Refresh depends for all r pkgs (#98)

* check depends for all r pkgs, fix arch

* fix archived url

* keep optional system libs

* precisely archive

* fix for special pkgs

BioArchLinux/r-adacgh2/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=ADaCGH2
 _pkgver=2.38.0
 pkgname=r-${_pkgname,,}
 pkgver=2.38.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Analysis of big data from aCGH experiments using parallel computing and ff objects'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -15,7 +15,6 @@ depends=(
   r-bit
   r-dnacopy
   r-ff
-  r-ffbase
   r-glad
   r-snapcgh
   r-tilingarray

BioArchLinux/r-adacgh2/lilac.yaml

@@ -7,7 +7,6 @@ repo_depends:
 - r-bit
 - r-dnacopy
 - r-ff
-- r-ffbase
 - r-glad
 - r-snapcgh
 - r-tilingarray

BioArchLinux/r-adehabitatma/PKGBUILD

@@ -4,14 +4,13 @@ _pkgname=adehabitatMA
 _pkgver=0.3.15
 pkgname=r-${_pkgname,,}
 pkgver=0.3.15
-pkgrel=1
+pkgrel=2
 pkgdesc='Tools to Deal with Raster Maps'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
 license=('GPL')
 depends=(
   r
-  r-filehash
   r-sp
 )
 optdepends=(

BioArchLinux/r-adehabitatma/lilac.yaml

@@ -3,7 +3,6 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-filehash
 - r-sp
 update_on:
 - regex: adehabitatMA_([\d._-]+).tar.gz

BioArchLinux/r-affypara/PKGBUILD

@@ -3,10 +3,10 @@ _pkgname=affyPara
 _pkgver=1.54.0
 pkgname=r-${_pkgname,,}
 pkgver=1.54.0
-pkgrel=2
+pkgrel=3
 pkgdesc='Sample size for RNAseq studies'
 arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/3.14/${_pkgname}"
 license=('GPL3')
 depends=(
   r
@@ -22,6 +22,7 @@ makedepends=(
   tar
 )
 optdepends=(
+  r-affy
   r-affydata
 )
 source=("git+https://git.bioconductor.org/packages/${_pkgname}.git")

BioArchLinux/r-affypara/lilac.yaml

@@ -4,10 +4,10 @@ maintainers:
   email: starsareintherose@outlook.com
 repo_depends:
 - r-affy
+- r-affyio
+- r-aplpack
 - r-snow
 - r-vsn
-- r-aplpack
-- r-affyio
 update_on:
 - regex: <td>(\d+.\d+.\d+)</td>
   source: regex

BioArchLinux/r-akima/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=akima
 _pkgver=0.6-3.4
 pkgname=r-${_pkgname,,}
 pkgver=0.6.3.4
-pkgrel=2
+pkgrel=3
 pkgdesc='Interpolation of Irregularly and Regularly Spaced Data'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -13,6 +13,9 @@ depends=(
   r
   r-sp
 )
+optdepends=(
+  r-tripack
+)
 makedepends=(
   gcc-fortran
 )

BioArchLinux/r-alevinqc/PKGBUILD

@@ -4,9 +4,9 @@ _pkgname=alevinQC
 _pkgver=1.14.0
 pkgname=r-${_pkgname,,}
 pkgver=1.14.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Generate QC Reports For Alevin Output'
-arch=('any')
+arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('MIT')
 depends=(
@@ -16,6 +16,7 @@ depends=(
   r-dt
   r-ggally
   r-ggplot2
+  r-rcpp
   r-rjson
   r-rlang
   r-rmarkdown
@@ -24,6 +25,7 @@ depends=(
   r-tximport
 )
 optdepends=(
+  r-biocmanager
   r-biocstyle
   r-knitr
   r-testthat

BioArchLinux/r-alevinqc/lilac.yaml

@@ -8,6 +8,7 @@ repo_depends:
 - r-dt
 - r-ggally
 - r-ggplot2
+- r-rcpp
 - r-rjson
 - r-rlang
 - r-rmarkdown

