Update BioConductor packages to BioC 3.20

recipes/bioconductor-a4/meta.yaml

@@ -1,47 +1,52 @@
-{% set version = "1.50.0" %}
+{% set version = "1.54.0" %}
 {% set name = "a4" %}
-{% set bioc = "3.18" %}
+{% set bioc = "3.20" %}
+
+about:
+  description: Umbrella package is available for the entire Automated Affymetrix Array Analysis suite of package.
+  home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html
+  license: GPL-3
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+  summary: Automated Affymetrix Array Analysis Umbrella Package
 
-package:
-  name: 'bioconductor-{{ name|lower }}'
-  version: '{{ version }}'
-source:
-  url:
-    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
-    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
-    - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
-    - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz'
-  md5: 54c9c4300db0c04edd9b531bb0f121a0
 build:
+  noarch: generic
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
   run_exports: '{{ pin_subpackage("bioconductor-a4", max_pin="x.x") }}'
-  noarch: generic
-# Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats
+
+package:
+  name: bioconductor-{{ name|lower }}
+  version: '{{ version }}'
+
+# Suggests: MLP, nlcv, ALL, Cairo, Rgraphviz, GOstats, hgu95av2.db
 requirements:
   host:
-    - 'bioconductor-a4base >=1.50.0,<1.51.0'
-    - 'bioconductor-a4classif >=1.50.0,<1.51.0'
-    - 'bioconductor-a4core >=1.50.0,<1.51.0'
-    - 'bioconductor-a4preproc >=1.50.0,<1.51.0'
-    - 'bioconductor-a4reporting >=1.50.0,<1.51.0'
+    - bioconductor-a4base >=1.54.0,<1.55.0
+    - bioconductor-a4classif >=1.54.0,<1.55.0
+    - bioconductor-a4core >=1.54.0,<1.55.0
+    - bioconductor-a4preproc >=1.54.0,<1.55.0
+    - bioconductor-a4reporting >=1.54.0,<1.55.0
     - r-base
   run:
-    - 'bioconductor-a4base >=1.50.0,<1.51.0'
-    - 'bioconductor-a4classif >=1.50.0,<1.51.0'
-    - 'bioconductor-a4core >=1.50.0,<1.51.0'
-    - 'bioconductor-a4preproc >=1.50.0,<1.51.0'
-    - 'bioconductor-a4reporting >=1.50.0,<1.51.0'
+    - bioconductor-a4base >=1.54.0,<1.55.0
+    - bioconductor-a4classif >=1.54.0,<1.55.0
+    - bioconductor-a4core >=1.54.0,<1.55.0
+    - bioconductor-a4preproc >=1.54.0,<1.55.0
+    - bioconductor-a4reporting >=1.54.0,<1.55.0
     - r-base
+
+source:
+  md5: 40f370dbf39df0f5d4182463c5bbd9d7
+  url:
+    - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz
+    - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz
+    - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz
+    - https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz
+
 test:
   commands:
-    - '$R -e "library(''{{ name }}'')"'
-about:
-  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-3
-  summary: 'Automated Affymetrix Array Analysis Umbrella Package'
-  description: 'Umbrella package is available for the entire Automated Affymetrix Array Analysis suite of package.'
-  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+    - $R -e "library('{{ name }}')"
 

recipes/bioconductor-a4base/meta.yaml

@@ -1,65 +1,71 @@
-{% set version = "1.50.0" %}
+{% set version = "1.54.0" %}
 {% set name = "a4Base" %}
-{% set bioc = "3.18" %}
+{% set bioc = "3.20" %}
+
+about:
+  description: Base utility functions are available for the Automated Affymetrix Array Analysis set of packages.
+  home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html
+  license: GPL-3
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+  summary: Automated Affymetrix Array Analysis Base Package
 
