Merge pull request #92 from BioArchLinux/update_depends

check `depends` and `optdepends` for 255 pkgs that failed to be built

BioArchLinux/r-airpart/PKGBUILD

@@ -38,6 +38,7 @@ optdepends=(
   r-rmarkdown
   r-roxygen2
   r-testthat
+  r-tidyr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('06b0adc3cfc81b2a0151e39692be4f9aa9b351ef1c90f1895f19b9b7dfb44a52')

BioArchLinux/r-ancombc/PKGBUILD

@@ -20,6 +20,7 @@ depends=(
   r-energy
   r-foreach
   r-hmisc
+  r-lme4
   r-lmertest
   r-magrittr
   r-mia
@@ -32,6 +33,7 @@ depends=(
   r-summarizedexperiment
   r-tibble
   r-tidyr
+  r-treesummarizedexperiment
 )
 optdepends=(
   r-caret

BioArchLinux/r-ancombc/lilac.yaml

@@ -3,27 +3,29 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-  - r-cvxr
+- r-cvxr
-  - r-desctools
+- r-desctools
-  - r-doparallel
+- r-doparallel
-  - r-dorng
+- r-dorng
-  - r-dplyr
+- r-dplyr
-  - r-emmeans
+- r-emmeans
-  - r-energy
+- r-energy
-  - r-foreach
+- r-foreach
-  - r-hmisc
+- r-hmisc
-  - r-lmertest
+- r-lme4
-  - r-magrittr
+- r-lmertest
-  - r-mia
+- r-magrittr
-  - r-nloptr
+- r-mia
-  - r-rdpack
+- r-nloptr
-  - r-rlang
+- r-rdpack
-  - r-rngtools
+- r-rlang
-  - r-s4vectors
+- r-rngtools
-  - r-singlecellexperiment
+- r-s4vectors
-  - r-summarizedexperiment
+- r-singlecellexperiment
-  - r-tibble
+- r-summarizedexperiment
-  - r-tidyr
+- r-tibble
+- r-tidyr
+- r-treesummarizedexperiment
 update_on:
 - regex: ANCOMBC_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-bambu/PKGBUILD

@@ -34,7 +34,6 @@ optdepends=(
   r-apeglm
   r-biocfilecache
   r-biostrings
-  r-bsgenome
   r-bsgenome.hsapiens.ncbi.grch38
   r-circlize
   r-complexheatmap
@@ -47,6 +46,7 @@ optdepends=(
   r-knitr
   r-nanoporernaseq
   r-parallel
+  r-purrr
   r-rmarkdown
   r-testthat
   r-txdb.hsapiens.ucsc.hg38.knowngene

BioArchLinux/r-bambu/lilac.yaml

@@ -5,6 +5,7 @@ maintainers:
 repo_depends:
 - r-biocgenerics
 - r-biocparallel
+- r-bsgenome
 - r-data.table
 - r-dplyr
 - r-genomeinfodb
@@ -19,7 +20,6 @@ repo_depends:
 - r-summarizedexperiment
 - r-tidyr
 - r-xgboost
-- r-bsgenome
 update_on:
 - regex: bambu_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-benchdamic/PKGBUILD

@@ -14,13 +14,14 @@ depends=(
   r-aldex2
   r-ancombc
   r-biocparallel
+  r-corncob
   r-cowplot
   r-dearseq
   r-deseq2
   r-edger
-  r-ffpe
   r-ggdendro
   r-ggplot2
+  r-ggridges
   r-limma
   r-mast
   r-metagenomeseq
@@ -38,10 +39,10 @@ depends=(
 )
 optdepends=(
   r-biocstyle
-  r-curatedmetagenomicdata
+  r-kableextra
-  r-hmp16sdata
   r-knitr
   r-rmarkdown
+  r-spsimseq
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-benchdamic/lilac.yaml

@@ -6,13 +6,14 @@ repo_depends:
 - r-aldex2
 - r-ancombc
 - r-biocparallel
+- r-corncob
 - r-cowplot
 - r-dearseq
 - r-deseq2
 - r-edger
-- r-ffpe
 - r-ggdendro
 - r-ggplot2
+- r-ggridges
 - r-limma
 - r-mast
 - r-metagenomeseq

BioArchLinux/r-bindingsitefinder/PKGBUILD

@@ -11,21 +11,23 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
   r
+  r-dplyr
+  r-genomeinfodb
   r-genomicranges
   r-ggforce
   r-ggplot2
+  r-gviz
   r-matrixstats
+  r-plyr
   r-rtracklayer
   r-s4vectors
+  r-tibble
   r-tidyr
-  r-plyr
 )
 optdepends=(
   r-biocstyle
   r-complexheatmap
-  r-dplyr
   r-forcats
-  r-genomeinfodb
   r-genomicalignments
   r-knitr
   r-rmarkdown

BioArchLinux/r-bindingsitefinder/lilac.yaml

@@ -3,14 +3,18 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-dplyr
+- r-genomeinfodb
 - r-genomicranges
 - r-ggforce
 - r-ggplot2
+- r-gviz
 - r-matrixstats
+- r-plyr
 - r-rtracklayer
 - r-s4vectors
+- r-tibble
 - r-tidyr
-- r-plyr
 update_on:
 - regex: BindingSiteFinder_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-biocancer/PKGBUILD

@@ -14,7 +14,6 @@ depends=(
   r-algdesign
   r-annotationdbi
   r-biobase
-  r-cgdsr
   r-clusterprofiler
   r-diagrammer
   r-dose
@@ -23,10 +22,13 @@ depends=(
   r-genetclassifier
   r-go.db
   r-htmlwidgets
+  r-httr
   r-import
   r-org.bt.eg.db
   r-org.hs.eg.db
   r-plyr
+  r-r.methodss3
+  r-r.oo
   r-radiant.data
   r-reactome.db
   r-reactomepa

BioArchLinux/r-biocancer/lilac.yaml

@@ -6,7 +6,6 @@ repo_depends:
 - r-algdesign
 - r-annotationdbi
 - r-biobase
-- r-cgdsr
 - r-clusterprofiler
 - r-diagrammer
 - r-dose
@@ -15,10 +14,13 @@ repo_depends:
 - r-genetclassifier
 - r-go.db
 - r-htmlwidgets
+- r-httr
 - r-import
 - r-org.bt.eg.db
 - r-org.hs.eg.db
 - r-plyr
+- r-r.methodss3
+- r-r.oo
 - r-radiant.data
 - r-reactome.db
 - r-reactomepa

