diff --git a/build-fail-blacklist b/build-fail-blacklist index b516db8473f59..c6f4b0e3d7ac6 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -816,13 +816,18 @@ 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 +recipes/bioconductor-dnacopy/1.48.0 recipes/bioconductor-ggbio/1.22.0 recipes/bioconductor-limma/3.28.2 recipes/bioconductor-limma/3.28.10 -recipes/bioconductor-dnacopy/1.48.0 -recipes/bioconductor-rgraphviz/2.13.0 +recipes/bioconductor-org.ce.eg.db/3.2.3 +recipes/bioconductor-org.ce.eg.db/3.4.1 +recipes/bioconductor-org.dm.eg.db/3.3.0 recipes/bioconductor-qdnaseq.mm10/1.4.0 +recipes/bioconductor-rgraphviz/2.13.0 +recipes/bioconductor-ropls/1.2.14 +recipes/r-seurat/1.4.0.16 +recipes/r-speaq/1.2.1 # Errors with bioconductor-skeleton recipes/bioconductor-mvgst @@ -833,6 +838,7 @@ recipes/bioconductor-jaspar2018 # new bioconductor blacklist recipes/bioconductor-rtandem recipes/bioconductor-msgfplus +recipes/bioconductor-msgfgui recipes/bioconductor-hpaanalyze recipes/bioconductor-hilbertvisgui recipes/bioconductor-glad diff --git a/recipes/bioconductor-biocsklearn/meta.yaml b/recipes/bioconductor-biocsklearn/meta.yaml index 3f3477c5f3f0f..df4f0b622af0c 100644 --- a/recipes/bioconductor-biocsklearn/meta.yaml +++ b/recipes/bioconductor-biocsklearn/meta.yaml @@ -27,6 +27,8 @@ requirements: - r-knitr - r-reticulate - python + - pandas + - h5py - scikit-learn run: - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' @@ -35,6 +37,8 @@ requirements: - r-knitr - r-reticulate - python + - pandas + - h5py - scikit-learn test: commands: diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index 3d5ebb83d2dc3..fca353c4a4bc8 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -36,6 +36,8 @@ requirements: - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-lattice + - gsl + - openblas build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 2c0b64fb1695e..7ae30ee6b82a5 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -12,7 +12,7 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' md5: 75cedfb5317f0d5e835779722a453fd7 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml index a27ff3cafabab..4380eef731350 100644 --- a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml +++ b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml @@ -29,6 +29,7 @@ requirements: - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-rcpp >=0.12.5' + - gsl run: - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - 'bioconductor-biocparallel >=1.16.0,<1.17.0' @@ -39,6 +40,7 @@ requirements: - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-rcpp >=0.12.5' + - gsl build: - {{ compiler('c') }} - {{ compiler('cxx') }} diff --git a/recipes/r-spp/meta.yaml b/recipes/r-spp/meta.yaml index e7b2bd13f1f52..c9cd194b970e3 100644 --- a/recipes/r-spp/meta.yaml +++ b/recipes/r-spp/meta.yaml @@ -15,10 +15,7 @@ source: build: merge_build_host: True # [win] - - number: 0 - skip: true # [win32] - + number: 1 rpaths: - lib/R/lib/ - lib/ diff --git a/recipes/r-wgcna/meta.yaml b/recipes/r-wgcna/meta.yaml index ec1c3029e84e9..b3474200e4668 100644 --- a/recipes/r-wgcna/meta.yaml +++ b/recipes/r-wgcna/meta.yaml @@ -1,4 +1,4 @@ -{% set version = '1.64-1' %} +{% set version = '1.66' %} {% set posix = 'm2-' if win else '' %} {% set native = 'm2w64-' if win else '' %} @@ -11,14 +11,10 @@ source: url: - {{ cran_mirror }}/src/contrib/WGCNA_{{ version }}.tar.gz - {{ cran_mirror }}/src/contrib/Archive/WGCNA/WGCNA_{{ version }}.tar.gz - sha256: 961a890cda40676ba533cd6de2b1d4f692addd16363f874c82ba8b65dd2d0db6 + sha256: 1b4b8d2a0b7c8c096a8b47810378fbfc475ff36f66a72f89b87e24eb3ef41666 build: - merge_build_host: True # [win] - number: 0 - skip: true # [win32] - rpaths: - lib/R/lib/ - lib/ @@ -36,40 +32,39 @@ requirements: host: - r-base - - 'bioconductor-annotationdbi >=1.42.0,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' + - bioconductor-annotationdbi + - bioconductor-go.db - r-hmisc - r-rcpp >=0.11.0 - r-doparallel - r-dynamictreecut >=1.62 - r-fastcluster - r-foreach - - 'bioconductor-impute >=1.54.0,<1.56.0' + - bioconductor-impute - r-matrixstats >=0.8.1 - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - bioconductor-preprocesscore - r-robust - r-survival run: - r-base - {{native}}gcc-libs # [win] - - 'bioconductor-annotationdbi >=1.42.0,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' + - bioconductor-annotationdbi + - bioconductor-go.db - r-hmisc - r-rcpp >=0.11.0 - r-doparallel - r-dynamictreecut >=1.62 - r-fastcluster - r-foreach - - 'bioconductor-impute >=1.54.0,<1.56.0' + - bioconductor-impute - r-matrixstats >=0.8.1 - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - bioconductor-preprocesscore - r-robust - r-survival test: commands: - - $R -e "library('WGCNA')" # [not win] - "\"%R%\" -e \"library('WGCNA')\"" # [win] @@ -87,11 +82,3 @@ extra: identifiers: - biotools:wgcna - doi:10.1186/1471-2105-9-559 - recipe-maintainers: - - MathiasHaudgaard - - FrodePedersen - - ArneKr - - johanneskoester - - bgruening - - daler - - jdblischak