diff --git a/.circleci/config.yml b/.circleci/config.yml index 6bcdb1d063e65..1046e0d9acbe5 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -229,6 +229,7 @@ workflows: ignore: - master - bulk + - /bulk.*/ matrix: parameters: os: diff --git a/.github/workflows/Bulk.yml b/.github/workflows/Bulk.yml index 539fb05adf79b..759c9db624c58 100644 --- a/.github/workflows/Bulk.yml +++ b/.github/workflows/Bulk.yml @@ -2,77 +2,8 @@ name: Bulk branch on: push: branches: - - bulk + - bulk-osx-failures jobs: - build-linux: - name: Bulk Linux Builds - if: "contains(github.event.head_commit.message, '[ci run]')" - runs-on: ubuntu-latest - strategy: - fail-fast: false - max-parallel: 6 - matrix: - runner: [0, 1, 2, 3, 4, 5] - steps: - - uses: actions/checkout@v4 - with: - # checkout as BiocondaBot in order to have the permission to push fail logs - token: ${{secrets.BIOCONDA_BOT_REPO_TOKEN}} - - - name: set git user - run: | - git config user.name BiocondaBot - git config user.email BiocondaBot@users.noreply.github.com - - - name: set path - run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH - - - name: Fetch conda install script - run: | - wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh - - - name: Restore cache - id: cache - uses: actions/cache@v4 - with: - path: /opt/mambaforge - key: ${{ runner.os }}--bulk--${{ hashFiles('install-and-set-up-conda.sh', 'common.sh', 'configure-conda.sh') }} - - - name: Set up bioconda-utils - if: steps.cache.outputs.cache-hit != 'true' - run: bash install-and-set-up-conda.sh - - # This script can be used to reconfigure conda to use the right channel setup. - # This has to be done after the cache is restored, because - # the channel setup is not cached as it resides in the home directory. - # We could use a system-wide (and therefore cached) channel setup, - # but mamba does not support that at the time of implementation - # (it ignores settings made with --system). - - name: Configure conda - run: bash configure-conda.sh - - - name: Build and upload - env: - ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }} - INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }} - QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }} - # Mimic circleci - OSTYPE: "linux-gnu" - CI: "true" - run: | - set -e - eval "$(conda shell.bash hook)" - conda activate bioconda - echo '============' - conda info --all - conda config --show-sources - python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' - echo '============' - bioconda-utils build recipes config.yml \ - --worker-offset ${{ matrix.runner }} --n-workers 6 \ - --docker --mulled-test --anaconda-upload --mulled-upload-target biocontainers \ - --lint --record-build-failures --skiplist-leafs - conda clean -y --all build-osx: name: Bulk OSX Builds @@ -80,9 +11,9 @@ jobs: runs-on: macos-13 strategy: fail-fast: false - max-parallel: 4 + max-parallel: 1 matrix: - runner: [0, 1, 2, 3] + runner: [0] #, 1, 2, 3] steps: - uses: actions/checkout@v4 with: @@ -99,7 +30,7 @@ jobs: - name: Fetch conda install script run: | - wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk/{common,install-and-set-up-conda,configure-conda}.sh + wget https://raw.githubusercontent.com/bioconda/bioconda-common/bulk-osx-failures/{common,install-and-set-up-conda,configure-conda}.sh - name: Restore cache id: cache @@ -133,17 +64,15 @@ jobs: set -e eval "$(conda shell.bash hook)" conda activate bioconda - - # The SDK isn't actually cached, so reinstall it + source common.sh run_conda_forge_build_setup - + echo $MACOSX_DEPLOYMENT_TARGET + echo $MACOSX_SDK_VERSION echo '============' conda info --all conda config --show-sources conda activate bioconda python -c 'import bioconda_utils.utils as u ; import pathlib as p ; print(*(f"{f}:\n{p.Path(f).read_text()}" for f in u.load_conda_build_config().exclusive_config_files), sep="\n")' echo '============' - bioconda-utils build recipes config.yml \ - --worker-offset ${{ matrix.runner }} --n-workers 4 \ - --lint --anaconda-upload --record-build-failures --skiplist-leafs + bioconda-utils build recipes config.yml --packages bowtie conda clean -y --all 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") }}