BioArchLinux/r-biocpkgtools/PKGBUILD

@@ -28,11 +28,10 @@ depends=(
   r-rbgl
   r-readr
   r-rlang
+  r-rorcid
   r-rvest
   r-stringr
   r-tibble
-  r-tidyr
-  r-tidyselect
   r-xml2
 )
 optdepends=(
@@ -42,8 +41,8 @@ optdepends=(
   r-diagrammer
   r-kableextra
   r-knitr
+  r-lubridate
   r-rmarkdown
-  r-snowballc
   r-summarizedexperiment
   r-testthat
   r-tm

BioArchLinux/r-biocpkgtools/lilac.yaml

@@ -19,11 +19,10 @@ repo_depends:
 - r-rbgl
 - r-readr
 - r-rlang
+- r-rorcid
 - r-rvest
 - r-stringr
 - r-tibble
-- r-tidyr
-- r-tidyselect
 - r-xml2
 update_on:
 - regex: BiocPkgTools_([\d._-]+).tar.gz

BioArchLinux/r-biosigner/PKGBUILD

@@ -13,9 +13,11 @@ depends=(
   r
   r-biobase
   r-e1071
+  r-multiassayexperiment
   r-multidataset
   r-randomforest
   r-ropls
+  r-summarizedexperiment
 )
 optdepends=(
   r-biocgenerics

BioArchLinux/r-biosigner/lilac.yaml

@@ -5,9 +5,11 @@ maintainers:
 repo_depends:
 - r-biobase
 - r-e1071
+- r-multiassayexperiment
 - r-multidataset
 - r-randomforest
 - r-ropls
+- r-summarizedexperiment
 update_on:
 - regex: biosigner_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-biscuiteer/PKGBUILD

@@ -25,6 +25,7 @@ depends=(
   r-hdf5array
   r-homo.sapiens
   r-impute
+  r-iranges
   r-matrixstats
   r-mus.musculus
   r-qdnaseq
@@ -38,6 +39,7 @@ depends=(
   r-variantannotation
 )
 optdepends=(
+  r-biocstyle
   r-covr
   r-dss
   r-knitr

BioArchLinux/r-biscuiteer/lilac.yaml

@@ -17,6 +17,7 @@ repo_depends:
 - r-hdf5array
 - r-homo.sapiens
 - r-impute
+- r-iranges
 - r-matrixstats
 - r-mus.musculus
 - r-qdnaseq

BioArchLinux/r-cbaf/PKGBUILD

@@ -12,12 +12,11 @@ license=('Artistic2.0')
 depends=(
   r
   r-biocfilecache
-  r-cgdsr
+  r-cbioportaldata
   r-genefilter
   r-gplots
   r-openxlsx
   r-rcolorbrewer
-  r-cbioportaldata
 )
 optdepends=(
   r-biocstyle

BioArchLinux/r-cbaf/lilac.yaml

@@ -4,12 +4,11 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biocfilecache
-- r-cgdsr
+- r-cbioportaldata
 - r-genefilter
 - r-gplots
 - r-openxlsx
 - r-rcolorbrewer
-- r-cbioportaldata
 update_on:
 - regex: cbaf_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-cellbarcode/PKGBUILD

@@ -11,6 +11,7 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('MIT')
 depends=(
   r
+  r-bh
   r-biostrings
   r-ckmeans.1d.dp
   r-data.table
@@ -20,8 +21,10 @@ depends=(
   r-plyr
   r-rcpp
   r-s4vectors
+  r-seqinr
   r-shortread
   r-stringr
+  r-zlibbioc
 )
 optdepends=(
   r-biocstyle

BioArchLinux/r-cellbarcode/lilac.yaml

@@ -3,6 +3,7 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-bh
 - r-biostrings
 - r-ckmeans.1d.dp
 - r-data.table
@@ -12,8 +13,10 @@ repo_depends:
 - r-plyr
 - r-rcpp
 - r-s4vectors
+- r-seqinr
 - r-shortread
 - r-stringr
+- r-zlibbioc
 update_on:
 - regex: CellBarcode_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-cellxgenedp/PKGBUILD

@@ -12,12 +12,12 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
   r
-  r-cpp11
   r-curl
   r-dplyr
   r-dt
   r-httr
   r-jsonlite
+  r-rjsoncons
   r-shiny
 )
 optdepends=(

BioArchLinux/r-cellxgenedp/lilac.yaml

@@ -3,12 +3,12 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-cpp11
 - r-curl
 - r-dplyr
 - r-dt
 - r-httr
 - r-jsonlite
+- r-rjsoncons
 - r-shiny
 update_on:
 - regex: cellxgenedp_([\d._-]+).tar.gz

BioArchLinux/r-cfdnapro/PKGBUILD

@@ -11,16 +11,25 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('GPL')
 depends=(
   r
+  r-biocgenerics
   r-dplyr
+  r-genomeinfodb
+  r-genomicalignments
+  r-genomicranges
   r-ggplot2
+  r-iranges
   r-magrittr
+  r-plyranges
   r-quantmod
   r-rlang
   r-rsamtools
   r-stringr
+  r-tibble
 )
 optdepends=(
   r-biocstyle
+  r-bsgenome.hsapiens.ucsc.hg19
+  r-bsgenome.hsapiens.ucsc.hg38
   r-devtools
   r-ggpubr
   r-knitr

BioArchLinux/r-cfdnapro/lilac.yaml

@@ -3,13 +3,20 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-biocgenerics
 - r-dplyr
+- r-genomeinfodb
+- r-genomicalignments
+- r-genomicranges
 - r-ggplot2
+- r-iranges
 - r-magrittr
+- r-plyranges
 - r-quantmod
 - r-rlang
 - r-rsamtools
 - r-stringr
+- r-tibble
 update_on:
 - regex: cfDNAPro_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-chipanalyser/PKGBUILD

@@ -17,6 +17,7 @@ depends=(
   r-genomeinfodb
   r-genomicranges
   r-iranges
+  r-rcolorbrewer
   r-rcpproll
   r-rocr
   r-rtracklayer
@@ -24,7 +25,7 @@ depends=(
 )
 optdepends=(
   r-biocgenerics
-  r-bsgenome.dmelanogaster.ucsc.dm3
+  r-bsgenome.dmelanogaster.ucsc.dm6
   r-knitr
   r-runit
 )

BioArchLinux/r-chipanalyser/lilac.yaml

@@ -9,6 +9,7 @@ repo_depends:
 - r-genomeinfodb
 - r-genomicranges
 - r-iranges
+- r-rcolorbrewer
 - r-rcpproll
 - r-rocr
 - r-rtracklayer

