diff --git a/build-fail-blacklist b/build-fail-blacklist index 99e03a2fdd90f..823c1eee268b7 100644 --- 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 index db04eccd8c503..cadeb659b66a5 100644 --- 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 index 62b076530efdf..95bb9f5a7e5e2 100644 --- 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 index 34eb9a0191557..25641d0abaf9f 100644 --- 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 new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ 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 new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ 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 index 512919c1bf4dc..81c17bbd5261a 100644 --- 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: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-harman/conda_build_config.yaml b/recipes/bioconductor-harman/conda_build_config.yaml new file mode 100644 index 0000000000000..d3da287204f8d --- /dev/null +++ b/recipes/bioconductor-harman/conda_build_config.yaml @@ -0,0 +1,2 @@ +r_base: + - 3.5.1 diff --git a/recipes/bioconductor-netreg/meta.yaml b/recipes/bioconductor-netreg/meta.yaml index 4e7d5a8fc0dfa..98700d1989d27 100644 --- a/recipes/bioconductor-netreg/meta.yaml +++ b/recipes/bioconductor-netreg/meta.yaml @@ -17,19 +17,21 @@ build: - lib/R/lib/ - lib/ requirements: + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make host: - r-base - r-rcpp - r-rcpparmadillo + - openblas run: - r-base - r-rcpp - r-rcpparmadillo - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make + - openblas test: commands: - '$R -e "library(''{{ name }}'')"' diff --git a/recipes/bioconductor-rsubread/meta.yaml b/recipes/bioconductor-rsubread/meta.yaml index 4d9d5b6a90963..16e1294e05aab 100644 --- 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 index 19737c3225aed..dd14915f1daec 100644 --- 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 index fd368e85ee8bb..edbad01298f9c 100644 --- 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) and Maliet et al. (2017) . 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 index 14caed9c5040b..937dbd9d96f58 100644 --- 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 index 2b4090c969731..c8f18a2bc188c 100644 --- 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 index 517978baf45d2..bb56331b4b9ac 100644 --- 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 index 8507ccdbbca90..c10101e4623d3 100644 --- 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 index 981ff7c2730a7..ec1c3029e84e9 100644 --- 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