[BULK] Bioconductor 3.8

recipes/bioconda-utils/meta.yaml

@@ -1,5 +1,5 @@
-{% set version = "0.15.3" %}
-{% set sha256 = "68c23754259fe7102edcc6c89ad55cf5a7ecfd453a2ea0f4e82a290129e4603c" %}
+{% set version = "0.15.2" %}
+{% set sha256 = "a51b1b8e872be08c5f69aaeb55c36379ef4f08039ce51abcabc8167b8577dda2" %}
 
 package:
   name: bioconda-utils

recipes/bioconductor-a4/build.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+mv DESCRIPTION DESCRIPTION.old
+grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+mkdir -p ~/.R
+echo -e "CC=$CC
+FC=$FC
+CXX=$CXX
+CXX98=$CXX
+CXX11=$CXX
+CXX14=$CXX" > ~/.R/Makevars
+$R CMD INSTALL --build .

recipes/bioconductor-a4/meta.yaml

@@ -0,0 +1,43 @@
+{% set version = "1.30.0" %}
+{% set name = "a4" %}
+{% set bioc = "3.8" %}
+
+package:
+  name: 'bioconductor-{{ name|lower }}'
+  version: '{{ version }}'
+source:
+  url:
+    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ 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: 4e44a4273b805b3fda0cbbd476566c25
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+  noarch: generic
+# Suggests: MLP, nlcv, ALL, Cairo
+requirements:
+  host:
+    - 'bioconductor-a4base >=1.30.0,<1.31.0'
+    - 'bioconductor-a4classif >=1.30.0,<1.31.0'
+    - 'bioconductor-a4core >=1.30.0,<1.31.0'
+    - 'bioconductor-a4preproc >=1.30.0,<1.31.0'
+    - 'bioconductor-a4reporting >=1.30.0,<1.31.0'
+    - r-base
+  run:
+    - 'bioconductor-a4base >=1.30.0,<1.31.0'
+    - 'bioconductor-a4classif >=1.30.0,<1.31.0'
+    - 'bioconductor-a4core >=1.30.0,<1.31.0'
+    - 'bioconductor-a4preproc >=1.30.0,<1.31.0'
+    - 'bioconductor-a4reporting >=1.30.0,<1.31.0'
+    - r-base
+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'
+

recipes/bioconductor-a4base/build.sh

@@ -1,4 +1,11 @@
 #!/bin/bash
 mv DESCRIPTION DESCRIPTION.old
 grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+mkdir -p ~/.R
+echo -e "CC=$CC
+FC=$FC
+CXX=$CXX
+CXX98=$CXX
+CXX11=$CXX
+CXX14=$CXX" > ~/.R/Makevars
 $R CMD INSTALL --build .

recipes/bioconductor-a4base/meta.yaml

@@ -1,6 +1,6 @@
-{% set version = "1.28.0" %}
+{% set version = "1.30.0" %}
 {% set name = "a4Base" %}
-{% set bioc = "3.7" %}
+{% set bioc = "3.8" %}
 