BioArchLinux/r-chipseeker/PKGBUILD

@@ -19,7 +19,6 @@ depends=(
   r-genomicfeatures
   r-genomicranges
   r-ggplot2
-  r-ggvenndiagram
   r-gplots
   r-gtools
   r-iranges
@@ -35,6 +34,7 @@ optdepends=(
   r-ggimage
   r-ggplotify
   r-ggupset
+  r-ggvenndiagram
   r-knitr
   r-org.hs.eg.db
   r-reactomepa

BioArchLinux/r-chipseeker/lilac.yaml

@@ -11,7 +11,6 @@ repo_depends:
 - r-genomicfeatures
 - r-genomicranges
 - r-ggplot2
-- r-ggvenndiagram
 - r-gplots
 - r-gtools
 - r-iranges

BioArchLinux/r-chromscape/PKGBUILD

@@ -24,7 +24,10 @@ depends=(
   r-forcats
   r-fs
   r-genomicranges
+  r-gggenes
   r-ggplot2
+  r-ggrepel
+  r-gridextra
   r-iranges
   r-irlba
   r-jsonlite
@@ -52,17 +55,19 @@ depends=(
   r-shinywidgets
   r-singlecellexperiment
   r-stringdist
+  r-stringr
   r-summarizedexperiment
-  r-sushi
   r-tibble
   r-tidyr
   r-umap
   r-viridis
-  r-gggenes
 )
 optdepends=(
   r-biocstyle
+  r-bluster
   r-future
+  r-httr
+  r-igraph
   r-knitr
   r-markdown
   r-rmarkdown

BioArchLinux/r-chromscape/lilac.yaml

@@ -16,7 +16,10 @@ repo_depends:
 - r-forcats
 - r-fs
 - r-genomicranges
+- r-gggenes
 - r-ggplot2
+- r-ggrepel
+- r-gridextra
 - r-iranges
 - r-irlba
 - r-jsonlite
@@ -44,13 +47,12 @@ repo_depends:
 - r-shinywidgets
 - r-singlecellexperiment
 - r-stringdist
+- r-stringr
 - r-summarizedexperiment
-- r-sushi
 - r-tibble
 - r-tidyr
 - r-umap
 - r-viridis
-- r-gggenes
 update_on:
 - regex: ChromSCape_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-cicero/PKGBUILD

@@ -37,6 +37,7 @@ optdepends=(
   r-annotationdbi
   r-covr
   r-knitr
+  r-markdown
   r-rmarkdown
   r-rtracklayer
   r-testthat

BioArchLinux/r-classifyr/PKGBUILD

@@ -12,11 +12,14 @@ license=('GPL')
 depends=(
   r
   r-biocparallel
-  r-locfit
+  r-dplyr
+  r-genefilter
+  r-generics
   r-multiassayexperiment
-  r-plyr
+  r-ranger
+  r-rlang
   r-s4vectors
-  r-randomforest
+  r-tidyr
 )
 optdepends=(
   r-biocstyle
@@ -25,7 +28,6 @@ optdepends=(
   r-cowplot
   r-e1071
   r-edger
-  r-genefilter
   r-ggplot2
   r-glmnet
   r-gridextra
@@ -34,13 +36,16 @@ optdepends=(
   r-iranges
   r-knitr
   r-limma
+  r-matrixmodels
   r-pamr
   r-parathyroidse
   r-poiclaclu
+  r-randomforestsrc
   r-rmarkdown
   r-rmixmod
   r-robustbase
   r-scales
+  r-xgboost
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('15115bd2058bba6a79d42a2e48b7175df23ddb6e0f08971cab9b893d028944a8')

BioArchLinux/r-classifyr/lilac.yaml

@@ -4,11 +4,14 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biocparallel
-- r-locfit
+- r-dplyr
+- r-genefilter
+- r-generics
 - r-multiassayexperiment
-- r-plyr
+- r-ranger
+- r-rlang
 - r-s4vectors
-- r-randomforest
+- r-tidyr
 update_on:
 - regex: ClassifyR_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-clusterprofiler/PKGBUILD

@@ -18,6 +18,7 @@ depends=(
   r-enrichplot
   r-go.db
   r-gosemsim
+  r-gson
   r-magrittr
   r-plyr
   r-qvalue

BioArchLinux/r-clusterprofiler/lilac.yaml

@@ -10,6 +10,7 @@ repo_depends:
 - r-enrichplot
 - r-go.db
 - r-gosemsim
+- r-gson
 - r-magrittr
 - r-plyr
 - r-qvalue

BioArchLinux/r-clustifyr/PKGBUILD

@@ -40,6 +40,7 @@ optdepends=(
   r-purrr
   r-remotes
   r-rmarkdown
+  r-seurat
   r-shiny
   r-testthat
 )

BioArchLinux/r-conclus/PKGBUILD

@@ -25,7 +25,10 @@ depends=(
   r-geoquery
   r-ggplot2
   r-gridextra
+  r-org.hs.eg.db
+  r-org.mm.eg.db
   r-pheatmap
+  r-rlang
   r-rtsne
   r-scales
   r-scater
@@ -33,8 +36,6 @@ depends=(
   r-singlecellexperiment
   r-stringr
   r-summarizedexperiment
-  r-org.mm.eg.db
-  r-org.hs.eg.db
 )
 optdepends=(
   r-biocstyle

BioArchLinux/r-conclus/lilac.yaml

@@ -17,7 +17,10 @@ repo_depends:
 - r-geoquery
 - r-ggplot2
 - r-gridextra
+- r-org.hs.eg.db
+- r-org.mm.eg.db
 - r-pheatmap
+- r-rlang
 - r-rtsne
 - r-scales
 - r-scater
@@ -25,8 +28,6 @@ repo_depends:
 - r-singlecellexperiment
 - r-stringr
 - r-summarizedexperiment
-- r-org.mm.eg.db
-- r-org.hs.eg.db
 update_on:
 - regex: conclus_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-condiments/lilac.yaml

@@ -4,6 +4,7 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biocparallel
+- r-distinct
 - r-dplyr
 - r-ecume
 - r-igraph
@@ -15,7 +16,6 @@ repo_depends:
 - r-slingshot
 - r-summarizedexperiment
 - r-trajectoryutils
-- r-distinct
 update_on:
 - regex: condiments_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-coregx/lilac.yaml

@@ -3,6 +3,7 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-bench
 - r-biobase
 - r-biocgenerics
 - r-biocparallel
@@ -18,7 +19,6 @@ repo_depends:
 - r-rlang
 - r-s4vectors
 - r-summarizedexperiment
-- r-bench
 update_on:
 - regex: CoreGx_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-corral/PKGBUILD

