R rebuild against R 3.3.2 from conda-forge (#4972)

* Add R package micropan * Add R package microseq * start rebuilding for R 3.3.2 without the r-channel * change channel order * various fixes * various fixes * fixes to bioc packages * fixes * remove blacklist * multiple fixes * multiple fixes * fixes * r fixes * change r to r-base * change r to r-base * change r to r-base * url fix * r fixes * r fixes * remove irganes 2.4.7 * r fixes * r fixes * r fixes * remove older version * r fixes * r fixes * r fixes * r fixes * r fixes * r fixes * r fixes * r fixes * rename folder * remove recipe * update bioc skeleton; fix tximport & biomformat * r fixes * fix syntax * r fixes * r fixes * update flowViz recipe * fix BiocStyle recipe * fix org.Hs.eg.db * fix bioconductor_skeleton to auto-find data packages * fix SummarizedExperiment * fix BiocParallel * fix fastseg * fix org.Dm.eg.db * R 3.3.2 has a different set of default packages * fix bioconductor-biomformat * r fixes * bioconductor_skeleton handles typos in DESCRIPTION * fix DEGreport * fix flowViz again * fix multtest * r fixes * more fixes to bioconductor_skeleton * fix org.{Hs,Dm}.eg.db * update the update_bioconductor_packages script to build topsorted dag * fix Category * fix genefilter * add matrix to summarizedexperiment * add urls for gostats * fix MotIV * urls for rGADEM * urls and built-ins for Ringo * urls for zlibbioc * r fixes * r fixes * remove old package * r fixes * r-fixes * r fixes * rpy * r fixes * Minor formatting * add readline to some failing R packages * remove old recipe * Remove micropan from this branch * remove libffi * remove old recipe * r fixes * pin rpy to conda-forge version * Apply comments bgruening * r fixes * enable more debug output * Disable debug logging. * Fix zifa source. * Imrpove cap-mirseq recipe. * r fixes * remove rpy2 * r fixes * r fixes * r fixes * r fixes * remove old version * add new version * r fixes * try some fixes * remove old package * r fixes * r fixes * skip this recipe, as it has to strict pinning * r fixes * remove old nanoraw package * fix osx version * r fixes * r fixes * remove older releases * this pkg is a bioc package * r fixes * remove old r-ggally version * readd older version * add R blacklist again * update blacklist * blacklist the rest of the packages * Change back to master branch
bioconda · fd2ecba171e1ffbfb94f65bc698e11c80852ba7e · bgruening committed with johanneskoester Jun 15, 2017 · Jun 15, 2017 · fd2ecba
1 parent 988233c
commit fd2ecba171e1ffbfb94f65bc698e11c80852ba7e
Unified Split

Showing 503 changed files with 1,632 additions and 4,158 deletions.
diff --git a/config.yml b/config.yml
@@ -12,7 +12,6 @@ docker_image: "condaforge/linux-anvil"
 # be added in reverse (from low to high priority).
 channels:
     - bioconda
-    - r
-    - defaults
     - conda-forge
+    - defaults
 docker_client_version: '1.20'
diff --git a/recipes/bcbio-rnaseq/meta.yaml b/recipes/bcbio-rnaseq/meta.yaml
@@ -13,7 +13,7 @@ build:
 requirements:
   run:
     - java-jdk
-    - r
+    - r-base
     - r-ggplot2
     - r-stringr
     - r-dplyr
diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml
@@ -18,15 +18,15 @@ requirements:
     - bioconductor-biocinstaller
     - bioconductor-preprocesscore
     - bioconductor-zlibbioc
-    - r
+    - r-base
   run:
     - 'bioconductor-affyio >=1.13.3'
     - 'bioconductor-biobase >=2.5.5'
     - 'bioconductor-biocgenerics >=0.1.12'
     - bioconductor-biocinstaller
     - bioconductor-preprocesscore
     - bioconductor-zlibbioc
-    - r
+    - r-base
 test:
   commands:
     - '$R -e "library(''affy'')"'
diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml
@@ -13,10 +13,10 @@ build:
 requirements:
   build:
     - bioconductor-zlibbioc
-    - r
+    - r-base
   run:
     - bioconductor-zlibbioc
-    - r
+    - r-base
 test:
   commands:
     - '$R -e "library(''affyio'')"'
diff --git a/recipes/bioconductor-alpine/meta.yaml b/recipes/bioconductor-alpine/meta.yaml
@@ -3,7 +3,7 @@ package:
   version: 1.0.0
 source:
   fn: alpine_1.0.0.tar.gz
-  url: http://bioconductor.org/packages/release/bioc/src/contrib/alpine_1.0.0.tar.gz
+  url: https://depot.galaxyproject.org/software/bioconductor-alpine/bioconductor-alpine_1.0.0_src_all.tar.gz
   md5: f70ca32c5336aca7745ee3875bbbf28f
 build:
   number: 0
@@ -23,7 +23,7 @@ requirements:
     - bioconductor-rsamtools
     - bioconductor-s4vectors
     - bioconductor-summarizedexperiment
-    - r
+    - r-base
     - r-speedglm
     - r-stringr
   run:
@@ -38,7 +38,7 @@ requirements:
     - bioconductor-rsamtools
     - bioconductor-s4vectors
     - bioconductor-summarizedexperiment
-    - r
+    - r-base
     - r-speedglm
     - r-stringr
 test:
diff --git a/recipes/bioconductor-annotate/meta.yaml b/recipes/bioconductor-annotate/meta.yaml
@@ -15,15 +15,15 @@ requirements:
     - 'bioconductor-annotationdbi >=1.27.5'
     - bioconductor-biobase
     - 'bioconductor-biocgenerics >=0.13.8'
-    - r
+    - r-base
     - r-dbi
     - r-xml
     - r-xtable
   run:
     - 'bioconductor-annotationdbi >=1.27.5'
     - bioconductor-biobase
     - 'bioconductor-biocgenerics >=0.13.8'
-    - r
+    - r-base
     - r-dbi
     - r-xml
     - r-xtable
diff --git a/recipes/bioconductor-annotationdbi/meta.yaml b/recipes/bioconductor-annotationdbi/meta.yaml
@@ -3,8 +3,8 @@ package:
   version: "1.38.0"
 
 source:
-  url: https://bioconductor.org/packages/release/bioc/src/contrib/AnnotationDbi_1.38.0.tar.gz
-  md5: e855f96541bbaf4565807d712a74abf1
+  url: https://depot.galaxyproject.org/software/bioconductor-annotationdbi/bioconductor-annotationdbi_1.38.0_src_all.tar.gz
+  sha256: 47bc40347c3383ffb992bfd31768a6f69860fc02d9b2231073f504a451aacef5
 
 build:
   number: 0
diff --git a/recipes/bioconductor-annotationforge/meta.yaml b/recipes/bioconductor-annotationforge/meta.yaml
@@ -16,7 +16,7 @@ requirements:
     - 'bioconductor-biobase >=1.17.0'
     - 'bioconductor-biocgenerics >=0.15.10'
     - bioconductor-s4vectors
-    - r
+    - r-base
     - r-dbi
     - r-rsqlite
     - r-xml
@@ -25,7 +25,7 @@ requirements:
     - 'bioconductor-biobase >=1.17.0'
     - 'bioconductor-biocgenerics >=0.15.10'
     - bioconductor-s4vectors
-    - r
+    - r-base
     - r-dbi
     - r-rsqlite
     - r-xml
diff --git a/recipes/bioconductor-annotationhub/meta.yaml b/recipes/bioconductor-annotationhub/meta.yaml
@@ -17,7 +17,7 @@ requirements:
     - bioconductor-biocinstaller
     - bioconductor-interactivedisplaybase
     - bioconductor-s4vectors
-    - r
+    - r-base
     - r-httr
     - r-rsqlite
   run:
@@ -26,7 +26,7 @@ requirements:
     - bioconductor-biocinstaller
     - bioconductor-interactivedisplaybase
     - bioconductor-s4vectors
-    - r
+    - r-base
     - r-httr
     - r-rsqlite
 test:
diff --git a/recipes/bioconductor-aroma.light/meta.yaml b/recipes/bioconductor-aroma.light/meta.yaml
@@ -15,13 +15,13 @@ build:
 