 package:
   name: 'bioconductor-{{ name|lower }}'
@@ -10,36 +10,37 @@ source:
     - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ 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'
-  sha256: ed117190a960d4e69725cf5fd1f2c7c785a5258c06eb897d80f0a57626ae7520
+  md5: a8238f64848e4f0974867b0a5f3dc920
 build:
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
+  noarch: generic
 # Suggests: Cairo, ALL
 requirements:
   host:
-    - 'bioconductor-a4core >=1.28.0,<1.30.0'
-    - 'bioconductor-a4preproc >=1.28.0,<1.30.0'
-    - 'bioconductor-annaffy >=1.52.0,<1.54.0'
-    - 'bioconductor-annotationdbi >=1.42.1,<1.44.0'
-    - 'bioconductor-biobase >=2.40.0,<2.42.0'
-    - 'bioconductor-genefilter >=1.62.0,<1.64.0'
-    - 'bioconductor-limma >=3.36.5,<3.38.0'
-    - 'bioconductor-multtest >=2.36.0,<2.38.0'
+    - 'bioconductor-a4core >=1.30.0,<1.31.0'
+    - 'bioconductor-a4preproc >=1.30.0,<1.31.0'
+    - 'bioconductor-annaffy >=1.54.0,<1.55.0'
+    - 'bioconductor-annotationdbi >=1.44.0,<1.45.0'
+    - 'bioconductor-biobase >=2.42.0,<2.43.0'
+    - 'bioconductor-genefilter >=1.64.0,<1.65.0'
+    - 'bioconductor-limma >=3.38.0,<3.39.0'
+    - 'bioconductor-multtest >=2.38.0,<2.39.0'
     - r-base
     - r-glmnet
     - r-gplots
     - r-mpm
   run:
-    - 'bioconductor-a4core >=1.28.0,<1.30.0'
-    - 'bioconductor-a4preproc >=1.28.0,<1.30.0'
-    - 'bioconductor-annaffy >=1.52.0,<1.54.0'
-    - 'bioconductor-annotationdbi >=1.42.1,<1.44.0'
-    - 'bioconductor-biobase >=2.40.0,<2.42.0'
-    - 'bioconductor-genefilter >=1.62.0,<1.64.0'
-    - 'bioconductor-limma >=3.36.5,<3.38.0'
-    - 'bioconductor-multtest >=2.36.0,<2.38.0'
+    - 'bioconductor-a4core >=1.30.0,<1.31.0'
+    - 'bioconductor-a4preproc >=1.30.0,<1.31.0'
+    - 'bioconductor-annaffy >=1.54.0,<1.55.0'
+    - 'bioconductor-annotationdbi >=1.44.0,<1.45.0'
+    - 'bioconductor-biobase >=2.42.0,<2.43.0'
+    - 'bioconductor-genefilter >=1.64.0,<1.65.0'
+    - 'bioconductor-limma >=3.38.0,<3.39.0'
+    - 'bioconductor-multtest >=2.38.0,<2.39.0'
     - r-base
     - r-glmnet
     - r-gplots
@@ -48,10 +49,15 @@ test:
   commands:
     - '$R -e "library(''{{ name }}'')"'
 about:
-  home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
+  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: GPL-3
   summary: 'Automated Affymetrix Array Analysis'
 extra:
   identifiers:
     - biotools:a4base
     - doi:10.1038/nmeth.3252
+  parent_recipe:
+    name: bioconductor-a4base
+    path: recipes/bioconductor-a4base
+    version: 1.28.0
+

recipes/bioconductor-a4classif/build.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+mv DESCRIPTION DESCRIPTION.old
+grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+mkdir -p ~/.R
+echo -e "CC=$CC
+FC=$FC
+CXX=$CXX
+CXX98=$CXX
+CXX11=$CXX
+CXX14=$CXX" > ~/.R/Makevars
+$R CMD INSTALL --build .

recipes/bioconductor-a4classif/meta.yaml

@@ -0,0 +1,47 @@
+{% set version = "1.30.0" %}
+{% set name = "a4Classif" %}
+{% set bioc = "3.8" %}
+
+package:
+  name: 'bioconductor-{{ name|lower }}'
+  version: '{{ version }}'
+source:
+  url:
+    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ 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: f3c574a15569caf4bc36badf16e2403a
+build:
+  number: 0
+  rpaths:
+    - lib/R/lib/
+    - lib/
+  noarch: generic
+# Suggests: ALL
+requirements:
+  host:
+    - 'bioconductor-a4core >=1.30.0,<1.31.0'
+    - 'bioconductor-a4preproc >=1.30.0,<1.31.0'
+    - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0'
+    - r-base
+    - r-glmnet
+    - r-pamr
+    - r-rocr
+    - r-varselrf
+  run:
+    - 'bioconductor-a4core >=1.30.0,<1.31.0'
+    - 'bioconductor-a4preproc >=1.30.0,<1.31.0'
+    - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0'
+    - r-base
+    - r-glmnet
+    - r-pamr
+    - r-rocr
+    - r-varselrf
+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'
+

recipes/bioconductor-a4core/build.sh

@@ -1,4 +1,11 @@
 #!/bin/bash
 mv DESCRIPTION DESCRIPTION.old
 grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+mkdir -p ~/.R
+echo -e "CC=$CC
+FC=$FC
+CXX=$CXX
+CXX98=$CXX
+CXX11=$CXX
+CXX14=$CXX" > ~/.R/Makevars
 $R CMD INSTALL --build .

