[BULK] Fixes for R/Bioconductor packages

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
+    - r-base >=3.5
     - '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
+    - r-base >=3.5
     - 'r-rcpp >=0.12.14'
   build:
     - {{ compiler('c') }}

recipes/bioconductor-chronos/meta.yaml

@@ -21,7 +21,7 @@ requirements:
     - 'bioconductor-biomart >=2.36.1,<2.38.0'
     - 'bioconductor-graph >=1.58.0,<1.60.0'
     - 'bioconductor-rbgl >=1.56.0,<1.58.0'
-    - r-base
+    - r-base >=3.5
     - r-circlize
     - r-doparallel
     - r-foreach
@@ -32,7 +32,7 @@ requirements:
     - 'bioconductor-biomart >=2.36.1,<2.38.0'
     - 'bioconductor-graph >=1.58.0,<1.60.0'
     - 'bioconductor-rbgl >=1.56.0,<1.58.0'
-    - r-base
+    - r-base >=3.5
     - r-circlize
     - r-doparallel
     - r-foreach

recipes/bioconductor-crisprvariants/meta.yaml

@@ -27,7 +27,7 @@ requirements:
     - 'bioconductor-iranges >=2.14.12,<2.16.0'
     - 'bioconductor-rsamtools >=1.32.3,<1.34.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base
+    - r-base >=3.5
     - 'r-ggplot2 >=2.2.0'
     - r-gridextra
     - r-reshape2
@@ -41,7 +41,7 @@ requirements:
     - 'bioconductor-iranges >=2.14.12,<2.16.0'
     - 'bioconductor-rsamtools >=1.32.3,<1.34.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
-    - r-base
+    - r-base >=3.5
     - 'r-ggplot2 >=2.2.0'
     - r-gridextra
     - r-reshape2

recipes/bioconductor-interactionset/meta.yaml

@@ -24,7 +24,7 @@ requirements:
     - 'bioconductor-iranges >=2.14.12,<2.16.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
     - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0'
-    - r-base
+    - r-base >=3.5
     - r-matrix
     - r-rcpp
   run:
@@ -34,7 +34,7 @@ requirements:
     - 'bioconductor-iranges >=2.14.12,<2.16.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
     - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0'
-    - r-base
+    - r-base >=3.5
     - r-matrix
     - r-rcpp
   build:

recipes/bioconductor-multiassayexperiment/meta.yaml

@@ -24,7 +24,7 @@ requirements:
     - 'bioconductor-iranges >=2.14.12,<2.16.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
     - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0'
-    - r-base
+    - r-base >=3.5
     - r-tidyr
   run:
     - 'bioconductor-biobase >=2.40.0,<2.42.0'
@@ -33,7 +33,7 @@ requirements:
     - 'bioconductor-iranges >=2.14.12,<2.16.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
     - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0'
-    - r-base
+    - r-base >=3.5
     - r-tidyr
 test:
   commands:

recipes/bioconductor-mzr/meta.yaml

@@ -23,6 +23,7 @@ requirements:
     - 'bioconductor-protgenerics >=1.12.0,<1.14.0'
     - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0'
     - 'bioconductor-zlibbioc >=1.26.0,<1.28.0'
+    - libnetcdf
     - r-base
     - 'r-rcpp >=0.10.1'
   run:
@@ -31,6 +32,7 @@ requirements:
     - 'bioconductor-protgenerics >=1.12.0,<1.14.0'
     - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0'
     - 'bioconductor-zlibbioc >=1.26.0,<1.28.0'
+    - libnetcdf
     - r-base
     - 'r-rcpp >=0.10.1'
   build:

recipes/bioconductor-singlecellexperiment/meta.yaml

@@ -21,12 +21,12 @@ requirements:
     - 'bioconductor-biocgenerics >=0.26.0,<0.28.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
     - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0'
-    - r-base
+    - r-base >=3.5
   run:
     - 'bioconductor-biocgenerics >=0.26.0,<0.28.0'
     - 'bioconductor-s4vectors >=0.18.3,<0.20.0'
     - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0'
-    - r-base
+    - r-base >=3.5
 test:
   commands:
     - '$R -e "library(''{{ name }}'')"'

recipes/r-dartr/meta.yaml

@@ -112,8 +112,6 @@ about:
     facilitate transfer of data between genlight/genind objects and newhybrids, related,
     phylip, structure, faststructure packages.
   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:
   container:
     # needed for libGL.so.1

recipes/r-exomedepth/meta.yaml

@@ -66,8 +66,6 @@ about:
   summary: Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing
     experiments designed to identify the genetic basis of Mendelian disorders.
   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:exomedepth

recipes/r-pscbs/meta.yaml

@@ -64,8 +64,6 @@ about:
     abnormal copy number within each parental chromosome.  Both tumor-normal paired
     and tumor-only analyses are supported.
   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