-package:
-  name: 'bioconductor-{{ name|lower }}'
-  version: '{{ version }}'
-source:
-  url:
-    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
-    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
-    - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
-    - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: 927ee5147653a1ee4df6380f52ad055a
 build:
+  noarch: generic
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
   run_exports: '{{ pin_subpackage("bioconductor-a4base", max_pin="x.x") }}'
-  noarch: generic
+
+extra:
+  identifiers:
+    - biotools:a4base
+    - doi:10.1038/nmeth.3252
+  parent_recipe:
+    name: bioconductor-a4base
+    path: recipes/bioconductor-a4base
+    version: 1.28.0
+
+package:
+  name: bioconductor-{{ name|lower }}
+  version: '{{ version }}'
+
 # Suggests: Cairo, ALL, hgu95av2.db, nlcv
 requirements:
   host:
-    - 'bioconductor-a4core >=1.50.0,<1.51.0'
-    - 'bioconductor-a4preproc >=1.50.0,<1.51.0'
-    - 'bioconductor-annaffy >=1.74.0,<1.75.0'
-    - 'bioconductor-biobase >=2.62.0,<2.63.0'
-    - 'bioconductor-genefilter >=1.84.0,<1.85.0'
-    - 'bioconductor-limma >=3.58.0,<3.59.0'
-    - 'bioconductor-multtest >=2.58.0,<2.59.0'
+    - bioconductor-a4core >=1.54.0,<1.55.0
+    - bioconductor-a4preproc >=1.54.0,<1.55.0
+    - bioconductor-annaffy >=1.78.0,<1.79.0
+    - bioconductor-biobase >=2.66.0,<2.67.0
+    - bioconductor-genefilter >=1.88.0,<1.89.0
+    - bioconductor-limma >=3.62.0,<3.63.0
+    - bioconductor-multtest >=2.62.0,<2.63.0
     - r-base
     - r-glmnet
     - r-gplots
     - r-mpm
   run:
-    - 'bioconductor-a4core >=1.50.0,<1.51.0'
-    - 'bioconductor-a4preproc >=1.50.0,<1.51.0'
-    - 'bioconductor-annaffy >=1.74.0,<1.75.0'
-    - 'bioconductor-biobase >=2.62.0,<2.63.0'
-    - 'bioconductor-genefilter >=1.84.0,<1.85.0'
-    - 'bioconductor-limma >=3.58.0,<3.59.0'
-    - 'bioconductor-multtest >=2.58.0,<2.59.0'
+    - bioconductor-a4core >=1.54.0,<1.55.0
+    - bioconductor-a4preproc >=1.54.0,<1.55.0
+    - bioconductor-annaffy >=1.78.0,<1.79.0
+    - bioconductor-biobase >=2.66.0,<2.67.0
+    - bioconductor-genefilter >=1.88.0,<1.89.0
+    - bioconductor-limma >=3.62.0,<3.63.0
+    - bioconductor-multtest >=2.62.0,<2.63.0
     - r-base
     - r-glmnet
     - r-gplots
     - r-mpm
+
+source:
+  md5: 4771171aad0490cd8cbde8837845b9a7
+  url:
+    - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz
+    - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz
+    - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz
+    - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz
+
 test:
   commands:
-    - '$R -e "library(''{{ name }}'')"'
-about:
-  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-3
-  summary: 'Automated Affymetrix Array Analysis Base Package'
-  description: 'Base utility functions are available for the Automated Affymetrix Array Analysis set of packages.'
-  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
-extra:
-  identifiers:
-    - biotools:a4base
-    - doi:10.1038/nmeth.3252
-  parent_recipe:
-    name: bioconductor-a4base
-    path: recipes/bioconductor-a4base
-    version: 1.28.0
+    - $R -e "library('{{ name }}')"
 

recipes/bioconductor-a4classif/meta.yaml

@@ -1,51 +1,56 @@
-{% set version = "1.50.0" %}
+{% set version = "1.54.0" %}
 {% set name = "a4Classif" %}
-{% set bioc = "3.18" %}
+{% set bioc = "3.20" %}
+
+about:
+  description: Functionalities for classification of Affymetrix microarray data, integrating within the Automated Affymetrix Array Analysis set of packages.
+  home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html
+  license: GPL-3
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+  summary: Automated Affymetrix Array Analysis Classification Package
 