BioArchLinux/r-alps/PKGBUILD

@@ -4,10 +4,10 @@ _pkgname=ALPS
 _pkgver=1.8.0
 pkgname=r-${_pkgname,,}
 pkgver=1.8.0
-pkgrel=4
+pkgrel=5
 pkgdesc='AnaLysis routines for ePigenomicS data'
 arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/3.14/${_pkgname}"
 license=('MIT')
 depends=(
   r
@@ -17,9 +17,9 @@ depends=(
   r-corrplot
   r-data.table
   r-dplyr
+  r-genefilter
   r-genomicranges
   r-ggally
-  r-genefilter
   r-gghalves
   r-ggplot2
   r-ggseqlogo
@@ -31,6 +31,8 @@ depends=(
   r-rtracklayer
   r-stringr
   r-tibble
+  r-tidyr
+  r-txdb.hsapiens.ucsc.hg19.knowngene
   r-txdb.hsapiens.ucsc.hg38.knowngene
 )
 optdepends=(

BioArchLinux/r-alps/lilac.yaml

@@ -9,9 +9,9 @@ repo_depends:
 - r-corrplot
 - r-data.table
 - r-dplyr
+- r-genefilter
 - r-genomicranges
 - r-ggally
-- r-genefilter
 - r-gghalves
 - r-ggplot2
 - r-ggseqlogo
@@ -23,12 +23,9 @@ repo_depends:
 - r-rtracklayer
 - r-stringr
 - r-tibble
+- r-tidyr
+- r-txdb.hsapiens.ucsc.hg19.knowngene
 - r-txdb.hsapiens.ucsc.hg38.knowngene
-- r-rmarkdown
-- r-knitr
-- r-complexheatmap
-- r-circlize
-- r-testthat
 update_on:
 - regex: <td>(\d+.\d+.\d+)</td>
   source: regex

BioArchLinux/r-alpsnmr/PKGBUILD

@@ -4,53 +4,57 @@ _pkgname=AlpsNMR
 _pkgver=4.0.2
 pkgname=r-${_pkgname,,}
 pkgver=4.0.2
-pkgrel=1
+pkgrel=2
 pkgdesc='Automated spectraL Processing System for NMR'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('MIT')
 depends=(
   r
-  r-assertthat
   r-baseline
   r-biocparallel
   r-dplyr
   r-fs
-  r-furrr
   r-future
-  r-ggally
+  r-generics
   r-ggplot2
-  r-ggrepel
   r-glue
   r-htmltools
   r-magrittr
   r-matrixstats
   r-mixomics
   r-pcapp
-  r-plyr
   r-purrr
   r-readxl
   r-reshape2
   r-rlang
   r-rmarkdown
-  r-s4vectors
+  r-scales
   r-signal
   r-speaq
   r-stringr
-  r-summarizedexperiment
   r-tibble
   r-tidyr
   r-tidyselect
   r-vctrs
-  r-writexl
-  r-zip
 )
 optdepends=(
+  r-biocstyle
   r-chemospec
+  r-cowplot
+  r-curl
   r-dt
+  r-ggally
+  r-ggrepel
+  r-gridextra
   r-knitr
   r-plotly
+  r-progressr
+  r-s4vectors
+  r-summarizedexperiment
   r-testthat
+  r-writexl
+  r-zip
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('f41e5f7db7f55cdf91ad2781274965dfd4e959e5f2734cb42d9b3a440dc398f8')

BioArchLinux/r-alpsnmr/lilac.yaml

@@ -3,39 +3,32 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-assertthat
 - r-baseline
 - r-biocparallel
 - r-dplyr
 - r-fs
-- r-furrr
 - r-future
-- r-ggally
+- r-generics
 - r-ggplot2
-- r-ggrepel
 - r-glue
 - r-htmltools
 - r-magrittr
 - r-matrixstats
 - r-mixomics
 - r-pcapp
-- r-plyr
 - r-purrr
 - r-readxl
 - r-reshape2
 - r-rlang
 - r-rmarkdown
-- r-s4vectors
+- r-scales
 - r-signal
 - r-speaq
 - r-stringr
-- r-summarizedexperiment
 - r-tibble
 - r-tidyr
 - r-tidyselect
 - r-vctrs
-- r-writexl
-- r-zip
 update_on:
 - regex: AlpsNMR_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-als/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=ALS
 _pkgver=0.0.6
 pkgname=r-${_pkgname,,}
 pkgver=0.0.6
-pkgrel=5
+pkgrel=6
 pkgdesc='Multivariate Curve Resolution Alternating Least Squares (MCR-ALS)'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -14,7 +14,7 @@ depends=(
   r-iso
   r-nnls
 )
-source=("https://cran.r-project.org/src/contrib/Archive/${_pkgname}/${_pkgname}_${_pkgver}.tar.gz")
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('ca90d27115ae9e476967f521bf6935723e410a3bf92477e7570e14bfd3b099eb')
 
 build() {

BioArchLinux/r-als/lilac.yaml

@@ -8,5 +8,5 @@ repo_depends:
 update_on:
 - regex: ALS_([\d._-]+).tar.gz
   source: regex
-  url: https://cran.r-project.org/src/contrib/Archive/ALS/
+  url: https://cran.r-project.org/package=ALS
 - alias: r

BioArchLinux/r-anvil/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=AnVIL
 _pkgver=1.10.1
 pkgname=r-${_pkgname,,}
 pkgver=1.10.1
-pkgrel=1
+pkgrel=2
 pkgdesc='Bioconductor on the AnVIL compute environment'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -13,22 +13,22 @@ depends=(
   r
   r-biocmanager
   r-dplyr
+  r-dt
   r-futile.logger
+  r-htmltools
   r-httr
   r-jsonlite
+  r-miniui
   r-rapiclient
   r-rlang
+  r-shiny
   r-tibble
   r-tidyr
   r-tidyselect
-  r-vctrs
-  r-shiny
-  r-dt
-  r-miniui
-  r-htmltools
 )
 optdepends=(
   r-biocstyle
+  r-devtools
   r-knitr
   r-parallel
   r-readr

BioArchLinux/r-anvil/lilac.yaml

@@ -5,19 +5,18 @@ maintainers:
 repo_depends:
 - r-biocmanager
 - r-dplyr
+- r-dt
 - r-futile.logger
+- r-htmltools
 - r-httr
 - r-jsonlite
+- r-miniui
 - r-rapiclient
 - r-rlang
+- r-shiny
 - r-tibble
 - r-tidyr
 - r-tidyselect
-- r-vctrs
-- r-shiny
-- r-dt
-- r-miniui
-- r-htmltools
 update_on:
 - regex: AnVIL_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-aods3/PKGBUILD

@@ -4,13 +4,16 @@ _pkgname=aods3
 _pkgver=0.4-1.2
 pkgname=r-${_pkgname,,}
 pkgver=0.4.1.2
-pkgrel=2
+pkgrel=3
 pkgdesc='Analysis of Overdispersed Data using S3 Methods'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
 license=('GPL')
 depends=(
   r
+)
+optdepends=(
+  r-boot
   r-lme4
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-apalyzer/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=APAlyzer
 _pkgver=1.12.0
 pkgname=r-${_pkgname,,}
 pkgver=1.12.0
-pkgrel=1
+pkgrel=2
 pkgdesc='A toolkit for APA analysis using RNA-seq data'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -13,12 +13,12 @@ depends=(
   r
   r-deseq2
   r-dplyr
-  r-ensembldb
   r-genomicalignments
   r-genomicfeatures
   r-genomicranges
   r-ggplot2
   r-ggrepel
+  r-hybridmtest
   r-repmis
   r-rsamtools
   r-rsubread
@@ -26,7 +26,6 @@ depends=(
   r-summarizedexperiment
   r-tidyr
   r-variantannotation
-  r-hybridmtest
 )
 optdepends=(
   r-annotationdbi