@@ -29,6 +29,7 @@ optdepends=(
   r-duoclustering2018
   r-knitr
   r-rmarkdown
+  r-scater
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-corral/lilac.yaml

@@ -9,10 +9,10 @@ repo_depends:
 - r-irlba
 - r-multiassayexperiment
 - r-pals
+- r-reshape2
 - r-singlecellexperiment
 - r-summarizedexperiment
 - r-transport
-- r-reshape2
 update_on:
 - regex: corral_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-countsimqc/PKGBUILD

@@ -19,6 +19,7 @@ depends=(
   r-genefilter
   r-genomeinfodbdata
   r-ggplot2
+  r-ragg
   r-randtests
   r-rmarkdown
   r-summarizedexperiment

BioArchLinux/r-countsimqc/lilac.yaml

@@ -11,6 +11,7 @@ repo_depends:
 - r-genefilter
 - r-genomeinfodbdata
 - r-ggplot2
+- r-ragg
 - r-randtests
 - r-rmarkdown
 - r-summarizedexperiment

BioArchLinux/r-cytomapper/PKGBUILD

@@ -18,6 +18,7 @@ depends=(
   r-ggplot2
   r-hdf5array
   r-matrixstats
+  r-nnls
   r-raster
   r-rcolorbrewer
   r-rhdf5
@@ -25,11 +26,11 @@ depends=(
   r-shiny
   r-shinydashboard
   r-singlecellexperiment
+  r-spatialexperiment
   r-summarizedexperiment
   r-svglite
   r-svgpanzoom
   r-viridis
-  r-nnls
 )
 optdepends=(
   r-biocstyle

BioArchLinux/r-cytomapper/lilac.yaml

@@ -10,6 +10,7 @@ repo_depends:
 - r-ggplot2
 - r-hdf5array
 - r-matrixstats
+- r-nnls
 - r-raster
 - r-rcolorbrewer
 - r-rhdf5
@@ -17,11 +18,11 @@ repo_depends:
 - r-shiny
 - r-shinydashboard
 - r-singlecellexperiment
+- r-spatialexperiment
 - r-summarizedexperiment
 - r-svglite
 - r-svgpanzoom
 - r-viridis
-- r-nnls
 update_on:
 - regex: cytomapper_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-daglogo/PKGBUILD

@@ -14,6 +14,7 @@ depends=(
   r-biocgenerics
   r-biomart
   r-biostrings
+  r-httr
   r-motifstack
   r-pheatmap
   r-uniprot.ws

BioArchLinux/r-daglogo/lilac.yaml

@@ -6,6 +6,7 @@ repo_depends:
 - r-biocgenerics
 - r-biomart
 - r-biostrings
+- r-httr
 - r-motifstack
 - r-pheatmap
 - r-uniprot.ws

BioArchLinux/r-dapar/PKGBUILD

@@ -11,13 +11,19 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
   r
+  r-biobase
+  r-dapardata
+  r-foreach
+  r-highcharter
+  r-msnbase
+)
+optdepends=(
   r-annotationdbi
   r-apcluster
-  r-biobase
+  r-biocstyle
-  r-cairo
+  r-cluster
   r-clusterprofiler
   r-cp4p
-  r-dapardata
   r-dendextend
   r-diptest
   r-doparallel
@@ -25,45 +31,41 @@ depends=(
   r-factoextra
   r-factominer
   r-forcats
-  r-foreach
   r-ggplot2
   r-gplots
   r-graph
-  r-highcharter
+  r-graphics
+  r-grdevices
   r-igraph
   r-imp4p
   r-impute
   r-knitr
   r-limma
   r-lme4
+  r-matrix
+  r-methods
   r-mfuzz
-  r-msnbase
   r-multcomp
   r-norm
   r-openxlsx
-  r-pcamethods
+  r-org.sc.sgd.db
-  r-png
+  r-parallel
   r-preprocesscore
   r-purrr
   r-rcolorbrewer
   r-readxl
   r-reshape2
   r-scales
-  r-siggenes
+  r-stats
   r-stringr
+  r-testthat
   r-tibble
   r-tidyr
   r-tidyverse
-  r-tmvtnorm
   r-vioplot
   r-visnetwork
   r-vsn
 )
-optdepends=(
-  r-biocgenerics
-  r-biocstyle
-  r-testthat
-)
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('7f28c77662ecbabeda7c8a5a50603a50fa283cd741bbd0306c659a230334f7fc')
 

BioArchLinux/r-dapar/lilac.yaml

@@ -3,53 +3,11 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-annotationdbi
-- r-apcluster
 - r-biobase
-- r-cairo
-- r-clusterprofiler
-- r-cp4p
 - r-dapardata
-- r-dendextend
-- r-diptest
-- r-doparallel
-- r-dplyr
-- r-factoextra
-- r-factominer
-- r-forcats
 - r-foreach
-- r-ggplot2
-- r-gplots
-- r-graph
 - r-highcharter
-- r-igraph
-- r-imp4p
-- r-impute
-- r-knitr
-- r-limma
-- r-lme4
-- r-mfuzz
 - r-msnbase
-- r-multcomp
-- r-norm
-- r-openxlsx
-- r-pcamethods
-- r-png
-- r-preprocesscore
-- r-purrr
-- r-rcolorbrewer
-- r-readxl
-- r-reshape2
-- r-scales
-- r-siggenes
-- r-stringr
-- r-tibble
-- r-tidyr
-- r-tidyverse
-- r-tmvtnorm
-- r-vioplot
-- r-visnetwork
-- r-vsn
 update_on:
 - regex: DAPAR_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-decoupler/PKGBUILD

@@ -11,35 +11,41 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('GPL')
 depends=(
   r
-  r-aucell
   r-broom
   r-dplyr
-  r-fgsea
-  r-gsva
   r-magrittr
   r-purrr
-  r-ranger
   r-rlang
-  r-robustrankaggreg
-  r-speedglm
   r-stringr
-  r-summarizedexperiment
   r-tibble
   r-tidyr
   r-tidyselect
-  r-viper
   r-withr
 )
 optdepends=(
+  r-aucell
   r-biocstyle
   r-covr
+  r-fgsea
+  r-ggplot2
+  r-ggrepel
+  r-glmnet
+  r-gsva
   r-knitr
+  r-omnipathr
+  r-patchwork
+  r-pheatmap
   r-pkgdown
+  r-ranger
   r-refmanager
   r-rmarkdown
   r-roxygen2
+  r-rpart
   r-sessioninfo
+  r-seurat
+  r-summarizedexperiment
   r-testthat
+  r-viper
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('354d165e9c6f0bf5211966242c63a797117ed2a78867f44b54a8f335b8473c60')

