[BULK] Don't use r-base >=3.5, use a conda_build_config.yaml instead (#…

…11452) * Don't use r-base >=3.5, use a conda_build_config.yaml instead * blacklist r-phangorn * Update variancepartition * R 3.5 for packages requiring singlecellexperiment * Update a few packages
bioconda · Oct 21, 2018 · 90868c8 · 90868c8
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diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -105,6 +105,7 @@ recipes/r-mlgt
 recipes/r-mqtl
 recipes/r-pamr
 recipes/r-patpro
+recipes/r-phangorn
 recipes/r-pinfsc50
 recipes/r-plasmidprofiler
 recipes/r-precrec

diff --git a/recipes/bioconductor-affy/conda_build_config.yaml b/recipes/bioconductor-affy/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml
@@ -24,15 +24,15 @@ requirements:
     - 'bioconductor-biocinstaller >=1.30.0,<1.32.0'
     - 'bioconductor-preprocesscore >=1.42.0,<1.44.0'
     - 'bioconductor-zlibbioc >=1.26.0,<1.28.0'
-    - r-base >=3.5
+    - r-base
   run:
     - 'bioconductor-affyio >=1.50.0,<1.52.0'
     - 'bioconductor-biobase >=2.40.0,<2.42.0'
     - 'bioconductor-biocgenerics >=0.26.0,<0.28.0'
     - 'bioconductor-biocinstaller >=1.30.0,<1.32.0'
     - 'bioconductor-preprocesscore >=1.42.0,<1.44.0'
     - 'bioconductor-zlibbioc >=1.26.0,<1.28.0'
-    - r-base >=3.5
+    - r-base
   build:
     - {{ compiler('c') }}
     - automake

diff --git a/recipes/bioconductor-affycontam/conda_build_config.yaml b/recipes/bioconductor-affycontam/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-affycontam/meta.yaml b/recipes/bioconductor-affycontam/meta.yaml
@@ -21,12 +21,12 @@ requirements:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
     - 'bioconductor-affydata >=1.28.0,<1.30.0'
     - 'bioconductor-biobase >=2.40.0,<2.42.0'
-    - r-base >=3.5
+    - r-base
   run:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
     - 'bioconductor-affydata >=1.28.0,<1.30.0'
     - 'bioconductor-biobase >=2.40.0,<2.42.0'
-    - r-base >=3.5
+    - r-base
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-affycoretools/conda_build_config.yaml b/recipes/bioconductor-affycoretools/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-affycoretools/meta.yaml b/recipes/bioconductor-affycoretools/meta.yaml
@@ -29,7 +29,7 @@ requirements:
     - 'bioconductor-oligoclasses >=1.42.0,<1.44.0'
     - 'bioconductor-reportingtools >=2.20.0,<2.22.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base >=3.5
+    - r-base
     - r-dbi
     - r-ggplot2
     - r-gplots
@@ -49,7 +49,7 @@ requirements:
     - 'bioconductor-oligoclasses >=1.42.0,<1.44.0'
     - 'bioconductor-reportingtools >=2.20.0,<2.22.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base >=3.5
+    - r-base
     - r-dbi
     - r-ggplot2
     - r-gplots

diff --git a/recipes/bioconductor-affydata/conda_build_config.yaml b/recipes/bioconductor-affydata/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-affydata/meta.yaml b/recipes/bioconductor-affydata/meta.yaml
@@ -19,10 +19,10 @@ build:
 requirements:
   host:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
-    - r-base >=3.5
+    - r-base
   run:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
-    - r-base >=3.5
+    - r-base
     - wget
 test:
   commands:

