From b58964265c510745857c8d14a60d393988212946 Mon Sep 17 00:00:00 2001 From: aliciaaevans Date: Fri, 27 Dec 2024 18:46:17 +0000 Subject: [PATCH] bioconductor-netpathminer: add zlib and liblzma-devel --- .../build_failure.linux-64.yaml | 104 ------------------ recipes/bioconductor-netpathminer/meta.yaml | 2 + 2 files changed, 2 insertions(+), 104 deletions(-) delete mode 100644 recipes/bioconductor-netpathminer/build_failure.linux-64.yaml diff --git a/recipes/bioconductor-netpathminer/build_failure.linux-64.yaml b/recipes/bioconductor-netpathminer/build_failure.linux-64.yaml deleted file mode 100644 index 112632c7f3e63..0000000000000 --- a/recipes/bioconductor-netpathminer/build_failure.linux-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: 80397652bc25f8257efb33b08ec900131e7096df29835427e3f6ba862f1e7410 # 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: |- - 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-netpathminer-1.42.0 -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-netpathminer-1.42.0 -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-netpathminer-1.42.0 -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-netpathminer-1.42.0 -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-netpathminer_1734193681777/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/library - * installing *source* package NetPathMiner ... - ** package NetPathMiner successfully unpacked and MD5 sums checked - ** using staged installation - 'config' variable 'CPP' is defunct - checking for x86_64-conda-linux-gnu-gcc... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc - checking whether the C compiler works... yes - checking for C compiler default output file name... a.out - checking for suffix of executables... - checking whether we are cross compiling... no - checking for suffix of object files... o - checking whether we are using the GNU C compiler... yes - checking whether $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc accepts -g... yes - checking for $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc option to accept ISO C89... none needed - checking how to run the C preprocessor... $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -E - checking for xmlParseFile in -lxml2... yes - checking for readSBML in -lsbml... no - SBML not found. - libXML2 found - checking for xml2-config... $PREFIX/bin/xml2-config - configure: creating ./config.status - config.status: creating src/Makevars - ** libs - using C compiler: x86_64-conda-linux-gnu-cc (conda-forge gcc 13.3.0-1) 13.3.0 - using C compiler: x86_64-conda-linux-gnu-c (conda-forge gcc 13.3.0-1) 13.3.0 - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-cc -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -DHAVE_XML -I$PREFIX/include/libxml2 -I$PREFIX/include -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 $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c handlesegfault.c -o handlesegfault.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,$PREFIX/lib -DHAVE_XML -I$PREFIX/include/libxml2 -I$PREFIX/include -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 $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c hme3m.c -o hme3m.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,$PREFIX/lib -DHAVE_XML -I$PREFIX/include/libxml2 -I$PREFIX/include -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 $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c init.c -o init.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -DHAVE_XML -I$PREFIX/include/libxml2 -I$PREFIX/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 $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c kgml_interface.cpp -o kgml_interface.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -DHAVE_XML -I$PREFIX/include/libxml2 -I$PREFIX/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 $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c methods.cpp -o methods.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -I"$PREFIX/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem $PREFIX/include -I$PREFIX/include -Wl,-rpath-link,$PREFIX/lib -DHAVE_XML -I$PREFIX/include/libxml2 -I$PREFIX/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 $PREFIX/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1732138515749/work=/usr/local/src/conda/r-base-4.4.2 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -c sbml_interface.cpp -o sbml_interface.o - $BUILD_PREFIX/bin/x86_64-conda-linux-gnu-c -shared -L$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$PREFIX/lib -o NetPathMiner.so handlesegfault.o hme3m.o init.o kgml_interface.o methods.o sbml_interface.o -lxml2 -L$PREFIX/lib -lxml2 -L$PREFIX/lib -lz -L$PREFIX/lib -llzma -L$PREFIX/lib -licui18n -licuuc -licudata -L$PREFIX/lib -liconv -lm -ldl -llapack -lblas -lgfortran -lm -lquadmath -L$PREFIX/lib/R/lib -lR - /opt/conda/conda-bld/bioconductor-netpathminer_1734193681777/_build_env/bin/../lib/gcc/x86_64-conda-linux-gnu/13.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: cannot find -lz: No such file or directory - collect2: error: ld returned 1 exit status - make: *** [/opt/conda/conda-bld/bioconductor-netpathminer_1734193681777/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/share/make/shlib.mk:10: NetPathMiner.so] Error 1 - ERROR: compilation failed for package NetPathMiner - * removing /opt/conda/conda-bld/bioconductor-netpathminer_1734193681777/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho/lib/R/library/NetPathMiner - 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-netpathminer_1734193681777/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-netpathminer_1734193681777/work/conda_build.sh']' returned non-zero exit status 1. -# Last 100 lines of the build log. diff --git a/recipes/bioconductor-netpathminer/meta.yaml b/recipes/bioconductor-netpathminer/meta.yaml index 3120f34d346ab..a37ea1410126a 100644 --- a/recipes/bioconductor-netpathminer/meta.yaml +++ b/recipes/bioconductor-netpathminer/meta.yaml @@ -42,6 +42,8 @@ requirements: - libblas - liblapack - libxml2 + - zlib + - liblzma-devel run: - r-base - r-igraph >=1.0