Update a number of recipes (#11482)

bioconda · Oct 22, 2018 · 4e205fa · 4e205fa
1 parent 90868c8
commit 4e205fa
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Showing 17 changed files with 35 additions and 28 deletions.
diff --git a/build-fail-blacklist b/build-fail-blacklist
@@ -834,6 +834,9 @@ recipes/bioconductor-rcytoscape
 recipes/bioconductor-edger/3.12.1
 recipes/bioconductor-masigpro/1.49.4
 
+# Old package, should we still build it?
+recipes/bioconductor-org.dm.eg.db/3.3.0
+
 # Errors with bioconductor-skeleton
 recipes/bioconductor-mvgst
 

diff --git a/recipes/bioconductor-amountain/meta.yaml b/recipes/bioconductor-amountain/meta.yaml
@@ -19,8 +19,10 @@ build:
 requirements:
   host:
     - r-base
+    - openblas
   run:
     - r-base
+    - openblas
   build:
     - {{ compiler('c') }}
     - make

diff --git a/recipes/bioconductor-annotationhubdata/meta.yaml b/recipes/bioconductor-annotationhubdata/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.10.2" %}
+{% set version = "1.10.3" %}
 {% set name = "AnnotationHubData" %}
 {% set bioc = "3.7" %}
 
@@ -10,7 +10,7 @@ source:
     - 'http://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: 4e18e50a99aefa9b9e2fc8c6a37659675a5bde5af8884c3b23360e2d4b4105c6
+  sha256: e91b48c7db39456601090dd66e6209023e849a2ccc0d49acab63b066806163f3
 build:
   number: 0
   rpaths:

diff --git a/recipes/bioconductor-derfinder/meta.yaml b/recipes/bioconductor-derfinder/meta.yaml
@@ -59,7 +59,11 @@ test:
 about:
   home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html'
   license: Artistic-2.0
-  summary: 'This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.'
+  summary: 'This package provides functions for annotation-agnostic differential
+    expression analysis of RNA-seq data. Two implementations of the DER Finder
+    approach are included in this package: (1) single base-level F-statistics
+    and (2) DER identification at the expressed regions-level. The DER Finder
+    approach can also be used to identify differentially bounded ChIP-seq peaks.'
 extra:
   identifiers:
     - biotools:derfinder
diff --git a/recipes/bioconductor-epivizr/conda_build_config.yaml b/recipes/bioconductor-epivizr/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-epivizrstandalone/conda_build_config.yaml b/recipes/bioconductor-epivizrstandalone/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-flowpeaks/meta.yaml b/recipes/bioconductor-flowpeaks/meta.yaml
@@ -17,14 +17,16 @@ build:
     - lib/R/lib/
     - lib/
 requirements:
-  host:
-    - r-base
-  run:
-    - r-base
   build:
     - {{ compiler('c') }}
     - {{ compiler('cxx') }}
     - make
+  host:
+    - r-base
+    - openblas
+  run:
+    - r-base
+    - openblas
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-harman/conda_build_config.yaml b/recipes/bioconductor-harman/conda_build_config.yaml
@@ -0,0 +1,2 @@
+r_base:
+  - 3.5.1
diff --git a/recipes/bioconductor-netreg/meta.yaml b/recipes/bioconductor-netreg/meta.yaml
@@ -17,19 +17,21 @@ build:
     - lib/R/lib/
     - lib/
 requirements:
+  build:
+    - {{ compiler('c') }}
+    - {{ compiler('cxx') }}
+    - automake
+    - make
   host:
     - r-base
     - r-rcpp
     - r-rcpparmadillo
+    - openblas
   run:
     - r-base
     - r-rcpp
     - r-rcpparmadillo
-  build:
-    - {{ compiler('c') }}
-    - {{ compiler('cxx') }}
-    - automake
-    - make
+    - openblas
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

diff --git a/recipes/bioconductor-rsubread/meta.yaml b/recipes/bioconductor-rsubread/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "1.30.8" %}
+{% set version = "1.30.9" %}
 {% set name = "Rsubread" %}
 {% set bioc = "3.7" %}
 