-package:
-  name: 'bioconductor-{{ name|lower }}'
-  version: '{{ version }}'
-source:
-  url:
-    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
-    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
-    - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
-    - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: 2af82160c9909dd6fdec620de5710cfa
 build:
+  noarch: generic
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
   run_exports: '{{ pin_subpackage("bioconductor-a4classif", max_pin="x.x") }}'
-  noarch: generic
+
+package:
+  name: bioconductor-{{ name|lower }}
+  version: '{{ version }}'
+
 # Suggests: ALL, hgu95av2.db, knitr, rmarkdown
 requirements:
   host:
-    - 'bioconductor-a4core >=1.50.0,<1.51.0'
-    - 'bioconductor-a4preproc >=1.50.0,<1.51.0'
-    - 'bioconductor-biobase >=2.62.0,<2.63.0'
+    - bioconductor-a4core >=1.54.0,<1.55.0
+    - bioconductor-a4preproc >=1.54.0,<1.55.0
+    - bioconductor-biobase >=2.66.0,<2.67.0
     - r-base
     - r-glmnet
     - r-pamr
     - r-rocr
     - r-varselrf
   run:
-    - 'bioconductor-a4core >=1.50.0,<1.51.0'
-    - 'bioconductor-a4preproc >=1.50.0,<1.51.0'
-    - 'bioconductor-biobase >=2.62.0,<2.63.0'
+    - bioconductor-a4core >=1.54.0,<1.55.0
+    - bioconductor-a4preproc >=1.54.0,<1.55.0
+    - bioconductor-biobase >=2.66.0,<2.67.0
     - r-base
     - r-glmnet
     - r-pamr
     - r-rocr
     - r-varselrf
+
+source:
+  md5: 05f58ff9cc5356d54f099b548556f1de
+  url:
+    - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz
+    - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz
+    - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz
+    - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz
+
 test:
   commands:
-    - '$R -e "library(''{{ name }}'')"'
-about:
-  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-3
-  summary: 'Automated Affymetrix Array Analysis Classification Package'
-  description: 'Functionalities for classification of Affymetrix microarray data, integrating within the Automated Affymetrix Array Analysis set of packages.'
-  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+    - $R -e "library('{{ name }}')"
 

recipes/bioconductor-a4core/meta.yaml

@@ -1,49 +1,55 @@
-{% set version = "1.50.0" %}
+{% set version = "1.54.0" %}
 {% set name = "a4Core" %}
-{% set bioc = "3.18" %}
+{% set bioc = "3.20" %}
+
+about:
+  description: Utility functions for the Automated Affymetrix Array Analysis set of packages.
+  home: https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html
+  license: GPL-3
+  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
+  summary: Automated Affymetrix Array Analysis Core Package
 
-package:
-  name: 'bioconductor-{{ name|lower }}'
-  version: '{{ version }}'
-source:
-  url:
-    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
-    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz'
-    - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz'
-    - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz'
-  md5: fdca418afe3a74d9114d8d28afca2037
 build:
+  noarch: generic
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
   run_exports: '{{ pin_subpackage("bioconductor-a4core", max_pin="x.x") }}'
-  noarch: generic
+
+extra:
+  identifiers:
+    - biotools:a4core
+    - doi:10.1038/nmeth.3252
+  parent_recipe:
+    name: bioconductor-a4core
+    path: recipes/bioconductor-a4core
+    version: 1.28.0
+
+package:
+  name: bioconductor-{{ name|lower }}
+  version: '{{ version }}'
+
 # Suggests: knitr, rmarkdown
 requirements:
   host:
-    - 'bioconductor-biobase >=2.62.0,<2.63.0'
+    - bioconductor-biobase >=2.66.0,<2.67.0
     - r-base
     - r-glmnet
   run:
-    - 'bioconductor-biobase >=2.62.0,<2.63.0'
+    - bioconductor-biobase >=2.66.0,<2.67.0
     - r-base
     - r-glmnet
+
+source:
+  md5: 5d5ce981344b7e509946fdf02ac78498
+  url:
+    - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz
+    - https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/Archive/{{ name }}/{{ name }}_{{ version }}.tar.gz
+    - https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz
+    - https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz
+
 test:
   commands:
-    - '$R -e "library(''{{ name }}'')"'
-about:
-  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
-  license: GPL-3
-  summary: 'Automated Affymetrix Array Analysis Core Package'
-  description: 'Utility functions for the Automated Affymetrix Array Analysis set of packages.'
-  license_file: '{{ environ["PREFIX"] }}/lib/R/share/licenses/GPL-3'
-extra:
-  identifiers:
-    - biotools:a4core
-    - doi:10.1038/nmeth.3252
-  parent_recipe:
-    name: bioconductor-a4core
-    path: recipes/bioconductor-a4core
-    version: 1.28.0
+    - $R -e "library('{{ name }}')"