BioArchLinux/r-decoupler/lilac.yaml

@@ -3,23 +3,15 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-aucell
 - r-broom
 - r-dplyr
-- r-fgsea
-- r-gsva
 - r-magrittr
 - r-purrr
-- r-ranger
 - r-rlang
-- r-robustrankaggreg
-- r-speedglm
 - r-stringr
-- r-summarizedexperiment
 - r-tibble
 - r-tidyr
 - r-tidyselect
-- r-viper
 - r-withr
 update_on:
 - regex: decoupleR_([\d._-]+).tar.gz

BioArchLinux/r-distinct/lilac.yaml

@@ -10,10 +10,10 @@ repo_depends:
 - r-limma
 - r-rcpp
 - r-rcpparmadillo
+- r-rfast
 - r-scater
 - r-singlecellexperiment
 - r-summarizedexperiment
-- r-rfast
 update_on:
 - regex: distinct_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-dmrcate/PKGBUILD

@@ -28,10 +28,13 @@ depends=(
 )
 optdepends=(
   r-biocgenerics
+  r-dmrcatedata
+  r-flowsorted.blood.epic
   r-illuminahumanmethylation450kanno.ilmn12.hg19
   r-illuminahumanmethylationepicanno.ilm10b4.hg19
   r-knitr
   r-runit
+  r-tissuetreg
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('5bdadf1c57ae1cc8d4f85ab9c184e0c94af45bc6eda7dff4d7b2dbd013fa0e50')

BioArchLinux/r-dose/PKGBUILD

@@ -13,15 +13,16 @@ depends=(
   r
   r-annotationdbi
   r-biocparallel
-  r-do.db
   r-fgsea
   r-ggplot2
   r-gosemsim
+  r-hdo.db
   r-qvalue
   r-reshape2
 )
 optdepends=(
   r-clusterprofiler
+  r-gson
   r-knitr
   r-org.hs.eg.db
   r-prettydoc

BioArchLinux/r-dose/lilac.yaml

@@ -5,10 +5,10 @@ maintainers:
 repo_depends:
 - r-annotationdbi
 - r-biocparallel
-- r-do.db
 - r-fgsea
 - r-ggplot2
 - r-gosemsim
+- r-hdo.db
 - r-qvalue
 - r-reshape2
 update_on:

BioArchLinux/r-easier/PKGBUILD

@@ -11,7 +11,6 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('MIT')
 depends=(
   r
-  r-arules
   r-biocparallel
   r-coin
   r-deseq2

BioArchLinux/r-easier/lilac.yaml

@@ -3,7 +3,6 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-arules
 - r-biocparallel
 - r-coin
 - r-deseq2

BioArchLinux/r-elmer/PKGBUILD

@@ -50,10 +50,12 @@ depends=(
   r-xml2
 )
 optdepends=(
+  r-annotationhub
   r-biocstyle
   r-covr
   r-data.table
   r-dt
+  r-experimenthub
   r-genomicinteractions
   r-knitr
   r-r.utils

BioArchLinux/r-enrichplot/PKGBUILD

@@ -13,6 +13,7 @@ depends=(
   r
   r-aplot
   r-dose
+  r-ggnewscale
   r-ggplot2
   r-ggraph
   r-ggtree
@@ -23,6 +24,7 @@ depends=(
   r-purrr
   r-rcolorbrewer
   r-reshape2
+  r-rlang
   r-scatterpie
   r-shadowtext
   r-yulab.utils
@@ -33,7 +35,6 @@ optdepends=(
   r-dplyr
   r-europepmc
   r-ggforce
-  r-ggnewscale
   r-ggplotify
   r-ggrepel
   r-ggridges
@@ -48,6 +49,7 @@ optdepends=(
   r-rmarkdown
   r-scales
   r-tibble
+  r-tidydr
   r-tidyr
   r-tidytree
   r-treeio

BioArchLinux/r-enrichplot/lilac.yaml

@@ -5,6 +5,7 @@ maintainers:
 repo_depends:
 - r-aplot
 - r-dose
+- r-ggnewscale
 - r-ggplot2
 - r-ggraph
 - r-ggtree
@@ -15,6 +16,7 @@ repo_depends:
 - r-purrr
 - r-rcolorbrewer
 - r-reshape2
+- r-rlang
 - r-scatterpie
 - r-shadowtext
 - r-yulab.utils

BioArchLinux/r-esatac/PKGBUILD

@@ -11,6 +11,7 @@ arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('GPL')
 depends=(
+  gcc
   r
   r-annotationdbi
   r-biocgenerics
@@ -22,6 +23,7 @@ depends=(
   r-corrplot
   r-digest
   r-genomeinfodb
+  r-genomicalignments
   r-genomicfeatures
   r-genomicranges
   r-ggplot2
@@ -43,7 +45,6 @@ depends=(
   r-shortread
   r-tfbstools
   r-venndiagram
-  gcc
 )
 optdepends=(
   r-bsgenome.hsapiens.ucsc.hg19

BioArchLinux/r-esatac/lilac.yaml

@@ -13,6 +13,7 @@ repo_depends:
 - r-corrplot
 - r-digest
 - r-genomeinfodb
+- r-genomicalignments
 - r-genomicfeatures
 - r-genomicranges
 - r-ggplot2

BioArchLinux/r-escape/PKGBUILD

@@ -12,25 +12,28 @@ license=('Apache')
 depends=(
   r
   r-biocparallel
+  r-broom
+  r-data.table
   r-dplyr
   r-ggplot2
   r-ggridges
   r-gseabase
   r-gsva
-  r-limma
+  r-matrixgenerics
   r-msigdbr
-  r-singlecellexperiment
-  r-broom
-  r-reshape2
   r-patchwork
+  r-reshape2
+  r-rlang
+  r-singlecellexperiment
   r-stringr
-  r-data.table
+  r-summarizedexperiment
   r-ucell
 )
 optdepends=(
   r-biocstyle
   r-dittoseq
   r-knitr
+  r-markdown
   r-rmarkdown
   r-seurat
   r-seuratobject

