Fixes (#12787)

* fix a few recipes * fix recipes * add new blacklisted recipes * remove old recipes * remove old recipes * add jackstraw * add orqa * add isogene
bioconda · Dec 21, 2018 · e83af43 · e83af43
1 parent 888dc48
commit e83af43
Show file tree

Hide file tree

Showing 44 changed files with 397 additions and 895 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -872,3 +872,23 @@ recipes/bioconductor-ramigo
 recipes/bioconductor-ncigraph
 recipes/bioconductor-lymphoseq
 recipes/bioconductor-universalmotif
+recipes/bioconductor-phantasus
+
+# r-feature missing/broken
+recipes/bioconductor-flowmerge
+recipes/bioconductor-flowmeans
+
+# some wired test error with the Docker tests
+recipes/bioconductor-flowstats
+recipes/bioconductor-nethet
+recipes/bioconductor-iterativebma
+recipes/bioconductor-narrowpeaks
+recipes/bioconductor-iwtomics
+
+# missing r-* deps
+recipes/bioconductor-mcagui
+recipes/bioconductor-rexposome
+
+
+# JVM errors
+recipes/bioconductor-rgmql
diff --git a/recipes/bioconductor-dnacopy/1.48.0/build.sh b/recipes/bioconductor-dnacopy/1.48.0/build.sh
diff --git a/recipes/bioconductor-dnacopy/1.48.0/meta.yaml b/recipes/bioconductor-dnacopy/1.48.0/meta.yaml
diff --git a/recipes/bioconductor-edger/3.12.1/build.sh b/recipes/bioconductor-edger/3.12.1/build.sh
diff --git a/recipes/bioconductor-edger/3.12.1/meta.yaml b/recipes/bioconductor-edger/3.12.1/meta.yaml
diff --git a/recipes/bioconductor-ggbio/1.22.0/build.sh b/recipes/bioconductor-ggbio/1.22.0/build.sh
diff --git a/recipes/bioconductor-ggbio/1.22.0/meta.yaml b/recipes/bioconductor-ggbio/1.22.0/meta.yaml
diff --git a/recipes/bioconductor-interminer/meta.yaml b/recipes/bioconductor-interminer/meta.yaml
@@ -10,7 +10,7 @@ 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'
-  md5: d41d8cd98f00b204e9800998ecf8427e
+  md5: 8b0b9de68ba80994ea1a0a7a6d90ee36
 build:
   number: 0
   rpaths:

diff --git a/recipes/bioconductor-limma/3.28.10/build.sh b/recipes/bioconductor-limma/3.28.10/build.sh
diff --git a/recipes/bioconductor-limma/3.28.10/meta.yaml b/recipes/bioconductor-limma/3.28.10/meta.yaml
diff --git a/recipes/bioconductor-limma/3.28.2/build.sh b/recipes/bioconductor-limma/3.28.2/build.sh
diff --git a/recipes/bioconductor-limma/3.28.2/meta.yaml b/recipes/bioconductor-limma/3.28.2/meta.yaml
diff --git a/recipes/bioconductor-masigpro/1.49.4/build.sh b/recipes/bioconductor-masigpro/1.49.4/build.sh
diff --git a/recipes/bioconductor-masigpro/1.49.4/meta.yaml b/recipes/bioconductor-masigpro/1.49.4/meta.yaml
diff --git a/recipes/bioconductor-normqpcr/meta.yaml b/recipes/bioconductor-normqpcr/meta.yaml
@@ -38,3 +38,7 @@ about:
   license: LGPL-3
   summary: 'Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data.'
 
+extra:
+  container:
+    # rgl
+    extended-base: true