 requirements:
   build:
-    - r
+    - r-base
     - 'r-matrixstats >=0.50.2'
     - 'r-r.methodss3 >=1.7.1'
     - 'r-r.oo >=1.20.0'
     - 'r-r.utils >=2.4.0'
   run:
-    - r
+    - r-base
     - 'r-matrixstats >=0.50.2'
     - 'r-r.methodss3 >=1.7.1'
     - 'r-r.oo >=1.20.0'
diff --git a/recipes/bioconductor-ballgown/meta.yaml b/recipes/bioconductor-ballgown/meta.yaml
@@ -20,7 +20,7 @@ requirements:
     - bioconductor-rtracklayer
     - bioconductor-s4vectors
     - bioconductor-sva
-    - r
+    - r-base
     - r-rcolorbrewer
   run:
     - bioconductor-biobase
@@ -31,7 +31,7 @@ requirements:
     - bioconductor-rtracklayer
     - bioconductor-s4vectors
     - bioconductor-sva
-    - r
+    - r-base
     - r-rcolorbrewer
 test:
   commands:
diff --git a/recipes/bioconductor-basic4cseq/meta.yaml b/recipes/bioconductor-basic4cseq/meta.yaml
@@ -16,15 +16,15 @@ requirements:
     - bioconductor-bsgenome.ecoli.ncbi.20080805
     - bioconductor-genomicalignments
     - bioconductor-genomicranges
-    - r
+    - r-base
     - r-catools
     - r-rcircos
   run:
     - bioconductor-biostrings
     - bioconductor-bsgenome.ecoli.ncbi.20080805
     - bioconductor-genomicalignments
     - bioconductor-genomicranges
-    - r
+    - r-base
     - r-catools
     - r-rcircos
 test:
diff --git a/recipes/bioconductor-biobase/meta.yaml b/recipes/bioconductor-biobase/meta.yaml
@@ -1,24 +1,29 @@
 package:
   name: bioconductor-biobase
   version: 2.34.0
+
 source:
-  url: https://bioconductor.org/packages/release/bioc/src/contrib/Biobase_2.34.0.tar.gz
-  md5: b761d9241462a4c6403731203c9fbb94
+  url: https://depot.galaxyproject.org/software/bioconductor-biobase/bioconductor-biobase_2.34.0_src_all.tar.gz
+  sha256: f4ab46c3a02e2c9e9f70b99d751c8749a5b528a53e5117c3290e698a7992494b
+
 build:
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
+
 requirements:
   build:
     - 'bioconductor-biocgenerics >=0.3.2'
     - r-base
   run:
     - 'bioconductor-biocgenerics >=0.3.2'
     - r-base
+
 test:
   commands:
     - '$R -e "library(''Biobase'')"'
+
 about:
   home: https://bioconductor.org/packages/release/bioc/html/Biobase.html
   license: Artistic-2.0
diff --git a/recipes/bioconductor-biocinstaller/meta.yaml b/recipes/bioconductor-biocinstaller/meta.yaml
@@ -1,25 +1,29 @@
 package:
   name: bioconductor-biocinstaller
-  version: 1.22.3
+  version: 1.24.0
+
 source:
-  fn: BiocInstaller_1.22.3.tar.gz
-  url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocInstaller_1.22.3.tar.gz
-  md5: b4547d5fd23d431f2e9ce78a1f619bac
+  fn: BiocInstaller_1.24.0.tar.gz
+  url: https://bioarchive.galaxyproject.org/BiocInstaller_1.24.0.tar.gz
+  sha256: 74d89e27db12d216cd22d99e12372f3e1ffbad5eb71ab6f446ab7190cbcb7943
+
 build:
   number: 0
   rpaths:
     - lib/R/lib/
     - lib/
+
 requirements:
   build:
-    - r
+    - r-base
   run:
-    - r
+    - r-base
+
 test:
   commands:
     - '$R -e "library(''BiocInstaller'')"'
+
 about:
   home: http://bioconductor.org/packages/release/bioc/html/BiocInstaller.html
   license: Artistic-2.0
-  summary: 'This package is used to install and update Bioconductor, CRAN, and (some)
-    github packages.'
+  summary: 'This package is used to install and update Bioconductor, CRAN, and (some) github packages.'
diff --git a/recipes/bioconductor-biocparallel/build.sh b/recipes/bioconductor-biocparallel/build.sh
@@ -1,17 +1,6 @@
 
