diff --git a/recipes/rmats/build_failure.osx-64.yaml b/recipes/rmats/build_failure.osx-64.yaml deleted file mode 100644 index 758d8e8d7dee2..0000000000000 --- a/recipes/rmats/build_failure.osx-64.yaml +++ /dev/null @@ -1,104 +0,0 @@ -recipe_sha: eb225f3a61251bb54e69e31c1b3d4ffe1b70c2f7cc8c20ac6a9433238022c11d # 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: |- - [ 3%] Building CXX object src/api/CMakeFiles/BamTools.dir/BamWriter.cpp.o - [ 4%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamHeader.cpp.o - [ 5%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgram.cpp.o - [ 6%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamProgramChain.cpp.o - [ 7%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroup.cpp.o - [ 8%] Building CXX object src/api/CMakeFiles/BamTools.dir/SamReadGroupDictionary.cpp.o - 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[ 31%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocket_p.cpp.o - [ 32%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_p.cpp.o - [ 33%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/io/TcpSocketEngine_unix_p.cpp.o - [ 34%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatParser_p.cpp.o - [ 35%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamFormatPrinter_p.cpp.o - [ 36%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/sam/SamHeaderValidator_p.cpp.o - [ 37%] Building CXX object src/api/CMakeFiles/BamTools.dir/internal/utils/BamException_p.cpp.o - [ 38%] Linking CXX shared library $SRC_DIR/bamtools/lib/libbamtools.dylib - make[3]: Leaving directory '$SRC_DIR/bamtools/build' - [ 38%] Built target BamTools - make[3]: Entering directory '$SRC_DIR/bamtools/build' - make[3]: Leaving directory '$SRC_DIR/bamtools/build' - make[3]: Entering directory '$SRC_DIR/bamtools/build' - [ 39%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamAlignment.cpp.o - [ 40%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamMultiReader.cpp.o - [ 41%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamReader.cpp.o - [ 42%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/BamWriter.cpp.o - [ 43%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamHeader.cpp.o - [ 44%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgram.cpp.o - [ 45%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamProgramChain.cpp.o - [ 46%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroup.cpp.o - [ 47%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamReadGroupDictionary.cpp.o - [ 48%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequence.cpp.o - [ 49%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/SamSequenceDictionary.cpp.o - [ 50%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/bam/BamHeader_p.cpp.o - 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[ 60%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamHttp_p.cpp.o - [ 61%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BamPipe_p.cpp.o - [ 62%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/BgzfStream_p.cpp.o - [ 63%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ByteArray_p.cpp.o - [ 64%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostAddress_p.cpp.o - [ 65%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HostInfo_p.cpp.o - [ 66%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/HttpHeader_p.cpp.o - [ 67%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/ILocalIODevice_p.cpp.o - [ 68%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/RollingBuffer_p.cpp.o - [ 69%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocket_p.cpp.o - [ 70%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_p.cpp.o - [ 71%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/io/TcpSocketEngine_unix_p.cpp.o - [ 72%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatParser_p.cpp.o - [ 73%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamFormatPrinter_p.cpp.o - [ 74%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/sam/SamHeaderValidator_p.cpp.o - [ 75%] Building CXX object src/api/CMakeFiles/BamTools-static.dir/internal/utils/BamException_p.cpp.o - [ 76%] Linking CXX static library $SRC_DIR/bamtools/lib/libbamtools.a - make[3]: Leaving directory '$SRC_DIR/bamtools/build' - [ 76%] Built target BamTools-static - make[3]: Entering directory '$SRC_DIR/bamtools/build' - make[3]: Leaving directory '$SRC_DIR/bamtools/build' - make[3]: Entering directory '$SRC_DIR/bamtools/build' - make[3]: Leaving directory '$SRC_DIR/bamtools/build' - [ 76%] Built target APIHeaders - make[3]: Entering directory '$SRC_DIR/bamtools/build' - make[3]: Leaving directory '$SRC_DIR/bamtools/build' - make[3]: Entering directory '$SRC_DIR/bamtools/build' - make[3]: Leaving directory '$SRC_DIR/bamtools/build' - [ 76%] Built target AlgorithmsHeaders - make[3]: Entering directory '$SRC_DIR/bamtools/build' - make[3]: Leaving directory '$SRC_DIR/bamtools/build' - make[3]: Entering directory '$SRC_DIR/bamtools/build' - [ 77%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_reader.cpp.o - [ 78%] Building CXX object src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/json_value.cpp.o - make[3]: Leaving directory '$SRC_DIR/bamtools/build' - make[2]: Leaving directory '$SRC_DIR/bamtools/build' - make[1]: Leaving directory '$SRC_DIR/bamtools/build' -# Last 100 lines of the build log. diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml index 6f36f750e1005..b09b14db10e21 100644 --- a/recipes/rmats/meta.yaml +++ b/recipes/rmats/meta.yaml @@ -8,9 +8,12 @@ package: source: sha256: c78e6411b7c6634cc31511b69d37a6a3da2e2e076e87609679818debd513aa7a url: https://github.com/Xinglab/rmats-turbo/releases/download/v{{ version }}/rmats_turbo_v{{ version|replace(".","_") }}.tar.gz + patches: + # remove patch when a release includes: https://github.com/Xinglab/rmats-turbo/pull/453 + - rmats_pipeline_setup.patch build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -26,16 +29,17 @@ requirements: - python - cython - numpy - - gsl 2.5 + - gsl - zlib - libblas - liblapack + - setuptools run: - python - numpy - - gsl 2.5 + - gsl - zlib - - star >=2.5 + - star >=2.5 # [not (osx and arm64)] test: commands: @@ -51,3 +55,4 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 diff --git a/recipes/rmats/rmats_pipeline_setup.patch b/recipes/rmats/rmats_pipeline_setup.patch new file mode 100644 index 0000000000000..eb31d6abbece5 --- /dev/null +++ b/recipes/rmats/rmats_pipeline_setup.patch @@ -0,0 +1,11 @@ +--- rMATS_pipeline/setup.py 2024-11-19 14:12:11.355314000 -0500 ++++ rMATS_pipeline/setup.py 2024-11-19 14:12:11.355314000 -0500 +@@ -1,6 +1,6 @@ + import os +-from distutils.core import setup +-from distutils.extension import Extension ++from setuptools import setup ++from setuptools import Extension + from Cython import __version__ as cython_version + from Cython.Build import cythonize + from Cython.Distutils import build_ext