diff --git a/recipes/bioconductor-affyexpress/conda_build_config.yaml b/recipes/bioconductor-affyexpress/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-affyexpress/meta.yaml b/recipes/bioconductor-affyexpress/meta.yaml
@@ -20,11 +20,11 @@ requirements:
   host:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
     - 'bioconductor-limma >=3.36.5,<3.38.0'
-    - r-base >=3.5
+    - r-base
   run:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
     - 'bioconductor-limma >=3.36.5,<3.38.0'
-    - r-base >=3.5
+    - r-base
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-affyilm/conda_build_config.yaml b/recipes/bioconductor-affyilm/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-affyilm/meta.yaml b/recipes/bioconductor-affyilm/meta.yaml
@@ -22,13 +22,13 @@ requirements:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
     - 'bioconductor-biobase >=2.40.0,<2.42.0'
     - 'bioconductor-gcrma >=2.52.0,<2.54.0'
-    - r-base >=3.5
+    - r-base
   run:
     - 'bioconductor-affxparser >=1.52.0,<1.54.0'
     - 'bioconductor-affy >=1.58.0,<1.60.0'
     - 'bioconductor-biobase >=2.40.0,<2.42.0'
     - 'bioconductor-gcrma >=2.52.0,<2.54.0'
-    - r-base >=3.5
+    - r-base
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-affypdnn/conda_build_config.yaml b/recipes/bioconductor-affypdnn/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-affypdnn/meta.yaml b/recipes/bioconductor-affypdnn/meta.yaml
@@ -19,10 +19,10 @@ build:
 requirements:
   host:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
-    - r-base >=3.5
+    - r-base
   run:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
-    - r-base >=3.5
+    - r-base
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-affyplm/conda_build_config.yaml b/recipes/bioconductor-affyplm/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-affyplm/meta.yaml b/recipes/bioconductor-affyplm/meta.yaml
@@ -24,15 +24,15 @@ requirements:
     - 'bioconductor-gcrma >=2.52.0,<2.54.0'
     - 'bioconductor-preprocesscore >=1.42.0,<1.44.0'
     - 'bioconductor-zlibbioc >=1.26.0,<1.28.0'
-    - r-base >=3.5
+    - r-base
   run:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
     - 'bioconductor-biobase >=2.40.0,<2.42.0'
     - 'bioconductor-biocgenerics >=0.26.0,<0.28.0'
     - 'bioconductor-gcrma >=2.52.0,<2.54.0'
     - 'bioconductor-preprocesscore >=1.42.0,<1.44.0'
     - 'bioconductor-zlibbioc >=1.26.0,<1.28.0'
-    - r-base >=3.5
+    - r-base
   build:
     - {{ compiler('c') }}
     - make

diff --git a/recipes/bioconductor-affyrnadegradation/conda_build_config.yaml b/recipes/bioconductor-affyrnadegradation/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-affyrnadegradation/meta.yaml b/recipes/bioconductor-affyrnadegradation/meta.yaml
@@ -19,10 +19,10 @@ build:
 requirements:
   host:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
-    - r-base >=3.5
+    - r-base
   run:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
-    - r-base >=3.5
+    - r-base
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-altcdfenvs/conda_build_config.yaml b/recipes/bioconductor-altcdfenvs/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-altcdfenvs/meta.yaml b/recipes/bioconductor-altcdfenvs/meta.yaml
@@ -25,7 +25,7 @@ requirements:
     - 'bioconductor-hypergraph >=1.52.0,<1.54.0'
     - 'bioconductor-makecdfenv >=1.56.0,<1.58.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base >=3.5
+    - r-base
   run:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
     - 'bioconductor-biobase >=2.40.0,<2.42.0'
@@ -34,7 +34,7 @@ requirements:
     - 'bioconductor-hypergraph >=1.52.0,<1.54.0'
     - 'bioconductor-makecdfenv >=1.56.0,<1.58.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base >=3.5
+    - r-base
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-annotationhub/conda_build_config.yaml b/recipes/bioconductor-annotationhub/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-annotationhub/meta.yaml b/recipes/bioconductor-annotationhub/meta.yaml
@@ -23,7 +23,7 @@ requirements:
     - 'bioconductor-biocinstaller >=1.30.0,<1.32.0'
     - 'bioconductor-interactivedisplaybase >=1.18.0,<1.20.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base >=3.5
+    - r-base
     - r-curl
     - r-httr
     - r-rsqlite
@@ -34,7 +34,7 @@ requirements:
     - 'bioconductor-biocinstaller >=1.30.0,<1.32.0'
     - 'bioconductor-interactivedisplaybase >=1.18.0,<1.20.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base >=3.5
+    - r-base
     - r-curl
     - r-httr
     - r-rsqlite