BioArchLinux/r-escape/lilac.yaml

@@ -4,19 +4,21 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biocparallel
+- r-broom
+- r-data.table
 - r-dplyr
 - r-ggplot2
 - r-ggridges
 - r-gseabase
 - r-gsva
-- r-limma
+- r-matrixgenerics
 - r-msigdbr
-- r-singlecellexperiment
-- r-broom
-- r-reshape2
 - r-patchwork
+- r-reshape2
+- r-rlang
+- r-singlecellexperiment
 - r-stringr
-- r-data.table
+- r-summarizedexperiment
 - r-ucell
 update_on:
 - regex: escape_([\d._-]+).tar.gz

BioArchLinux/r-eventpointer/PKGBUILD

@@ -40,6 +40,7 @@ depends=(
   r-sgseq
   r-speedglm
   r-stringr
+  r-summarizedexperiment
   r-tximport
 )
 optdepends=(

BioArchLinux/r-eventpointer/lilac.yaml

@@ -32,6 +32,7 @@ repo_depends:
 - r-sgseq
 - r-speedglm
 - r-stringr
+- r-summarizedexperiment
 - r-tximport
 update_on:
 - regex: EventPointer_([\d._-]+).tar.gz

BioArchLinux/r-famat/PKGBUILD

@@ -11,6 +11,7 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('GPL')
 depends=(
   r
+  r-biasedurn
   r-clusterprofiler
   r-dplyr
   r-dt
@@ -18,7 +19,6 @@ depends=(
   r-gprofiler2
   r-keggrest
   r-magrittr
-  r-mpinet
   r-ontologyindex
   r-org.hs.eg.db
   r-plotly

BioArchLinux/r-famat/lilac.yaml

@@ -3,6 +3,7 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-biasedurn
 - r-clusterprofiler
 - r-dplyr
 - r-dt
@@ -10,7 +11,6 @@ repo_depends:
 - r-gprofiler2
 - r-keggrest
 - r-magrittr
-- r-mpinet
 - r-ontologyindex
 - r-org.hs.eg.db
 - r-plotly

BioArchLinux/r-fgarch/PKGBUILD

@@ -11,6 +11,7 @@ url="https://cran.r-project.org/package=${_pkgname}"
 license=('GPL')
 depends=(
   r
+  r-cvar
   r-fastica
   r-fbasics
   r-timedate

BioArchLinux/r-fgarch/lilac.yaml

@@ -3,6 +3,7 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-cvar
 - r-fastica
 - r-fbasics
 - r-timedate

BioArchLinux/r-fgsea/PKGBUILD

@@ -11,21 +11,23 @@ arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('MIT')
 depends=(
+  gcc
   r
   r-bh
   r-biocparallel
+  r-cowplot
   r-data.table
   r-fastmatch
   r-ggplot2
-  r-gridextra
   r-rcpp
-  gcc
 )
 optdepends=(
+  r-aggregation
   r-annotationdbi
   r-geoquery
   r-knitr
   r-limma
+  r-msigdbr
   r-org.mm.eg.db
   r-parallel
   r-reactome.db

BioArchLinux/r-fgsea/lilac.yaml

@@ -5,10 +5,10 @@ maintainers:
 repo_depends:
 - r-bh
 - r-biocparallel
+- r-cowplot
 - r-data.table
 - r-fastmatch
 - r-ggplot2
-- r-gridextra
 - r-rcpp
 update_on:
 - regex: fgsea_([\d._-]+).tar.gz

BioArchLinux/r-flames/PKGBUILD

@@ -12,30 +12,38 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('GPL')
 depends=(
   r
+  r-bambu
   r-basilisk
+  r-biocgenerics
+  r-biostrings
+  r-circlize
+  r-complexheatmap
+  r-cowplot
   r-dplyr
+  r-genomeinfodb
+  r-genomicfeatures
+  r-genomicranges
+  r-ggbio
+  r-ggplot2
+  r-gridextra
+  r-igraph
   r-magrittr
+  r-rcolorbrewer
   r-rcpp
   r-reticulate
   r-rhtslib
   r-rsamtools
+  r-rtracklayer
   r-s4vectors
   r-scater
+  r-scran
   r-scuttle
   r-singlecellexperiment
+  r-stringr
   r-summarizedexperiment
   r-tidyr
+  r-withr
   r-zlibbioc
-  r-complexheatmap
-  r-rtracklayer
-  r-igraph
-  r-ggbio
-  r-scran
-  r-genomicfeatures
-  r-circlize
-  r-cowplot
-  r-stringr
-  r-bambu
 )
 optdepends=(
   r-biocfilecache

BioArchLinux/r-flames/lilac.yaml

@@ -3,30 +3,38 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-bambu
 - r-basilisk
+- r-biocgenerics
+- r-biostrings
+- r-circlize
+- r-complexheatmap
+- r-cowplot
 - r-dplyr
+- r-genomeinfodb
+- r-genomicfeatures
+- r-genomicranges
+- r-ggbio
+- r-ggplot2
+- r-gridextra
+- r-igraph
 - r-magrittr
+- r-rcolorbrewer
 - r-rcpp
 - r-reticulate
 - r-rhtslib
 - r-rsamtools
+- r-rtracklayer
 - r-s4vectors
 - r-scater
+- r-scran
 - r-scuttle
 - r-singlecellexperiment
+- r-stringr
 - r-summarizedexperiment
 - r-tidyr
+- r-withr
 - r-zlibbioc
-- r-complexheatmap
-- r-rtracklayer
-- r-igraph
-- r-ggbio
-- r-scran
-- r-genomicfeatures
-- r-circlize
-- r-cowplot
-- r-stringr
-- r-bambu
 update_on:
 - regex: FLAMES_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-glmsparsenet/PKGBUILD

@@ -12,19 +12,18 @@ license=('GPL')
 depends=(
   r
   r-biomart
+  r-digest
   r-dplyr
   r-forcats
   r-futile.logger
+  r-futile.options
   r-ggplot2
   r-glmnet
   r-glue
   r-httr
-  r-loose.rock
   r-multiassayexperiment
   r-readr
   r-reshape2
-  r-sparsebn
-  r-sparsebnutils
   r-stringr
   r-summarizedexperiment
   r-survminer

BioArchLinux/r-glmsparsenet/lilac.yaml

@@ -4,19 +4,18 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biomart
+- r-digest
 - r-dplyr
 - r-forcats
 - r-futile.logger
+- r-futile.options
 - r-ggplot2
 - r-glmnet
 - r-glue
 - r-httr
-- r-loose.rock
 - r-multiassayexperiment
 - r-readr
 - r-reshape2
-- r-sparsebn
-- r-sparsebnutils
 - r-stringr
 - r-summarizedexperiment
 - r-survminer

