Merge pull request #92 from BioArchLinux/update_depends

check `depends` and `optdepends` for 255 pkgs that failed to be built
2025-03-10 12:02:42 +00:00 · 2022-11-07 12:51:14 +08:00 · 2022-11-07 12:51:14 +08:00 · c399728b36
commit c399728b36
parent 9b2c00ea71 06275804f0
193 changed files with 740 additions and 452 deletions
--- a/BioArchLinux/r-airpart/PKGBUILD
+++ b/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')
--- a/BioArchLinux/r-ancombc/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-ancombc/lilac.yaml
+++ b/BioArchLinux/r-ancombc/lilac.yaml
@ -3,27 +3,29 @@ maintainers:
 - github: starsareintherose
  email: kuoi@bioarchlinux.org
 repo_depends:
-  - r-cvxr
-  - r-desctools
-  - r-doparallel
-  - r-dorng
-  - r-dplyr
-  - r-emmeans
-  - r-energy
-  - r-foreach
-  - r-hmisc
-  - r-lmertest
-  - r-magrittr
-  - r-mia
-  - r-nloptr
-  - r-rdpack
-  - r-rlang
-  - r-rngtools
-  - r-s4vectors
-  - r-singlecellexperiment
-  - r-summarizedexperiment
-  - r-tibble
-  - r-tidyr
+- r-cvxr
+- r-desctools
+- r-doparallel
+- r-dorng
+- r-dplyr
+- r-emmeans
+- r-energy
+- r-foreach
+- r-hmisc
+- r-lme4
+- r-lmertest
+- r-magrittr
+- r-mia
+- r-nloptr
+- r-rdpack
+- r-rlang
+- r-rngtools
+- r-s4vectors
+- r-singlecellexperiment
+- r-summarizedexperiment
+- r-tibble
+- r-tidyr
+- r-treesummarizedexperiment
 update_on:
 - regex: ANCOMBC_([\d._-]+).tar.gz
  source: regex
--- a/BioArchLinux/r-bambu/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-bambu/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-benchdamic/PKGBUILD
+++ b/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-hmp16sdata
+  r-kableextra
  r-knitr
  r-rmarkdown
+  r-spsimseq
  r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
--- a/BioArchLinux/r-benchdamic/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-bindingsitefinder/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-bindingsitefinder/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-biocancer/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-biocancer/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-biocpkgtools/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-biocpkgtools/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-biosigner/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-biosigner/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-biscuiteer/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-biscuiteer/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-cbaf/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-cbaf/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-cellbarcode/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-cellbarcode/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-cellxgenedp/PKGBUILD
+++ b/BioArchLinux/r-cellxgenedp/PKGBUILD
@ -12,12 +12,12 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
  r
-  r-cpp11
  r-curl
  r-dplyr
  r-dt
  r-httr
  r-jsonlite
+  r-rjsoncons
  r-shiny
 )
 optdepends=(
--- a/BioArchLinux/r-cellxgenedp/lilac.yaml
+++ b/BioArchLinux/r-cellxgenedp/lilac.yaml
@ -3,12 +3,12 @@ maintainers:
 - github: starsareintherose
  email: kuoi@bioarchlinux.org
 repo_depends:
- r-cpp11
 - r-curl
 - r-dplyr
 - r-dt
 - r-httr
 - r-jsonlite
+- r-rjsoncons
 - r-shiny
 update_on:
 - regex: cellxgenedp_([\d._-]+).tar.gz
--- a/BioArchLinux/r-cfdnapro/PKGBUILD