BioArchLinux/r-apalyzer/lilac.yaml

@@ -5,12 +5,12 @@ maintainers:
 repo_depends:
 - r-deseq2
 - r-dplyr
-- r-ensembldb
 - r-genomicalignments
 - r-genomicfeatures
 - r-genomicranges
 - r-ggplot2
 - r-ggrepel
+- r-hybridmtest
 - r-repmis
 - r-rsamtools
 - r-rsubread
@@ -18,7 +18,6 @@ repo_depends:
 - r-summarizedexperiment
 - r-tidyr
 - r-variantannotation
-- r-hybridmtest
 update_on:
 - regex: APAlyzer_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-apcluster/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=apcluster
 _pkgver=1.4.10
 pkgname=r-${_pkgname,,}
 pkgver=1.4.10
-pkgrel=2
+pkgrel=3
 pkgdesc='Affinity Propagation Clustering'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -14,8 +14,6 @@ depends=(
   r-rcpp
 )
 optdepends=(
-  r-biostrings
-  r-kebabs
   r-knitr
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-aplot/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=aplot
 _pkgver=0.1.9
 pkgname=r-${_pkgname,,}
 pkgver=0.1.9
-pkgrel=1
+pkgrel=2
 pkgdesc="Decorate a 'ggplot' with Associated Information"
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -16,7 +16,6 @@ depends=(
   r-ggplotify
   r-magrittr
   r-patchwork
-  r-yulab.utils
 )
 optdepends=(
   r-ggtree

BioArchLinux/r-aplot/lilac.yaml

@@ -8,7 +8,6 @@ repo_depends:
 - r-ggplotify
 - r-magrittr
 - r-patchwork
-- r-yulab.utils
 update_on:
 - regex: aplot_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-arrow/PKGBUILD

@@ -5,24 +5,29 @@ _pkgname=arrow
 _pkgver=10.0.0
 pkgname=r-${_pkgname,,}
 pkgver=10.0.0
-pkgrel=1
+pkgrel=2
 pkgdesc="Integration to 'Apache' 'Arrow'"
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
 license=('Apache')
 depends=(
+  gcc
   r
   r-assertthat
   r-bit64
+  r-cpp11
+  r-glue
   r-purrr
   r-r6
   r-rlang
   r-tidyselect
   r-vctrs
-  gcc
-  r-cpp11
 )
 optdepends=(
+  libcurl-compat
+  openssl
+  r-blob
+  r-cli
   r-dbi
   r-dbplyr
   r-decor
@@ -32,16 +37,17 @@ optdepends=(
   r-hms
   r-knitr
   r-lubridate
+  r-pillar
   r-pkgload
   r-reticulate
   r-rmarkdown
   r-stringi
   r-stringr
+  r-sys
   r-testthat
   r-tibble
+  r-tzdb
   r-withr
-  libcurl-compat
-  openssl
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('e855b5ea913e93935d20be11b342f45193437404945c9fc39e9c61fd91911a13')

BioArchLinux/r-arrow/lilac.yaml

@@ -5,12 +5,13 @@ maintainers:
 repo_depends:
 - r-assertthat
 - r-bit64
+- r-cpp11
+- r-glue
 - r-purrr
 - r-r6
 - r-rlang
 - r-tidyselect
 - r-vctrs
-- r-cpp11
 update_on:
 - regex: arrow_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-arules/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=arules
 _pkgver=1.7-5
 pkgname=r-${_pkgname,,}
 pkgver=1.7.5
-pkgrel=1
+pkgrel=2
 pkgdesc='Mining Association Rules and Frequent Itemsets'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -17,6 +17,7 @@ optdepends=(
   r-arulescba
   r-arulesviz
   r-pmml
+  r-proxy
   r-testthat
   r-xml
 )