diff --git a/recipes/bioconductor-annotationhubdata/conda_build_config.yaml b/recipes/bioconductor-annotationhubdata/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-annotationhubdata/meta.yaml b/recipes/bioconductor-annotationhubdata/meta.yaml
@@ -36,7 +36,7 @@ requirements:
     - 'bioconductor-rsamtools >=1.32.3,<1.34.0'
     - 'bioconductor-rtracklayer >=1.40.6,<1.42.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base >=3.5
+    - r-base
     - r-dbi
     - 'r-futile.logger >=1.3.0'
     - r-jsonlite
@@ -62,7 +62,7 @@ requirements:
     - 'bioconductor-rsamtools >=1.32.3,<1.34.0'
     - 'bioconductor-rtracklayer >=1.40.6,<1.42.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base >=3.5
+    - r-base
     - r-dbi
     - 'r-futile.logger >=1.3.0'
     - r-jsonlite

diff --git a/recipes/bioconductor-arrayqualitymetrics/conda_build_config.yaml b/recipes/bioconductor-arrayqualitymetrics/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-arrayqualitymetrics/meta.yaml b/recipes/bioconductor-arrayqualitymetrics/meta.yaml
@@ -25,7 +25,7 @@ requirements:
     - 'bioconductor-genefilter >=1.62.0,<1.64.0'
     - 'bioconductor-limma >=3.36.5,<3.38.0'
     - 'bioconductor-vsn >=3.48.1,<3.50.0'
-    - r-base >=3.5
+    - r-base
     - 'r-cairo >=1.4-6'
     - 'r-gridsvg >=1.4-3'
     - r-hmisc
@@ -43,7 +43,7 @@ requirements:
     - 'bioconductor-genefilter >=1.62.0,<1.64.0'
     - 'bioconductor-limma >=3.36.5,<3.38.0'
     - 'bioconductor-vsn >=3.48.1,<3.50.0'
-    - r-base >=3.5
+    - r-base
     - 'r-cairo >=1.4-6'
     - 'r-gridsvg >=1.4-3'
     - r-hmisc

diff --git a/recipes/bioconductor-arraytools/conda_build_config.yaml b/recipes/bioconductor-arraytools/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-arraytools/meta.yaml b/recipes/bioconductor-arraytools/meta.yaml
@@ -21,13 +21,13 @@ requirements:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
     - 'bioconductor-biobase >=2.40.0,<2.42.0'
     - 'bioconductor-limma >=3.36.5,<3.38.0'
-    - r-base >=3.5
+    - r-base
     - r-xtable
   run:
     - 'bioconductor-affy >=1.58.0,<1.60.0'
     - 'bioconductor-biobase >=2.40.0,<2.42.0'
     - 'bioconductor-limma >=3.36.5,<3.38.0'
-    - r-base >=3.5
+    - r-base
     - r-xtable
 test:
   commands:

diff --git a/recipes/bioconductor-atacseqqc/conda_build_config.yaml b/recipes/bioconductor-atacseqqc/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-atacseqqc/meta.yaml b/recipes/bioconductor-atacseqqc/meta.yaml
@@ -32,7 +32,7 @@ requirements:
     - 'bioconductor-rsamtools >=1.32.3,<1.34.0'
     - 'bioconductor-rtracklayer >=1.40.6,<1.42.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base >=3.5
+    - r-base
     - r-kernsmooth
     - r-preseqr
     - r-randomforest
@@ -51,7 +51,7 @@ requirements:
     - 'bioconductor-rsamtools >=1.32.3,<1.34.0'
     - 'bioconductor-rtracklayer >=1.40.6,<1.42.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base >=3.5
+    - r-base
     - r-kernsmooth
     - r-preseqr
     - r-randomforest