+++ b/BioArchLinux/r-cfdnapro/PKGBUILD
@ -11,16 +11,25 @@ url="https://bioconductor.org/packages/${_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
--- a/BioArchLinux/r-cfdnapro/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-chipanalyser/PKGBUILD
+++ b/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
 )
--- a/BioArchLinux/r-chipanalyser/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-chipseeker/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-chipseeker/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-chromscape/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-chromscape/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-cicero/PKGBUILD
+++ b/BioArchLinux/r-cicero/PKGBUILD
@ -37,6 +37,7 @@ optdepends=(
  r-annotationdbi
  r-covr
  r-knitr
+  r-markdown
  r-rmarkdown
  r-rtracklayer
  r-testthat
--- a/BioArchLinux/r-classifyr/PKGBUILD
+++ b/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')
--- a/BioArchLinux/r-classifyr/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-clusterprofiler/PKGBUILD
+++ b/BioArchLinux/r-clusterprofiler/PKGBUILD
@ -18,6 +18,7 @@ depends=(
  r-enrichplot
  r-go.db
  r-gosemsim
+  r-gson
  r-magrittr
  r-plyr
  r-qvalue
--- a/BioArchLinux/r-clusterprofiler/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-clustifyr/PKGBUILD
+++ b/BioArchLinux/r-clustifyr/PKGBUILD
@ -40,6 +40,7 @@ optdepends=(
  r-purrr
  r-remotes
  r-rmarkdown
+  r-seurat
  r-shiny
  r-testthat
 )
--- a/BioArchLinux/r-conclus/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-conclus/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-condiments/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-coregx/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-corral/PKGBUILD
+++ b/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")
--- a/BioArchLinux/r-corral/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-countsimqc/PKGBUILD
+++ b/BioArchLinux/r-countsimqc/PKGBUILD
@ -19,6 +19,7 @@ depends=(
  r-genefilter
  r-genomeinfodbdata
  r-ggplot2
+  r-ragg
  r-randtests
  r-rmarkdown
  r-summarizedexperiment
--- a/BioArchLinux/r-countsimqc/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-cytomapper/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-cytomapper/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-daglogo/PKGBUILD
+++ b/BioArchLinux/r-daglogo/PKGBUILD
@ -14,6 +14,7 @@ depends=(
  r-biocgenerics
  r-biomart
  r-biostrings
+  r-httr
  r-motifstack
  r-pheatmap
  r-uniprot.ws
--- a/BioArchLinux/r-daglogo/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-dapar/PKGBUILD
+++ b/BioArchLinux/r-dapar/PKGBUILD
@ -11,13 +11,19 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
  r
+  r-biobase
+  r-dapardata
+  r-foreach
+  r-highcharter
+  r-msnbase
+)
+optdepends=(
  r-annotationdbi
  r-apcluster
-  r-biobase
-  r-cairo
+  r-biocstyle
+  r-cluster
  r-clusterprofiler
  r-cp4p
-  r-dapardata
  r-dendextend
  r-diptest
  r-doparallel
@ -25,45 +31,41 @@ depends=(
  r-factoextra
  r-factominer
  r-forcats
-  r-foreach
  r-ggplot2
  r-gplots
  r-graph
-  r-highcharter
+  r-graphics
+  r-grdevices
  r-igraph
  r-imp4p
  r-impute
  r-knitr
  r-limma
  r-lme4
+  r-matrix
+  r-methods
  r-mfuzz
-  r-msnbase
  r-multcomp
  r-norm
  r-openxlsx
-  r-pcamethods
-  r-png
+  r-org.sc.sgd.db
+  r-parallel
  r-preprocesscore