BioArchLinux/r-atena/PKGBUILD

@@ -4,26 +4,27 @@ _pkgname=atena
 _pkgver=1.4.0
 pkgname=r-${_pkgname,,}
 pkgver=1.4.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Analysis of Transposable Elements'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
   r
+  r-annotationhub
   r-biocgenerics
   r-biocparallel
   r-genomeinfodb
   r-genomicalignments
   r-genomicranges
   r-iranges
+  r-matrixstats
   r-rsamtools
   r-s4vectors
+  r-scales
   r-sparsematrixstats
   r-squarem
   r-summarizedexperiment
-  r-annotationhub
-  r-scales
 )
 optdepends=(
   r-biocstyle

BioArchLinux/r-atena/lilac.yaml

@@ -3,19 +3,20 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-annotationhub
 - r-biocgenerics
 - r-biocparallel
 - r-genomeinfodb
 - r-genomicalignments
 - r-genomicranges
 - r-iranges
+- r-matrixstats
 - r-rsamtools
 - r-s4vectors
+- r-scales
 - r-sparsematrixstats
 - r-squarem
 - r-summarizedexperiment
-- r-annotationhub
-- r-scales
 update_on:
 - regex: atena_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-aucell/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=AUCell
 _pkgver=1.20.1
 pkgname=r-${_pkgname,,}
 pkgver=1.20.1
-pkgrel=1
+pkgrel=2
 pkgdesc="AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)"
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -13,13 +13,13 @@ depends=(
   r
   r-biocgenerics
   r-data.table
+  r-delayedarray
+  r-delayedmatrixstats
   r-gseabase
   r-mixtools
   r-r.utils
-  r-s4vectors
   r-shiny
   r-summarizedexperiment
-  r-delayedmatrixstats
 )
 optdepends=(
   r-biobase

BioArchLinux/r-aucell/lilac.yaml

@@ -5,13 +5,13 @@ maintainers:
 repo_depends:
 - r-biocgenerics
 - r-data.table
+- r-delayedarray
+- r-delayedmatrixstats
 - r-gseabase
 - r-mixtools
 - r-r.utils
-- r-s4vectors
 - r-shiny
 - r-summarizedexperiment
-- r-delayedmatrixstats
 update_on:
 - regex: AUCell_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-available/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=available
 _pkgver=1.1.0
 pkgname=r-${_pkgname,,}
 pkgver=1.1.0
-pkgrel=2
+pkgrel=3
 pkgdesc='Check if the Title of a Package is Available, Appropriate and Interesting'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -22,7 +22,6 @@ depends=(
   r-stringdist
   r-tibble
   r-tidytext
-  r-udapi
   r-yesno
 )
 optdepends=(

BioArchLinux/r-available/lilac.yaml

@@ -14,7 +14,6 @@ repo_depends:
 - r-stringdist
 - r-tibble
 - r-tidytext
-- r-udapi
 - r-yesno
 update_on:
 - regex: available_([\d._-]+).tar.gz

BioArchLinux/r-babelgene/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=babelgene
 _pkgver=22.9
 pkgname=r-${_pkgname,,}
 pkgver=22.9
-pkgrel=1
+pkgrel=2
 pkgdesc='Gene Orthologs for Model Organisms in a Tidy Data Format'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -13,7 +13,6 @@ depends=(
   r
   r-dplyr
   r-rlang
-  r-vctrs
 )
 optdepends=(
   r-covr

BioArchLinux/r-babelgene/lilac.yaml

@@ -5,7 +5,6 @@ maintainers:
 repo_depends:
 - r-dplyr
 - r-rlang
-- r-vctrs
 update_on:
 - regex: babelgene_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-backbone/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=backbone
 _pkgver=2.1.1
 pkgname=r-${_pkgname,,}
 pkgver=2.1.1
-pkgrel=1
+pkgrel=2
 pkgdesc='Extracts the Backbone from Graphs'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -12,15 +12,12 @@ license=('GPL')
 depends=(
   r
   r-igraph
-  r-network
-  r-poissonbinomial
   r-rcpp
 )
 optdepends=(
   r-knitr
-  r-mass
   r-rmarkdown
-  r-testthat
+  r-tinytest
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('0748ed4031739b793a9dcb39476848a0ef80049a66b86ea4facef3d12e0500ac')

