From 1b400a9428900f3ddafc7ef7fe89bda58b922441 Mon Sep 17 00:00:00 2001 From: Eric Kutschera Date: Tue, 19 Nov 2024 09:42:14 -0500 Subject: [PATCH 1/4] Add osx-arm64 * Remove build_failure.osx-64.yaml * Increment build number --- recipes/rmats/build_failure.osx-64.yaml | 104 ------------------------ recipes/rmats/meta.yaml | 3 +- 2 files changed, 2 insertions(+), 105 deletions(-) delete mode 100644 recipes/rmats/build_failure.osx-64.yaml 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 - 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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..3a8956afbb937 100644 --- a/recipes/rmats/meta.yaml +++ b/recipes/rmats/meta.yaml @@ -10,7 +10,7 @@ source: url: https://github.com/Xinglab/rmats-turbo/releases/download/v{{ version }}/rmats_turbo_v{{ version|replace(".","_") }}.tar.gz build: - number: 3 + number: 4 run_exports: - {{ pin_subpackage(name, max_pin="x") }} @@ -51,3 +51,4 @@ about: extra: additional-platforms: - linux-aarch64 + - osx-arm64 From 7ec94429c0d1a394740c7a932ab1f0eecbf0ba50 Mon Sep 17 00:00:00 2001 From: Eric Kutschera Date: Tue, 19 Nov 2024 14:31:35 -0500 Subject: [PATCH 2/4] Address build errors * Unpin gsl + WARNING: failed to get package records, retrying. exception was: Unsatisfiable dependencies for platform osx-arm64: {MatchSpec("gsl=2.5")} * Use setuptools instead of distutils + rMATS_pipeline/setup.py:2: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives + ModuleNotFoundError: No module named 'distutils' --- recipes/rmats/meta.yaml | 8 ++++++-- recipes/rmats/rmats_pipeline_setup.patch | 11 +++++++++++ 2 files changed, 17 insertions(+), 2 deletions(-) create mode 100644 recipes/rmats/rmats_pipeline_setup.patch diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml index 3a8956afbb937..c349c530ec5d7 100644 --- a/recipes/rmats/meta.yaml +++ b/recipes/rmats/meta.yaml @@ -8,6 +8,9 @@ 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: 4 @@ -26,14 +29,15 @@ requirements: - python - cython - numpy - - gsl 2.5 + - gsl - zlib - libblas - liblapack + - setuptools run: - python - numpy - - gsl 2.5 + - gsl - zlib - star >=2.5 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 From 59829473341bfcfd0be42e2f61ad93ae26f03df2 Mon Sep 17 00:00:00 2001 From: Eric Kutschera Date: Tue, 19 Nov 2024 15:54:23 -0500 Subject: [PATCH 3/4] Do not include STAR as a dependency for osx-arm64 * STAR is only needed by rmats when starting with fastq files * WARNING: failed to get package records, retrying. exception was: Unsatisfiable dependencies for platform osx-arm64: {MatchSpec("star[version='>=2.5']")} + STAR --version [...]run_test.sh: line 7: [...]/bin/STAR: Bad CPU type in executable --- recipes/rmats/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml index c349c530ec5d7..8d69496dc25a9 100644 --- a/recipes/rmats/meta.yaml +++ b/recipes/rmats/meta.yaml @@ -39,7 +39,7 @@ requirements: - numpy - gsl - zlib - - star >=2.5 + - star >=2.5 # [not osx-arm64] test: commands: From 5c685be0b9b4f9887f18e4e993a2a05e0fc60dca Mon Sep 17 00:00:00 2001 From: Eric Kutschera Date: Wed, 20 Nov 2024 07:36:14 -0500 Subject: [PATCH 4/4] Fix condition for not requiring STAR --- recipes/rmats/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/rmats/meta.yaml b/recipes/rmats/meta.yaml index 8d69496dc25a9..b09b14db10e21 100644 --- a/recipes/rmats/meta.yaml +++ b/recipes/rmats/meta.yaml @@ -39,7 +39,7 @@ requirements: - numpy - gsl - zlib - - star >=2.5 # [not osx-arm64] + - star >=2.5 # [not (osx and arm64)] test: commands: