From 5c18b75cc548bd446ef40f765d13cb92b539ae7c Mon Sep 17 00:00:00 2001 From: aliciaaevans Date: Fri, 7 Jun 2024 16:17:30 -0400 Subject: [PATCH] rebuild bowtie --- recipes/bowtie/build_failure.osx-64.yaml | 104 ----------------------- recipes/bowtie/meta.yaml | 1 - 2 files changed, 105 deletions(-) delete mode 100644 recipes/bowtie/build_failure.osx-64.yaml diff --git a/recipes/bowtie/build_failure.osx-64.yaml b/recipes/bowtie/build_failure.osx-64.yaml deleted file mode 100644 index 52d72157ec1d0..0000000000000 --- a/recipes/bowtie/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c2a8312eada5f447d81c5780f388e40fc17487b8966607e43b2708bd9986e45b # 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: |- - In file included from /opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/_build_env/bin/../include/c/v1/__std_mbstate_t.h:14: - In file included from /opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/_build_env/bin/../include/c/v1/__mbstate_t.h:45: - /Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/usr/include/sys/_types/_mbstate_t.h:31:9: error: unknown type name '__darwin_mbstate_t' - typedef __darwin_mbstate_t mbstate_t; - ^ - In file included from bowtie_build_main.cpp:13: - ./ds.h:4077:8: warning: variable 'thru' set but not used [-Wunused-but-set-variable] - int thru = 0; - ^ - 1 warning and 1 error generated. - make: *** [Makefile:237: bowtie-build-s] Error 1 - Extracting download - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bowtie/rename_version_to_version_txt.patch - Traceback (most recent call last): - File "/opt/mambaforge/envs/bioconda/bin/conda-build", line 11, in - sys.exit(execute()) - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/cli/main_build.py", line 590, in execute - api.build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/api.py", line 250, in build - return build_tree( - Applying patch: /Users/runner/work/bioconda-recipes/bioconda-recipes/recipes/bowtie/rename_version_to_version_txt.patch with args: - ['-Np1', '-i', '/tmp/tmp1sqf2v3x/rename_version_to_version_txt.patch.native', '--binary'] - Patch analysis gives: - [[ RA-MD1LOVE ]] - [[ rename_version_to_version_txt.patch ]] - - Key: - - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 3638, in build_tree - packages_from_this = build( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/build.py", line 2506, in build - utils.check_call_env( - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 405, in check_call_env - return _func_defaulting_env_to_os_environ("call", *popenargs, **kwargs) - R :: Reversible A :: Applicable - File "/opt/mambaforge/envs/bioconda/lib/python3.10/site-packages/conda_build/utils.py", line 381, in _func_defaulting_env_to_os_environ - raise subprocess.CalledProcessError(proc.returncode, _args) - Y :: Build-prefix patch in use M :: Minimal, non-amalgamated - D :: Dry-runnable N :: Patch level (1 is preferred) - L :: Patch level not-ambiguous O :: Patch applies without offsets - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/work/conda_build.sh']' returned non-zero exit status 2. - V :: Patch applies without fuzz E :: Patch applies without emitting to stderr - - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/work - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/_build_env - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/bowtie_1717779480345/work - INFO: activate_clang_osx-64.sh made the following environmental changes: - AR=x86_64-apple-darwin13.4.0-ar - AS=x86_64-apple-darwin13.4.0-as - CC=x86_64-apple-darwin13.4.0-clang - CC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CHECKSYMS=x86_64-apple-darwin13.4.0-checksyms - CLANG=x86_64-apple-darwin13.4.0-clang - CMAKE_ARGS=-DCMAKE_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_CXX_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_C_COMPILER_AR=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ar -DCMAKE_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_CXX_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_C_COMPILER_RANLIB=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ranlib -DCMAKE_LINKER=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-ld -DCMAKE_STRIP=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-strip -DCMAKE_INSTALL_NAME_TOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-install_name_tool -DCMAKE_LIBTOOL=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-libtool -DCMAKE_OSX_DEPLOYMENT_TARGET=10.9 -DCMAKE_BUILD_TYPE=Release -DCMAKE_OSX_SYSROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk -DCMAKE_FIND_FRAMEWORK=LAST -DCMAKE_FIND_APPBUNDLE=LAST -DCMAKE_INSTALL_PREFIX=$PREFIX -DCMAKE_INSTALL_LIBDIR=lib -DCMAKE_PROGRAM_PATH=$BUILD_PREFIX/bin;$PREFIX/bin - CMAKE_PREFIX_PATH=:$PREFIX - CONDA_TOOLCHAIN_BUILD=x86_64-apple-darwin13.4.0 - CONDA_TOOLCHAIN_HOST=x86_64-apple-darwin13.4.0 - CPPFLAGS=-D_FORTIFY_SOURCE=2 -isystem $PREFIX/include -mmacosx-version-min=10.9 - DEBUG_CFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - HOST=x86_64-apple-darwin13.4.0 - INSTALL_NAME_TOOL=x86_64-apple-darwin13.4.0-install_name_tool - LD=x86_64-apple-darwin13.4.0-ld - LDFLAGS=-Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib - LDFLAGS_LD=-headerpad_max_install_names -dead_strip_dylibs -rpath $PREFIX/lib -L$PREFIX/lib - LIBTOOL=x86_64-apple-darwin13.4.0-libtool - LIPO=x86_64-apple-darwin13.4.0-lipo - MESON_ARGS=--buildtype release --prefix=$PREFIX -Dlibdir=lib - NM=x86_64-apple-darwin13.4.0-nm - NMEDIT=x86_64-apple-darwin13.4.0-nmedit - OBJC=x86_64-apple-darwin13.4.0-clang - OBJC_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - OTOOL=x86_64-apple-darwin13.4.0-otool - PAGESTUFF=x86_64-apple-darwin13.4.0-pagestuff - RANLIB=x86_64-apple-darwin13.4.0-ranlib - REDO_PREBINDING=x86_64-apple-darwin13.4.0-redo_prebinding - SDKROOT=/Applications/Xcode_15.0.1.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk - SEGEDIT=x86_64-apple-darwin13.4.0-segedit - SEG_ADDR_TABLE=x86_64-apple-darwin13.4.0-seg_addr_table - SEG_HACK=x86_64-apple-darwin13.4.0-seg_hack - SIZE=x86_64-apple-darwin13.4.0-size - STRINGS=x86_64-apple-darwin13.4.0-strings - STRIP=x86_64-apple-darwin13.4.0-strip - _CONDA_PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_x86_64_apple_darwin13_4_0 - ac_cv_func_malloc_0_nonnull=yes - ac_cv_func_realloc_0_nonnull=yes - build_alias=x86_64-apple-darwin13.4.0 - host_alias=x86_64-apple-darwin13.4.0 - INFO: activate_clangxx_osx-64.sh made the following environmental changes: - CLANGXX=x86_64-apple-darwin13.4.0-clang - CXX=x86_64-apple-darwin13.4.0-clang - CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - CXX_FOR_BUILD=$BUILD_PREFIX/bin/x86_64-apple-darwin13.4.0-clang - DEBUG_CXXFLAGS=-march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -Og -g -Wall -Wextra -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix - x86_64-apple-darwin13.4.0-clang -O3 -DCOMPILER_OPTIONS="\"-O3 -DPOPCNT_CAPABILITY -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix \"" -DPOPCNT_CAPABILITY -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -stdlib=libc -fvisibility-inlines-hidden -fmessage-length=0 -isystem $PREFIX/include -fdebug-prefix-map=$SRC_DIR=/usr/local/src/conda/bowtie-1.3.1 -fdebug-prefix-map=$PREFIX=/usr/local/src/conda-prefix \ - -fno-strict-aliasing -DBOWTIE_VERSION="\"cat VERSION.txt\"" -DBUILD_HOST="\"hostname\"" -DBUILD_TIME="\"2024-06-07T16:59:50\"" -DCOMPILER_VERSION="\"x86_64-apple-darwin13.4.0-clang -v 2>&1 | tail -1\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder \ - -I third_party \ - -o bowtie-build-s ebwt_build.cpp \ - ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp bowtie_build_main.cpp \ - -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,$PREFIX/lib -L$PREFIX/lib -lz -lpthread -# Last 100 lines of the build log. diff --git a/recipes/bowtie/meta.yaml b/recipes/bowtie/meta.yaml index 069e9a1bd54ef..32cfcadbc62c2 100644 --- a/recipes/bowtie/meta.yaml +++ b/recipes/bowtie/meta.yaml @@ -12,7 +12,6 @@ source: - rename_version_to_version_txt.patch build: - skip: True # [py<30] number: 8 run_exports: - {{ pin_subpackage("bowtie", max_pin="x.x") }}