@@ -10,7 +10,7 @@ source:
     - 'http://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: ea984b97e9762ff84879567c24d7cdd2d76eb77f27a69aa83ad1a4bb395b6d7a
+  sha256: 57673882455021a2656e56798da722864b2b1e0aaa9ab5783952179e6af7b323
 build:
   number: 0
   rpaths:

diff --git a/recipes/bioconductor-uniprot.ws/meta.yaml b/recipes/bioconductor-uniprot.ws/meta.yaml
@@ -1,4 +1,4 @@
-{% set version = "2.20.2" %}
+{% set version = "2.20.4" %}
 {% set name = "UniProt.ws" %}
 {% set bioc = "3.7" %}
 
@@ -10,7 +10,7 @@ source:
     - 'http://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: bda659895edf820e7a63267e39ae5739880a605930f0f6304570e08a7c713805
+  sha256: 38f80df3370c7beb0de96666b5df08efddbb66bd91c2a58aed2ac20d7dfa60ab
 build:
   number: 0
   rpaths:

diff --git a/recipes/r-aptreeshape/meta.yaml b/recipes/r-aptreeshape/meta.yaml
@@ -59,8 +59,6 @@ about:
     be converted easily. Implements methods described in Bortolussi et al. (2005) <doi:10.1093/bioinformatics/bti798>
     and Maliet et al. (2017)  <doi:10.1101/224295>.
   license_family: GPL3
-  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
-  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
 extra:
   recipe-maintainers:
     - MathiasHaudgaard

diff --git a/recipes/r-canopy/meta.yaml b/recipes/r-canopy/meta.yaml
@@ -61,8 +61,6 @@ about:
     evolutionary configurations consistent with the data, Canopy outputs  all configurations
     along with their confidence assessment.
   license_family: GPL2
-  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-2'  # [unix]
-  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-2'  # [win]
 extra:
   recipe-maintainers:
     - MathiasHaudgaard

diff --git a/recipes/r-geiger/meta.yaml b/recipes/r-geiger/meta.yaml
@@ -71,8 +71,6 @@ about:
   license: GPL (>= 2)
   summary: Methods for fitting macroevolutionary models to phylogenetic trees.
   license_family: GPL3
-  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
-  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
 extra:
   recipe-maintainers:
     - MathiasHaudgaard

diff --git a/recipes/r-maldiquantforeign/meta.yaml b/recipes/r-maldiquantforeign/meta.yaml
@@ -57,8 +57,6 @@ about:
     7.5, CDF, mMass MSD) and writing (tab, csv, mMass MSD, mzML, imzML) different file
     formats of mass spectrometry data into/from 'MALDIquant' objects.
   license_family: GPL3
-  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
-  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
 extra:
   recipe-maintainers:
     - MathiasHaudgaard

diff --git a/recipes/r-maldirppa/meta.yaml b/recipes/r-maldirppa/meta.yaml
@@ -54,8 +54,6 @@ about:
   summary: Provides methods for quality control and robust pre-processing and analysis of MALDI
     mass spectrometry data.
   license_family: GPL3
-  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
-  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
 extra:
   recipe-maintainers:
     - MathiasHaudgaard

diff --git a/recipes/r-wgcna/meta.yaml b/recipes/r-wgcna/meta.yaml
@@ -83,8 +83,6 @@ about:
     summarization, and relating of variables and modules to sample traits. Also includes
     a number of utility functions for data manipulation and visualization.
   license_family: GPL3
-  license_file: '{{ environ["PREFIX"] }}\/lib\/R\/share\/licenses\/GPL-3'  # [unix]
-  license_file: '{{ environ["PREFIX"] }}\R\share\licenses\GPL-3'  # [win]
 extra:
   identifiers:
     - biotools:wgcna