BioArchLinux/r-gsean/PKGBUILD

@@ -17,7 +17,6 @@ depends=(
 optdepends=(
   r-knitr
   r-plotly
-  r-ranks
   r-rmarkdown
   r-summarizedexperiment
   r-wgcna

BioArchLinux/r-guideseq/PKGBUILD

@@ -12,7 +12,6 @@ license=('GPL')
 depends=(
   r
   r-biocgenerics
-  r-biocparallel
   r-biostrings
   r-bsgenome
   r-chippeakanno
@@ -21,20 +20,32 @@ depends=(
   r-dplyr
   r-genomeinfodb
   r-genomicalignments
+  r-genomicfeatures
   r-genomicranges
+  r-ggplot2
   r-hash
   r-iranges
   r-limma
   r-matrixstats
+  r-multtest
+  r-openxlsx
+  r-patchwork
+  r-purrr
+  r-rio
+  r-rlang
   r-rsamtools
   r-s4vectors
+  r-stringr
+  r-tidyr
 )
 optdepends=(
   r-biocstyle
   r-bsgenome.hsapiens.ucsc.hg19
+  r-bsgenome.hsapiens.ucsc.hg38
   r-knitr
   r-org.hs.eg.db
   r-runit
+  r-testthat
   r-txdb.hsapiens.ucsc.hg19.knowngene
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-guideseq/lilac.yaml

@@ -4,7 +4,6 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biocgenerics
-- r-biocparallel
 - r-biostrings
 - r-bsgenome
 - r-chippeakanno
@@ -13,13 +12,23 @@ repo_depends:
 - r-dplyr
 - r-genomeinfodb
 - r-genomicalignments
+- r-genomicfeatures
 - r-genomicranges
+- r-ggplot2
 - r-hash
 - r-iranges
 - r-limma
 - r-matrixstats
+- r-multtest
+- r-openxlsx
+- r-patchwork
+- r-purrr
+- r-rio
+- r-rlang
 - r-rsamtools
 - r-s4vectors
+- r-stringr
+- r-tidyr
 update_on:
 - regex: GUIDEseq_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-imcrtools/PKGBUILD

@@ -17,6 +17,7 @@ depends=(
   r-concaveman
   r-cytomapper
   r-data.table
+  r-distances
   r-dplyr
   r-dt
   r-ebimage
@@ -24,6 +25,7 @@ depends=(
   r-ggraph
   r-igraph
   r-magrittr
+  r-matrixgenerics
   r-pheatmap
   r-readr
   r-rtriangle
@@ -35,6 +37,7 @@ depends=(
   r-stringr
   r-summarizedexperiment
   r-tidygraph
+  r-tidyselect
   r-viridis
   r-vroom
 )
@@ -46,7 +49,6 @@ optdepends=(
   r-markdown
   r-rmarkdown
   r-testthat
-  r-tidyr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('dc7d7dc805ad18d23fce68c5fd60fe036343af2b89b254893a5d1093ea554fa8')

BioArchLinux/r-imcrtools/lilac.yaml

@@ -9,6 +9,7 @@ repo_depends:
 - r-concaveman
 - r-cytomapper
 - r-data.table
+- r-distances
 - r-dplyr
 - r-dt
 - r-ebimage
@@ -16,6 +17,7 @@ repo_depends:
 - r-ggraph
 - r-igraph
 - r-magrittr
+- r-matrixgenerics
 - r-pheatmap
 - r-readr
 - r-rtriangle
@@ -27,6 +29,7 @@ repo_depends:
 - r-stringr
 - r-summarizedexperiment
 - r-tidygraph
+- r-tidyselect
 - r-viridis
 - r-vroom
 update_on:

BioArchLinux/r-iseeu/PKGBUILD

@@ -16,6 +16,7 @@ depends=(
   r-ggplot2
   r-iranges
   r-isee
+  r-iseehex
   r-s4vectors
   r-shiny
   r-shinyace

BioArchLinux/r-iseeu/lilac.yaml

@@ -8,6 +8,7 @@ repo_depends:
 - r-ggplot2
 - r-iranges
 - r-isee
+- r-iseehex
 - r-s4vectors
 - r-shiny
 - r-shinyace

BioArchLinux/r-lace/PKGBUILD

@@ -11,41 +11,45 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('custom')
 depends=(
   r
-  r-data.tree
+  r-biomart
-  r-igraph
+  r-bsplus
-  r-rcolorbrewer
+  r-callr
-  r-rfast
-  r-summarizedexperiment
-  r-curl
-  r-foreach
-  r-doparallel
-  r-sortable
-  r-dplyr
-  r-purrr
-  r-stringr
-  r-tidyr
-  r-jsonlite
-  r-readr
   r-configr
-  r-dt
+  r-curl
-  r-fs
   r-data.table
+  r-data.tree
+  r-doparallel
+  r-dplyr
+  r-dt
+  r-foreach
+  r-fs
   r-htmltools
   r-htmlwidgets
-  r-bsplus
+  r-igraph
+  r-jsonlite
+  r-logr
+  r-purrr
+  r-rcolorbrewer
+  r-readr
+  r-rfast
   r-shiny
-  r-shinythemes
-  r-shinyfiles
-  r-shinyjs
   r-shinybs
   r-shinydashboard
-  r-biomart
+  r-shinyfiles
-  r-callr
+  r-shinyjs
+  r-shinythemes
+  r-shinyvalidate
+  r-sortable
+  r-stringi
+  r-stringr
+  r-summarizedexperiment
+  r-tidyr
 )
 optdepends=(
   r-biocgenerics
   r-biocstyle
   r-knitr
+  r-rmarkdown
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-lace/lilac.yaml

@@ -3,36 +3,39 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-data.tree
+- r-biomart
-- r-igraph
+- r-bsplus
-- r-rcolorbrewer
+- r-callr
-- r-rfast
-- r-summarizedexperiment
-- r-curl
-- r-foreach
-- r-doparallel
-- r-sortable
-- r-dplyr
-- r-purrr
-- r-stringr
-- r-tidyr
-- r-jsonlite
-- r-readr
 - r-configr
-- r-dt
+- r-curl
-- r-fs
 - r-data.table
+- r-data.tree
+- r-doparallel
+- r-dplyr
+- r-dt
+- r-foreach
+- r-fs
 - r-htmltools
 - r-htmlwidgets
-- r-bsplus
+- r-igraph
+- r-jsonlite
+- r-logr
+- r-purrr
+- r-rcolorbrewer
+- r-readr
+- r-rfast
 - r-shiny
-- r-shinythemes
-- r-shinyfiles
-- r-shinyjs
 - r-shinybs
 - r-shinydashboard
-- r-biomart
+- r-shinyfiles
-- r-callr
+- r-shinyjs
+- r-shinythemes
+- r-shinyvalidate
+- r-sortable
+- r-stringi
+- r-stringr
+- r-summarizedexperiment
+- r-tidyr
 update_on:
 - regex: LACE_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-lisaclust/PKGBUILD