BioArchLinux/r-backbone/lilac.yaml

@@ -4,8 +4,6 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-igraph
-- r-network
-- r-poissonbinomial
 - r-rcpp
 update_on:
 - regex: backbone_([\d._-]+).tar.gz

BioArchLinux/r-bamlss/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=bamlss
 _pkgver=1.1-9
 pkgname=r-${_pkgname,,}
 pkgver=1.1.9
-pkgrel=1
+pkgrel=2
 pkgdesc='Bayesian Additive Models for Location, Scale, and Shape (and Beyond)'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -19,17 +19,15 @@ depends=(
   r-sp
 )
 optdepends=(
-  r-akima
   r-bayesx
   r-bit
   r-ff
-  r-ffbase
   r-fields
   r-gamlss
   r-gamlss.dist
-  r-geor
   r-glmnet
   r-glogis
+  r-interp
   r-keras
   r-knitr
   r-mapdata

BioArchLinux/r-banocc/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=banocc
 _pkgver=1.22.0
 pkgname=r-${_pkgname,,}
 pkgver=1.22.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Bayesian ANalysis Of Compositional Covariance'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -17,6 +17,7 @@ depends=(
   r-stringr
 )
 optdepends=(
+  r-biocstyle
   r-knitr
   r-methods
   r-rmarkdown

BioArchLinux/r-basilisk.utils/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=basilisk.utils
 _pkgver=1.10.0
 pkgname=r-${_pkgname,,}
 pkgver=1.10.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Basilisk Installation Utilities'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -16,6 +16,7 @@ depends=(
 optdepends=(
   r-biocstyle
   r-knitr
+  r-reticulate
   r-rmarkdown
   r-testthat
 )

BioArchLinux/r-bayesfactor/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=BayesFactor
 _pkgver=0.9.12-4.4
 pkgname=r-${_pkgname,,}
 pkgver=0.9.12.4.4
-pkgrel=2
+pkgrel=3
 pkgdesc='Computation of Bayes Factors for Common Designs'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -12,7 +12,6 @@ license=('GPL')
 depends=(
   r
   r-coda
-  r-gtools
   r-hypergeo
   r-matrixmodels
   r-mvtnorm

BioArchLinux/r-bayesfactor/lilac.yaml

@@ -1,18 +1,17 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: sukanka
+- github: sukanka
 repo_depends:
-  - r-coda
-  - r-gtools
-  - r-hypergeo
-  - r-matrixmodels
-  - r-mvtnorm
-  - r-pbapply
-  - r-rcpp
-  - r-rcppeigen
-  - r-stringr
+- r-coda
+- r-hypergeo
+- r-matrixmodels
+- r-mvtnorm
+- r-pbapply
+- r-rcpp
+- r-rcppeigen
+- r-stringr
 update_on:
-  - regex: BayesFactor_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=BayesFactor
-  - alias: r
+- regex: BayesFactor_([\d._-]+).tar.gz
+  source: regex
+  url: https://cran.r-project.org/package=BayesFactor
+- alias: r

BioArchLinux/r-bayestestr/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=bayestestR
 _pkgver=0.13.0
 pkgname=r-${_pkgname,,}
 pkgver=0.13.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Understand and Describe Bayesian Models and Posterior Distributions'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -16,16 +16,18 @@ depends=(
 )
 optdepends=(
   r-bayesfactor
+  r-bayesplot
   r-bayesqr
+  r-bh
   r-blavaan
   r-bridgesampling
   r-brms
-  r-dplyr
   r-effectsize
   r-emmeans
-  r-ggally
+  r-gamm4
+  r-ggdist
   r-ggplot2
-  r-ggridges
+  r-glmmtmb
   r-httr
   r-kernsmooth
   r-knitr
@@ -37,15 +39,16 @@ optdepends=(
   r-mediation
   r-modelbased
   r-parameters
+  r-patchwork
   r-performance
+  r-posterior
+  r-quadprog
+  r-rcppeigen
   r-rmarkdown
   r-rstan
   r-rstanarm
   r-see
-  r-spelling
-  r-stringr
   r-testthat
-  r-tidyr
   r-tweedie
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-bayestestr/lilac.yaml