  r-purrr
  r-rcolorbrewer
  r-readxl
  r-reshape2
  r-scales
-  r-siggenes
+  r-stats
  r-stringr
+  r-testthat
  r-tibble
  r-tidyr
  r-tidyverse
-  r-tmvtnorm
  r-vioplot
  r-visnetwork
  r-vsn
 )
-optdepends=(
-  r-biocgenerics
-  r-biocstyle
-  r-testthat
-)
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('7f28c77662ecbabeda7c8a5a50603a50fa283cd741bbd0306c659a230334f7fc')

--- a/BioArchLinux/r-dapar/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-decoupler/PKGBUILD
+++ b/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}_${_pkgver}.tar.gz")
 sha256sums=('354d165e9c6f0bf5211966242c63a797117ed2a78867f44b54a8f335b8473c60')
--- a/BioArchLinux/r-decoupler/lilac.yaml
+++ b/BioArchLinux/r-decoupler/lilac.yaml
@ -3,23 +3,15 @@ maintainers:
 - github: starsareintherose
  email: kuoi@bioarchlinux.org
 repo_depends:
- r-aucell
 - r-broom
 - r-dplyr
- r-fgsea
- r-gsva
 - r-magrittr
 - r-purrr
- r-ranger
 - r-rlang
- r-robustrankaggreg
- r-speedglm
 - r-stringr
- r-summarizedexperiment
 - r-tibble
 - r-tidyr
 - r-tidyselect
- r-viper
 - r-withr
 update_on:
 - regex: decoupleR_([\d._-]+).tar.gz
--- a/BioArchLinux/r-distinct/lilac.yaml
+++ b/BioArchLinux/r-distinct/lilac.yaml
@ -10,10 +10,10 @@ repo_depends:
 - r-limma
 - r-rcpp
 - r-rcpparmadillo
+- r-rfast
 - r-scater
 - r-singlecellexperiment
 - r-summarizedexperiment
- r-rfast
 update_on:
 - regex: distinct_([\d._-]+).tar.gz
  source: regex
--- a/BioArchLinux/r-dmrcate/PKGBUILD
+++ b/BioArchLinux/r-dmrcate/PKGBUILD
@ -28,10 +28,13 @@ depends=(
 )
 optdepends=(
  r-biocgenerics
+  r-dmrcatedata
+  r-flowsorted.blood.epic
  r-illuminahumanmethylation450kanno.ilmn12.hg19
  r-illuminahumanmethylationepicanno.ilm10b4.hg19
  r-knitr
  r-runit
+  r-tissuetreg
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('5bdadf1c57ae1cc8d4f85ab9c184e0c94af45bc6eda7dff4d7b2dbd013fa0e50')
--- a/BioArchLinux/r-dose/PKGBUILD
+++ b/BioArchLinux/r-dose/PKGBUILD
@ -13,15 +13,16 @@ depends=(
  r
  r-annotationdbi
  r-biocparallel
-  r-do.db
  r-fgsea
  r-ggplot2
  r-gosemsim
+  r-hdo.db
  r-qvalue
  r-reshape2
 )
 optdepends=(
  r-clusterprofiler
+  r-gson
  r-knitr
  r-org.hs.eg.db
  r-prettydoc
--- a/BioArchLinux/r-dose/lilac.yaml
+++ b/BioArchLinux/r-dose/lilac.yaml
@ -5,10 +5,10 @@ maintainers:
 repo_depends:
 - r-annotationdbi
 - r-biocparallel
- r-do.db
 - r-fgsea
 - r-ggplot2
 - r-gosemsim
+- r-hdo.db
 - r-qvalue
 - r-reshape2
 update_on:
--- a/BioArchLinux/r-easier/PKGBUILD
+++ b/BioArchLinux/r-easier/PKGBUILD
@ -11,7 +11,6 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('MIT')
 depends=(
  r
-  r-arules
  r-biocparallel
  r-coin
  r-deseq2
--- a/BioArchLinux/r-easier/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-elmer/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-enrichplot/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-enrichplot/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-esatac/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-esatac/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-escape/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-escape/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-eventpointer/PKGBUILD
+++ b/BioArchLinux/r-eventpointer/PKGBUILD
@ -40,6 +40,7 @@ depends=(
  r-sgseq
  r-speedglm
  r-stringr
+  r-summarizedexperiment
  r-tximport
 )
 optdepends=(
--- a/BioArchLinux/r-eventpointer/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-famat/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-famat/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-fgarch/PKGBUILD
+++ b/BioArchLinux/r-fgarch/PKGBUILD
@ -11,6 +11,7 @@ url="https://cran.r-project.org/package=${_pkgname}"
 license=('GPL')
 depends=(
  r
+  r-cvar
  r-fastica
  r-fbasics
  r-timedate
--- a/BioArchLinux/r-fgarch/lilac.yaml
+++ b/BioArchLinux/r-fgarch/lilac.yaml
@ -3,6 +3,7 @@ maintainers:
 - github: starsareintherose
  email: kuoi@bioarchlinux.org
 repo_depends:
+- r-cvar
 - r-fastica
 - r-fbasics
 - r-timedate
--- a/BioArchLinux/r-fgsea/PKGBUILD
+++ b/BioArchLinux/r-fgsea/PKGBUILD
@ -11,21 +11,23 @@ arch=('x86_64')
 url="https://bioconductor.org/packages/${_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
--- a/BioArchLinux/r-fgsea/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-flames/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-flames/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-glmsparsenet/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-glmsparsenet/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-gsean/PKGBUILD
+++ b/BioArchLinux/r-gsean/PKGBUILD
@ -17,7 +17,6 @@ depends=(
 optdepends=(
  r-knitr
  r-plotly
-  r-ranks
  r-rmarkdown
  r-summarizedexperiment
  r-wgcna
--- a/BioArchLinux/r-guideseq/PKGBUILD
+++ b/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}_${_pkgver}.tar.gz")
--- a/BioArchLinux/r-guideseq/lilac.yaml
+++ b/BioArchLinux/r-guideseq/lilac.yaml
@ -4,7 +4,6 @@ maintainers:
  email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biocgenerics
- r-biocparallel
 - r-biostrings
 - r-bsgenome
 - r-chippeakanno
@ -13,13 +12,23 @@ repo_depends:
 - r-dplyr
 - r-genomeinfodb
 - r-genomicalignments
+- r-genomicfeatures
 - r-genomicranges
+- r-ggplot2
 - r-hash
 - r-iranges
 - r-limma
 - r-matrixstats
+- r-multtest
+- r-openxlsx
+- r-patchwork
+- r-purrr
+- r-rio
+- r-rlang
 - r-rsamtools
 - r-s4vectors
+- r-stringr
+- r-tidyr
 update_on:
 - regex: GUIDEseq_([\d._-]+).tar.gz
  source: regex
--- a/BioArchLinux/r-imcrtools/PKGBUILD
+++ b/BioArchLinux/r-imcrtools/PKGBUILD
@ -17,6 +17,7 @@ depends=(
  r-concaveman
  r-cytomapper
  r-data.table
+  r-distances
  r-dplyr
  r-dt
  r-ebimage
@ -24,6 +25,7 @@ depends=(
  r-ggraph
  r-igraph
  r-magrittr
+  r-matrixgenerics
  r-pheatmap
  r-readr
  r-rtriangle
@ -35,6 +37,7 @@ depends=(
  r-stringr
  r-summarizedexperiment
  r-tidygraph
+  r-tidyselect
  r-viridis
  r-vroom
 )
@ -46,7 +49,6 @@ optdepends=(
  r-markdown
  r-rmarkdown
  r-testthat
-  r-tidyr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('dc7d7dc805ad18d23fce68c5fd60fe036343af2b89b254893a5d1093ea554fa8')
--- a/BioArchLinux/r-imcrtools/lilac.yaml
+++ b/BioArchLinux/r-imcrtools/lilac.yaml
@ -9,6 +9,7 @@ repo_depends:
 - r-concaveman
 - r-cytomapper
 - r-data.table
+- r-distances
 - r-dplyr
 - r-dt
 - r-ebimage
@ -16,6 +17,7 @@ repo_depends:
 - r-ggraph
 - r-igraph
 - r-magrittr
+- r-matrixgenerics
 - r-pheatmap
 - r-readr
 - r-rtriangle
@ -27,6 +29,7 @@ repo_depends:
 - r-stringr
 - r-summarizedexperiment
 - r-tidygraph
+- r-tidyselect
 - r-viridis
 - r-vroom
 update_on:
--- a/BioArchLinux/r-iseeu/PKGBUILD
+++ b/BioArchLinux/r-iseeu/PKGBUILD
@ -16,6 +16,7 @@ depends=(
  r-ggplot2
  r-iranges
  r-isee
+  r-iseehex