recipes/bioconductor-a4core/meta.yaml

@@ -1,38 +1,44 @@
-{% set version = "1.28.0" %}
+{% set version = "1.30.0" %}
 {% set name = "a4Core" %}
-{% set bioc = "3.7" %}
+{% set bioc = "3.8" %}
 
 package:
   name: 'bioconductor-{{ name|lower }}'
   version: '{{ version }}'
 source:
   url:
-    - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
+    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ 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'
-  sha256: 3e71939ec82a11b5d9be7e28e744903fde2a3e58aa4ecc65138c7e8eaec4ac6b
+  md5: 1c18ebb284225195642263519f84089b
 build:
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
+  noarch: generic
 requirements:
   host:
-    - 'bioconductor-biobase >=2.40.0,<2.42.0'
+    - 'bioconductor-biobase >=2.42.0,<2.43.0'
     - r-base
     - r-glmnet
   run:
-    - 'bioconductor-biobase >=2.40.0,<2.42.0'
+    - 'bioconductor-biobase >=2.42.0,<2.43.0'
     - r-base
     - r-glmnet
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'
 about:
-  home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
+  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: GPL-3
   summary: 'Automated Affymetrix Array Analysis Core Package'
 extra:
   identifiers:
     - biotools:a4core
     - doi:10.1038/nmeth.3252
+  parent_recipe:
+    name: bioconductor-a4core
+    path: recipes/bioconductor-a4core
+    version: 1.28.0
+

recipes/bioconductor-a4preproc/build.sh

@@ -1,4 +1,11 @@
 #!/bin/bash
 mv DESCRIPTION DESCRIPTION.old
 grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+mkdir -p ~/.R
+echo -e "CC=$CC
+FC=$FC
+CXX=$CXX
+CXX98=$CXX
+CXX11=$CXX
+CXX14=$CXX" > ~/.R/Makevars
 $R CMD INSTALL --build .

recipes/bioconductor-a4preproc/meta.yaml

@@ -1,36 +1,43 @@
-{% set version = "1.28.0" %}
+{% set version = "1.30.0" %}
 {% set name = "a4Preproc" %}
-{% set bioc = "3.7" %}
+{% set bioc = "3.8" %}
 
 package:
   name: 'bioconductor-{{ name|lower }}'
   version: '{{ version }}'
 source:
   url:
-    - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz'
+    - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ 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'
-  sha256: 84408d2da7e19431824560f1cd9cdd952539550dcfe5607b244220cc88e71042
+  md5: 79f088fcd94c8cf56ca40b40a59b8e97
 build:
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
+  noarch: generic
+# Suggests: ALL, hgu95av2.db
 requirements:
   host:
-    - 'bioconductor-annotationdbi >=1.42.1,<1.44.0'
+    - 'bioconductor-annotationdbi >=1.44.0,<1.45.0'
     - r-base
   run:
-    - 'bioconductor-annotationdbi >=1.42.1,<1.44.0'
+    - 'bioconductor-annotationdbi >=1.44.0,<1.45.0'
     - r-base
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'
 about:
-  home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
+  home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: GPL-3
   summary: 'Automated Affymetrix Array Analysis Preprocessing Package'
 extra:
   identifiers:
     - biotools:a4preproc
     - doi:10.1038/nmeth.3252
+  parent_recipe:
+    name: bioconductor-a4preproc
+    path: recipes/bioconductor-a4preproc
+    version: 1.28.0
+

recipes/bioconductor-a4reporting/build.sh

@@ -1,4 +1,11 @@
 #!/bin/bash
 mv DESCRIPTION DESCRIPTION.old
 grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
+mkdir -p ~/.R
+echo -e "CC=$CC
+FC=$FC
+CXX=$CXX
+CXX98=$CXX
+CXX11=$CXX
+CXX14=$CXX" > ~/.R/Makevars
 $R CMD INSTALL --build .