@@ -1,11 +1,11 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: hubutui
+- github: hubutui
 repo_depends:
-  - r-datawizard
-  - r-insight
+- r-datawizard
+- r-insight
 update_on:
-  - regex: bayestestR_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=bayestestR
-  - alias: r
+- regex: bayestestR_([\d._-]+).tar.gz
+  source: regex
+  url: https://cran.r-project.org/package=bayestestR
+- alias: r

BioArchLinux/r-bayestools/PKGBUILD

@@ -5,12 +5,13 @@ _pkgname=BayesTools
 _pkgver=0.2.13
 pkgname=r-${_pkgname,,}
 pkgver=0.2.13
-pkgrel=1
+pkgrel=2
 pkgdesc='Tools for Bayesian Analyses'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
 license=('GPL')
 depends=(
+  jags
   r
   r-bridgesampling
   r-coda
@@ -18,16 +19,15 @@ depends=(
   r-ggplot2
   r-mvtnorm
   r-rdpack
-  r-rjags
-  r-runjags
-  jags
 )
 optdepends=(
   r-bayesfactor
   r-covr
   r-knitr
+  r-rjags
   r-rmarkdown
   r-rstan
+  r-runjags
   r-scales
   r-testthat
   r-vdiffr

BioArchLinux/r-bayestools/lilac.yaml

@@ -1,18 +1,16 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: sukanka
+- github: sukanka
 repo_depends:
-  - r-bridgesampling
-  - r-coda
-  - r-extradistr
-  - r-ggplot2
-  - r-mvtnorm
-  - r-rdpack
-  - r-rjags
-  - r-runjags
-  - jags
+- jags
+- r-bridgesampling
+- r-coda
+- r-extradistr
+- r-ggplot2
+- r-mvtnorm
+- r-rdpack
 update_on:
-  - regex: BayesTools_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=BayesTools
-  - alias: r
+- regex: BayesTools_([\d._-]+).tar.gz
+  source: regex
+  url: https://cran.r-project.org/package=BayesTools
+- alias: r

BioArchLinux/r-beclear/PKGBUILD

@@ -5,29 +5,29 @@ _pkgname=BEclear
 _pkgver=2.14.0
 pkgname=r-${_pkgname,,}
 pkgver=2.14.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Correction of batch effects in DNA methylation data'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('GPL')
 depends=(
+  gcc
   r
   r-abind
   r-biocparallel
   r-data.table
+  r-dixontest
   r-futile.logger
   r-ids
-  r-outliers
   r-rcpp
   r-rdpack
-  r-dixontest
-  gcc
 )
 optdepends=(
   r-biocstyle
   r-knitr
   r-pander
   r-rmarkdown
+  r-seewave
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-beclear/lilac.yaml

@@ -6,12 +6,11 @@ repo_depends:
 - r-abind
 - r-biocparallel
 - r-data.table
+- r-dixontest
 - r-futile.logger
 - r-ids
-- r-outliers
 - r-rcpp
 - r-rdpack
-- r-dixontest
 update_on:
 - regex: BEclear_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-bigmemory.sri/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=bigmemory.sri
 _pkgver=0.1.6
 pkgname=r-${_pkgname,,}
 pkgver=0.1.6
-pkgrel=1
+pkgrel=2
 pkgdesc='A shared resource interface for Bigmemory Project packages'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -14,7 +14,6 @@ depends=(
 )
 optdepends=(
   r-bigmemory
-  r-synchronicity
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('3bfa6ac966ce0ea93283f5856a853d0ee5ff85aedd7a7d1ca8a93d0aa642860c')