@@ -17,11 +17,15 @@ depends=(
   r-data.table
   r-dplyr
   r-ggplot2
+  r-pheatmap
   r-purrr
   r-s4vectors
+  r-singlecellexperiment
+  r-spatialexperiment
   r-spatstat.core
   r-spatstat.geom
   r-spicyr
+  r-summarizedexperiment
   r-tidyr
 )
 optdepends=(

BioArchLinux/r-lisaclust/lilac.yaml

@@ -9,11 +9,15 @@ repo_depends:
 - r-data.table
 - r-dplyr
 - r-ggplot2
+- r-pheatmap
 - r-purrr
 - r-s4vectors
+- r-singlecellexperiment
+- r-spatialexperiment
 - r-spatstat.core
 - r-spatstat.geom
 - r-spicyr
+- r-summarizedexperiment
 - r-tidyr
 update_on:
 - regex: lisaClust_([\d._-]+).tar.gz

BioArchLinux/r-lowmaca/PKGBUILD

@@ -11,24 +11,24 @@ arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('GPL')
 depends=(
+  clustal-omega
+  ghostscript
+  perl
+  perl-lwp-protocol-https
+  perl-xml-simple
   r
   r-biocparallel
   r-biostrings
   r-cbioportaldata
-  r-cgdsr
   r-data.table
   r-gridbase
   r-httr
   r-lowmacaannotation
   r-motifstack
+  r-plyr
   r-rcolorbrewer
   r-reshape2
   r-stringr
-  ghostscript
-  perl
-  perl-lwp-protocol-https
-  perl-xml-simple
-  clustal-omega
 )
 optdepends=(
   r-biocstyle

BioArchLinux/r-lowmaca/lilac.yaml

@@ -3,19 +3,19 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- clustal-omega
 - r-biocparallel
 - r-biostrings
 - r-cbioportaldata
-- r-cgdsr
 - r-data.table
 - r-gridbase
 - r-httr
 - r-lowmacaannotation
 - r-motifstack
+- r-plyr
 - r-rcolorbrewer
 - r-reshape2
 - r-stringr
-- clustal-omega
 update_on:
 - regex: LowMACA_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-lubridate/PKGBUILD

@@ -11,14 +11,15 @@ arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
 license=('GPL')
 depends=(
-  r
-  r-cpp11
-  r-generics
   gcc
+  r
+  r-generics
+  r-timechange
 )
 optdepends=(
   r-chron
   r-covr
+  r-data.table
   r-knitr
   r-rmarkdown
   r-testthat

BioArchLinux/r-lubridate/lilac.yaml

@@ -3,8 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-cpp11
 - r-generics
+- r-timechange
 update_on:
 - regex: lubridate_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-mageckflute/PKGBUILD

@@ -13,27 +13,27 @@ depends=(
   r
   r-biobase
   r-clusterprofiler
+  r-depmap
+  r-dose
   r-enrichplot
   r-ggplot2
   r-ggrepel
   r-gridextra
-  r-reshape2
   r-msigdbr
   r-pathview
-  r-depmap
+  r-reshape2
 )
 optdepends=(
+  r-biocmanager
   r-biocstyle
   r-biomart
   r-dendextend
-  r-dose
   r-graphics
   r-knitr
   r-pheatmap
   r-png
   r-scales
   r-sva
-  r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('5580217e7f29318ad4b8acddcb5cda450a0e9b7302e6a3f75686d782ca3d8e6d')

BioArchLinux/r-mageckflute/lilac.yaml

@@ -5,14 +5,15 @@ maintainers:
 repo_depends:
 - r-biobase
 - r-clusterprofiler
+- r-depmap
+- r-dose
 - r-enrichplot
 - r-ggplot2
 - r-ggrepel
 - r-gridextra
-- r-reshape2
 - r-msigdbr
 - r-pathview
-- r-depmap
+- r-reshape2
 update_on:
 - regex: MAGeCKFlute_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-metapone/PKGBUILD

@@ -12,11 +12,12 @@ license=('Artistic2.0')
 depends=(
   r
   r-biocparallel
-  r-fields
-  r-markdown
   r-fdrtool
   r-fgsea
+  r-fields
+  r-ggplot2
   r-ggrepel
+  r-markdown
 )
 optdepends=(
   r-knitr

BioArchLinux/r-metapone/lilac.yaml

@@ -4,11 +4,12 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biocparallel
-- r-fields
-- r-markdown
 - r-fdrtool
 - r-fgsea
+- r-fields
+- r-ggplot2
 - r-ggrepel
+- r-markdown
 update_on:
 - regex: metapone_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-metcirc/PKGBUILD

@@ -14,18 +14,17 @@ depends=(
   r-amap
   r-circlize
   r-ggplot2
-  r-msnbase
+  r-mscoreutils
   r-s4vectors
   r-scales
   r-shiny
+  r-spectra
 )
 optdepends=(
   r-biocgenerics
   r-graphics
   r-grdevices
   r-knitr
-  r-methods
-  r-stats
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-metcirc/lilac.yaml

@@ -6,10 +6,11 @@ repo_depends:
 - r-amap
 - r-circlize
 - r-ggplot2
-- r-msnbase
+- r-mscoreutils
 - r-s4vectors
 - r-scales
 - r-shiny
+- r-spectra
 update_on:
 - regex: MetCirc_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-methreg/PKGBUILD

@@ -11,8 +11,10 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('GPL')
 depends=(
   r
+  r-annotationhub
   r-delayedarray
   r-dplyr
+  r-experimenthub
   r-genomicranges
   r-ggplot2
   r-ggpubr
@@ -23,13 +25,13 @@ depends=(
   r-readr
   r-rlang
   r-s4vectors
+  r-sesame
   r-sesamedata
   r-sfsmisc
   r-stringr
   r-summarizedexperiment
   r-tibble
   r-tidyr
-  r-sesame
 )
 optdepends=(
   r-biocfilecache
@@ -41,7 +43,7 @@ optdepends=(
   r-dorothea
   r-downloader
   r-htmltools
-  r-jaspar2020
+  r-jaspar2022
   r-jpeg
   r-knitr
   r-matrixstats