  r-s4vectors
  r-shiny
  r-shinyace
--- a/BioArchLinux/r-iseeu/lilac.yaml
+++ b/BioArchLinux/r-iseeu/lilac.yaml
@ -8,6 +8,7 @@ repo_depends:
 - r-ggplot2
 - r-iranges
 - r-isee
+- r-iseehex
 - r-s4vectors
 - r-shiny
 - r-shinyace
--- a/BioArchLinux/r-lace/PKGBUILD
+++ b/BioArchLinux/r-lace/PKGBUILD
@ -11,41 +11,45 @@ url="https://bioconductor.org/packages/${_pkgname}"
 license=('custom')
 depends=(
  r
-  r-data.tree
-  r-igraph
-  r-rcolorbrewer
-  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-biomart
+  r-bsplus
+  r-callr
  r-configr
-  r-dt
-  r-fs
+  r-curl
  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-callr
+  r-shinyfiles
+  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")
--- a/BioArchLinux/r-lace/lilac.yaml
+++ b/BioArchLinux/r-lace/lilac.yaml
@ -3,36 +3,39 @@ maintainers:
 - github: starsareintherose
  email: kuoi@bioarchlinux.org
 repo_depends:
- r-data.tree
- r-igraph
- r-rcolorbrewer
- 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-biomart
+- r-bsplus
+- r-callr
 - r-configr
- r-dt
- r-fs
+- r-curl
 - 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-callr
+- r-shinyfiles
+- 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
--- a/BioArchLinux/r-lisaclust/PKGBUILD
+++ b/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=(
--- a/BioArchLinux/r-lisaclust/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-lowmaca/PKGBUILD
+++ b/BioArchLinux/r-lowmaca/PKGBUILD
@ -11,24 +11,24 @@ arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('GPL')
 depends=(
+  clustal-omega
+  ghostscript
+  perl
+  perl-lwp-protocol-https
+  perl-xml-simple
  r
  r-biocparallel
  r-biostrings
  r-cbioportaldata
-  r-cgdsr
  r-data.table
  r-gridbase
  r-httr
  r-lowmacaannotation
  r-motifstack
+  r-plyr
  r-rcolorbrewer
  r-reshape2
  r-stringr
-  ghostscript
-  perl
-  perl-lwp-protocol-https
-  perl-xml-simple
-  clustal-omega
 )
 optdepends=(
  r-biocstyle
--- a/BioArchLinux/r-lowmaca/lilac.yaml
+++ b/BioArchLinux/r-lowmaca/lilac.yaml
@ -3,19 +3,19 @@ maintainers:
 - github: starsareintherose
  email: kuoi@bioarchlinux.org
 repo_depends:
+- clustal-omega
 - r-biocparallel
 - r-biostrings
 - r-cbioportaldata
- r-cgdsr
 - r-data.table
 - r-gridbase
 - r-httr
 - r-lowmacaannotation
 - r-motifstack
+- r-plyr
 - r-rcolorbrewer
 - r-reshape2
 - r-stringr
- clustal-omega
 update_on:
 - regex: LowMACA_([\d._-]+).tar.gz
  source: regex
--- a/BioArchLinux/r-lubridate/PKGBUILD
+++ b/BioArchLinux/r-lubridate/PKGBUILD
@ -11,14 +11,15 @@ arch=('x86_64')
 url="https://cran.r-project.org/package=${_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
--- a/BioArchLinux/r-lubridate/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-mageckflute/PKGBUILD
+++ b/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')
--- a/BioArchLinux/r-mageckflute/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-metapone/PKGBUILD
+++ b/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
--- a/BioArchLinux/r-metapone/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-metcirc/PKGBUILD
+++ b/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")
--- a/BioArchLinux/r-metcirc/lilac.yaml
+++ b/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
--- a/BioArchLinux/r-methreg/PKGBUILD
+++ b/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
--- a/Show more
+++ b/Show more