 #!/bin/bash
-
-# R refuses to build packages that mark themselves as
-# "Priority: Recommended"
 mv DESCRIPTION DESCRIPTION.old
 grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
-#
 $R CMD INSTALL --build .
-#
-# # Add more build steps here, if they are necessary.
-#
-# See
-# http://docs.continuum.io/conda/build.html
-# for a list of environment variables that are set during the build
-# process.
 # 
diff --git a/recipes/bioconductor-biocparallel/meta.yaml b/recipes/bioconductor-biocparallel/meta.yaml
@@ -3,27 +3,29 @@ package:
   version: 1.6.6
 source:
   fn: BiocParallel_1.6.6.tar.gz
-  url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocParallel_1.6.6.tar.gz
+  url:
+    - http://bioconductor.org/packages/3.3/bioc/src/contrib/BiocParallel_1.6.6.tar.gz
+    - https://depot.galaxyproject.org/software/BiocParallel/BiocParallel_1.6.6_src_all.tar.gz
   md5: 445ec78a20e348d678d2e7b8dc5b4354
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
 requirements:
   build:
-    - r
+    - r-base
     - r-futile.logger
     - r-snow
   run:
-    - r
+    - r-base
     - r-futile.logger
     - r-snow
 test:
   commands:
     - '$R -e "library(''BiocParallel'')"'
 about:
-  home: http://bioconductor.org/packages/release/bioc/html/BiocParallel.html
+  home: http://bioconductor.org/packages/3.5/bioc/html/BiocParallel.html
   license: 'GPL-2 | GPL-3'
   summary: 'This package provides modified versions and novel implementation of functions
     for parallel evaluation, tailored to use with Bioconductor objects.'
diff --git a/recipes/bioconductor-biocstyle/build.sh b/recipes/bioconductor-biocstyle/build.sh
@@ -1,17 +1,6 @@
 
 #!/bin/bash
-
-# R refuses to build packages that mark themselves as
-# "Priority: Recommended"
 mv DESCRIPTION DESCRIPTION.old
 grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION
-#
 $R CMD INSTALL --build .
-#
-# # Add more build steps here, if they are necessary.
-#
-# See
-# http://docs.continuum.io/conda/build.html
-# for a list of environment variables that are set during the build
-# process.
 # 
diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml
@@ -3,23 +3,25 @@ package:
   version: 2.0.3
 source:
   fn: BiocStyle_2.0.3.tar.gz
-  url: http://bioconductor.org/packages/release/bioc/src/contrib/BiocStyle_2.0.3.tar.gz
+  url:
+    - http://bioconductor.org/packages/3.3/bioc/src/contrib/BiocStyle_2.0.3.tar.gz
+    - https://depot.galaxyproject.org/software/BiocStyle/BiocStyle_2.0.3_src_all.tar.gz
   md5: 426dcf23e33d0d29b10b6d40cae2054e
 build:
-  number: 0
+  number: 1
   rpaths:
     - lib/R/lib/
     - lib/
 requirements:
   build:
-    - r
+    - r-base
   run:
-    - r
+    - r-base
 test:
   commands:
     - '$R -e "library(''BiocStyle'')"'
 about:
-  home: http://bioconductor.org/packages/release/bioc/html/BiocStyle.html
+  home: http://bioconductor.org/packages/3.5/bioc/html/BiocStyle.html
   license: Artistic-2.0
   summary: 'Provides standard formatting styles for Bioconductor PDF and HTML documents.
     Package vignettes illustrate use and functionality.'
diff --git a/recipes/bioconductor-biomart/meta.yaml b/recipes/bioconductor-biomart/meta.yaml
@@ -13,12 +13,12 @@ build:
 requirements:
   build:
     - bioconductor-annotationdbi
-    - r
+    - r-base
     - r-rcurl
     - r-xml
   run:
     - bioconductor-annotationdbi
-    - r
+    - r-base
     - r-rcurl
     - r-xml
 test: