Add Linux aarch64 build for more Bioconductor packages (#47789)

* iAdd Linux aarch64 build for more Bioconductor packages - bamsignals - bcrank - bcseq - beachmat - chromdraw - hdf5array - rsamtools Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org> * Add linux-aarch64 build for bioconductor-rhdf5 too Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org> * Add `tapi` as a dependency for bioconductor-beachmat ``` (ERR) dyld[44564]: Library not loaded: '@rpath/libtapi.dylib'␛[0m 2024-05-09T12:56:36.5989360Z 12:56:34 ␛[32mBIOCONDA INFO␛[0m (ERR) Referenced from: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/x86_64-apple-darwin13.4.0-ld'␛[0m 2024-05-09T12:56:36.5991920Z 12:56:34 ␛[32mBIOCONDA INFO␛[0m (ERR) Reason: tried: '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/../lib/libtapi.dylib' (no such file), '/opt/mambaforge/envs/bioconda/pkgs/ld64_osx-64-609-h0fd476b_15/bin/../lib/libtapi.dylib' (no such file), '/usr/local/lib/libtapi.dylib' (no such file), '/usr/lib/libtapi.dylib' (no such file)␛[0m 2024-05-09T12:56:36.5995710Z 12:56:34 ␛[32mBIOCONDA INFO␛[0m (ERR) clang-15: error: unable to execute command: Abort trap: 6␛[0m ``` Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org> * Do not build bioc-bcseq and bioc-rsamtools for now. The build on OSX fails Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org> --------- Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
bioconda · May 10, 2024 · 420bee3 · 420bee3
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diff --git a/recipes/bioconductor-bamsignals/meta.yaml b/recipes/bioconductor-bamsignals/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: e7b42351aa9651bdf7d429a6377143f5
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -48,11 +48,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-2
+  license: GPL-2.0-only
   summary: 'Extract read count signals from bam files'
   description: 'This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:bamsignals
     - doi:10.1038/nmeth.3252

diff --git a/recipes/bioconductor-bcrank/meta.yaml b/recipes/bioconductor-bcrank/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: 6c551ab389af456ab76449642c01881a
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -36,11 +36,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-2
+  license: GPL-2.0-only
   summary: 'Predicting binding site consensus from ranked DNA sequences'
   description: 'Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-2'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:bcrank
     - doi:10.1093/nar/gkp381

diff --git a/recipes/bioconductor-beachmat/meta.yaml b/recipes/bioconductor-beachmat/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: ec47172a09aba997192731b4a5f2f284
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -30,13 +30,16 @@ requirements:
     - r-rcpp
     - libblas
     - liblapack
+    - tapi # [osx]
   run:
     - 'bioconductor-biocgenerics >=0.48.0,<0.49.0'
     - 'bioconductor-delayedarray >=0.28.0,<0.29.0'
     - 'bioconductor-sparsearray >=1.2.0,<1.3.0'
     - r-base
     - r-matrix
     - r-rcpp
+    - tapi
+    - tapi # [osx]
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
@@ -46,11 +49,15 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-3
+  license: GPL-3.0-only
   summary: 'Compiling Bioconductor to Handle Each Matrix Type'
   description: 'Provides a consistent C++ class interface for reading from a variety of commonly used matrix types. Ordinary matrices and several sparse/dense Matrix classes are directly supported, along with a subset of the delayed operations implemented in the DelayedArray package. All other matrix-like objects are supported by calling back into R.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
 extra:
+  additional-platforms:
+    - linux-aarch64
+  identifiers:
+    - biotools:{{ name|lower }}
   parent_recipe:
     name: bioconductor-beachmat
     path: recipes/bioconductor-beachmat

diff --git a/recipes/bioconductor-chromdraw/meta.yaml b/recipes/bioconductor-chromdraw/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: a2cb0f03cdde9853f68662b1783a2edb
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -39,11 +39,13 @@ test:
     - '$R -e "library(''{{ name }}'')"'
 about:
   home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-3
+  license: GPL-3.0-only
   summary: 'chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion.'
   description: 'ChromDraw is a R package for drawing the schemes of karyotype(s) in the linear and circular fashion. It is possible to visualized cytogenetic marsk on the chromosomes. This tool has own input data format. Input data can be imported from the GenomicRanges data structure. This package can visualized the data in the BED file format. Here is requirement on to the first nine fields of the BED format. Output files format are *.eps and *.svg.'
   license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:chromdraw
   parent_recipe:

diff --git a/recipes/bioconductor-hdf5array/meta.yaml b/recipes/bioconductor-hdf5array/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
   md5: c59fcd283e0f9877f68457524b9d86bb
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -57,6 +57,8 @@ about:
   summary: 'HDF5 backend for DelayedArray objects'
   description: 'Implement the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:hdf5array
     - doi:10.1038/nmeth.3252

diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml
@@ -13,7 +13,7 @@ source:
     - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
   md5: 947e662fe5f427ed0cc839e8049b431e
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
@@ -47,6 +47,8 @@ about:
   summary: 'R Interface to HDF5'
   description: 'This package provides an interface between HDF5 and R. HDF5''s main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.'
 extra:
+  additional-platforms:
+    - linux-aarch64
   identifiers:
     - biotools:rhdf5
   parent_recipe: