~~~~~ | ||
| compilation terminated. | ||
| make: *** [/opt/conda/conda-bld/bioconductor-methylkit_1735251216058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/etc/Makeconf:204: methCall.o] Error 1 | ||
| ERROR: compilation failed for package methylKit | ||
| * removing /opt/conda/conda-bld/bioconductor-methylkit_1735251216058/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/lib/R/library/methylKit | ||
| 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-methylkit_1735251216058/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-methylkit_1735251216058/work/conda_build.sh']' returned non-zero exit status 1. | ||
| # Last 100 lines of the build log. |