From 8ded14776654889aae08c30f4a48d5fd814d415f Mon Sep 17 00:00:00 2001 From: Bioconda Bot <47040946+BiocondaBot@users.noreply.github.com> Date: Mon, 11 Nov 2024 11:58:32 -0500 Subject: [PATCH] Update emu-pca to 1.1 (#52035) * Update emu-pca to 1.1 * edit dependencies * edit dependencies --------- Co-authored-by: mencian --- recipes/emu-pca/build_failure.osx-64.yaml | 104 ---------------------- recipes/emu-pca/meta.yaml | 12 +-- 2 files changed, 7 insertions(+), 109 deletions(-) delete mode 100644 recipes/emu-pca/build_failure.osx-64.yaml diff --git a/recipes/emu-pca/build_failure.osx-64.yaml b/recipes/emu-pca/build_failure.osx-64.yaml deleted file mode 100644 index faf6c61b044ce..0000000000000 --- a/recipes/emu-pca/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: c8fdd7d1be49e7c2e5e03c78e8ef8e5da084a2de40931b17429baec27d330480 # 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- - ERROR: Failed building wheel for emu - ERROR: Could not build wheels for emu, which is required to install pyproject.toml-based projects - Extracting download - source tree in: /opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work - 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( - 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) - 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) - export PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeh - export BUILD_PREFIX=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/_build_env - subprocess.CalledProcessError: Command '['/bin/bash', '-o', 'errexit', '/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/work/conda_build.sh']' returned non-zero exit status 1. - export SRC_DIR=/opt/mambaforge/envs/bioconda/conda-bld/emu-pca_1717514596039/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/emu-pca-1.0 -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/emu-pca-1.0 -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 - Using pip 24.0 from $PREFIX/lib/python3.12/site-packages/pip (python 3.12) - Non-user install because user site-packages disabled - Ignoring indexes: https://pypi.org/simple - Created temporary directory: /private/tmp/pip-build-tracker-pcf71fuv - Initialized build tracking at /private/tmp/pip-build-tracker-pcf71fuv - Created build tracker: /private/tmp/pip-build-tracker-pcf71fuv - Entered build tracker: /private/tmp/pip-build-tracker-pcf71fuv - Created temporary directory: /private/tmp/pip-install-_4p1fpa8 - Created temporary directory: /private/tmp/pip-ephem-wheel-cache-pg6d97ox - Processing $SRC_DIR - Added file://$SRC_DIR to build tracker '/private/tmp/pip-build-tracker-pcf71fuv' - Created temporary directory: /private/tmp/pip-modern-metadata-x9ykve7d - Preparing metadata (pyproject.toml): started - Preparing metadata (pyproject.toml): finished with status 'done' - Source in $SRC_DIR has version 1.0, which satisfies requirement emu==1.0 from file://$SRC_DIR - Removed emu==1.0 from file://$SRC_DIR from build tracker '/private/tmp/pip-build-tracker-pcf71fuv' - Created temporary directory: /private/tmp/pip-unpack-ylygux9m - Building wheels for collected packages: emu - Created temporary directory: /private/tmp/pip-wheel-f2hnm5l2 - Destination directory: /private/tmp/pip-wheel-f2hnm5l2 - Building wheel for emu (pyproject.toml): started - Building wheel for emu (pyproject.toml): finished with status 'error' - Failed to build emu - Exception information: - Traceback (most recent call last): - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper - status = run_func(*args) - ^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/cli/req_command.py", line 245, in wrapper - return func(self, options, args) - ^^^^^^^^^^^^^^^^^^^^^^^^^ - File "$PREFIX/lib/python3.12/site-packages/pip/_internal/commands/install.py", line 429, in run - raise InstallationError( - pip._internal.exceptions.InstallationError: Could not build wheels for emu, which is required to install pyproject.toml-based projects - Removed build tracker: '/private/tmp/pip-build-tracker-pcf71fuv' -# Last 100 lines of the build log. diff --git a/recipes/emu-pca/meta.yaml b/recipes/emu-pca/meta.yaml index 3606b1fe2ba7c..f299b78443ca6 100644 --- a/recipes/emu-pca/meta.yaml +++ b/recipes/emu-pca/meta.yaml @@ -1,5 +1,5 @@ {% set name = "emu-pca" %} -{% set version = "1.0" %} +{% set version = "1.1" %} package: name: "{{ name|lower }}" @@ -7,12 +7,15 @@ package: source: url: 'https://github.com/Rosemeis/emu/archive/refs/tags/v{{ version }}.tar.gz' - md5: b79e9a2f72b8b83361a5542edc1c4ca7 + sha256: a309849df3cbd2255718ba27d413b931b835ed869a67a93cd20320d1a04d31fb build: - number: 1 + number: 0 + skip: True # [py < 310] script: - - "{{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation" + - "{{ PYTHON }} -m pip install . -vvv --no-deps --no-build-isolation --no-cache-dir" + entry_points: + - emu=emu.main:main run_exports: {{ pin_subpackage('emu-pca', max_pin="x") }} @@ -37,4 +40,3 @@ about: license_file: LICENSE summary: EM-PCA for Ultra-low Coverage Sequencing Data. dev_url: https://github.com/Rosemeis/emu -