diff --git a/recipes/bioconductor-beachmat/conda_build_config.yaml b/recipes/bioconductor-beachmat/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-beachmat/meta.yaml b/recipes/bioconductor-beachmat/meta.yaml
@@ -22,14 +22,14 @@ requirements:
     - 'bioconductor-hdf5array >=1.8.1,<1.10.0'
     - 'bioconductor-rhdf5 >=2.24.0,<2.26.0'
     - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0'
-    - r-base >=3.5
+    - r-base
     - 'r-rcpp >=0.12.14'
   run:
     - 'bioconductor-delayedarray >=0.6.6,<0.8.0'
     - 'bioconductor-hdf5array >=1.8.1,<1.10.0'
     - 'bioconductor-rhdf5 >=2.24.0,<2.26.0'
     - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0'
-    - r-base >=3.5
+    - r-base
     - 'r-rcpp >=0.12.14'
   build:
     - {{ compiler('c') }}

diff --git a/recipes/bioconductor-biocinstaller/conda_build_config.yaml b/recipes/bioconductor-biocinstaller/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-biocinstaller/meta.yaml b/recipes/bioconductor-biocinstaller/meta.yaml
@@ -18,9 +18,9 @@ build:
     - lib/
 requirements:
   host:
-    - r-base >=3.5.0
+    - r-base
   run:
-    - r-base >=3.5.0
+    - r-base
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-cager/conda_build_config.yaml b/recipes/bioconductor-cager/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-cager/meta.yaml b/recipes/bioconductor-cager/meta.yaml
@@ -31,7 +31,7 @@ requirements:
     - 'bioconductor-rtracklayer >=1.40.6,<1.42.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
     - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0'
-    - r-base >=3.5
+    - r-base
     - r-beanplot
     - r-data.table
     - 'r-ggplot2 >=2.2.0'
@@ -59,7 +59,7 @@ requirements:
     - 'bioconductor-rtracklayer >=1.40.6,<1.42.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
     - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0'
-    - r-base >=3.5
+    - r-base
     - r-beanplot
     - r-data.table
     - 'r-ggplot2 >=2.2.0'

diff --git a/recipes/bioconductor-cellhts2/conda_build_config.yaml b/recipes/bioconductor-cellhts2/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-cellhts2/meta.yaml b/recipes/bioconductor-cellhts2/meta.yaml
@@ -26,7 +26,7 @@ requirements:
     - 'bioconductor-prada >=1.56.0,<1.58.0'
     - 'bioconductor-splots >=1.46.0,<1.48.0'
     - 'bioconductor-vsn >=3.48.1,<3.50.0'
-    - r-base >=3.5
+    - r-base
     - r-hwriter
     - r-locfit
     - r-rcolorbrewer
@@ -39,7 +39,7 @@ requirements:
     - 'bioconductor-prada >=1.56.0,<1.58.0'
     - 'bioconductor-splots >=1.46.0,<1.48.0'
     - 'bioconductor-vsn >=3.48.1,<3.50.0'
-    - r-base >=3.5
+    - r-base
     - r-hwriter
     - r-locfit
     - r-rcolorbrewer

diff --git a/recipes/bioconductor-chippeakanno/conda_build_config.yaml b/recipes/bioconductor-chippeakanno/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-chippeakanno/meta.yaml b/recipes/bioconductor-chippeakanno/meta.yaml
@@ -41,7 +41,7 @@ requirements:
     - 'bioconductor-rsamtools >=1.32.3,<1.34.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
     - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0'
-    - r-base >=3.5
+    - r-base
     - r-dbi
     - r-idr
     - r-matrixstats
@@ -71,7 +71,7 @@ requirements:
     - 'bioconductor-rsamtools >=1.32.3,<1.34.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
     - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0'
-    - r-base >=3.5
+    - r-base
     - r-dbi
     - r-idr
     - r-matrixstats

diff --git a/recipes/bioconductor-chipxpress/conda_build_config.yaml b/recipes/bioconductor-chipxpress/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1