BioArchLinux/r-bigmemory/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=bigmemory
 _pkgver=4.6.1
 pkgname=r-${_pkgname,,}
 pkgver=4.6.1
-pkgrel=2
+pkgrel=3
 pkgdesc='Manage Massive Matrices with Shared Memory and Memory-Mapped Files'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -19,6 +19,7 @@ depends=(
 optdepends=(
   r-biganalytics
   r-bigtabulate
+  r-remotes
   r-testthat
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-bigstatsr/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=bigstatsr
 _pkgver=1.5.12
 pkgname=r-${_pkgname,,}
 pkgver=1.5.12
-pkgrel=1
+pkgrel=2
 pkgdesc='Statistical Tools for Filebacked Big Matrices'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -24,7 +24,6 @@ depends=(
   r-tibble
 )
 optdepends=(
-  r-biglasso
   r-bigmemory
   r-bigreadr
   r-covr
@@ -34,6 +33,7 @@ optdepends=(
   r-hexbin
   r-memuse
   r-modelmetrics
+  r-plotly
   r-ppcor
   r-rhpcblasctl
   r-spelling

BioArchLinux/r-biobase/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=Biobase
 _pkgver=2.58.0
 pkgname=r-${_pkgname,,}
 pkgver=2.58.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Biobase: Base functions for Bioconductor'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -15,7 +15,9 @@ depends=(
 )
 optdepends=(
   r-all
+  r-biocstyle
   r-golubesets
+  r-knitr
   r-runit
   r-tkwidgets
   r-tools

BioArchLinux/r-bioccheck/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=BiocCheck
 _pkgver=1.34.2
 pkgname=r-${_pkgname,,}
 pkgver=1.34.2
-pkgrel=1
+pkgrel=2
 pkgdesc='Bioconductor-specific package checks'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -16,16 +16,17 @@ depends=(
   r-graph
   r-httr
   r-knitr
-  r-optparse
   r-stringdist
 )
 optdepends=(
   r-biobase
   r-biocgenerics
   r-biocstyle
+  r-callr
   r-codetoolsbioc
   r-devtools
-  r-rjsonio
+  r-downloader
+  r-jsonlite
   r-rmarkdown
   r-runit
   r-usethis

BioArchLinux/r-bioccheck/lilac.yaml

@@ -8,7 +8,6 @@ repo_depends:
 - r-graph
 - r-httr
 - r-knitr
-- r-optparse
 - r-stringdist
 update_on:
 - regex: BiocCheck_([\d._-]+).tar.gz

BioArchLinux/r-biocparallel/PKGBUILD

@@ -5,7 +5,7 @@ _pkgname=BiocParallel
 _pkgver=1.32.3
 pkgname=r-${_pkgname,,}
 pkgver=1.32.3
-pkgrel=1
+pkgrel=2
 pkgdesc='Bioconductor facilities for parallel evaluation'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -23,7 +23,6 @@ optdepends=(
   r-bbmisc
   r-biocgenerics
   r-biocstyle
-  r-codetools
   r-data.table
   r-doparallel
   r-foreach

BioArchLinux/r-biocparallel/lilac.yaml

@@ -4,9 +4,9 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-bh
+- r-cpp11
 - r-futile.logger
 - r-snow
-- r-cpp11
 update_on:
 - regex: BiocParallel_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-biocsklearn/PKGBUILD

@@ -5,27 +5,27 @@ _pkgname=BiocSklearn
 _pkgver=1.20.0
 pkgname=r-${_pkgname,,}
 pkgver=1.20.0
-pkgrel=1
+pkgrel=2
 pkgdesc='interface to python sklearn via Rstudio reticulate'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
-  r
-  r-basilisk
-  r-knitr
-  r-rcpp
-  r-reticulate
-  r-summarizedexperiment
   python
-  python-scikit-learn
+  python-h5py
   python-numpy
   python-pandas
-  python-h5py
+  python-scikit-learn
+  r
+  r-basilisk
+  r-basilisk.utils
+  r-reticulate
+  r-summarizedexperiment
 )
 optdepends=(
   r-biocstyle
   r-hdf5array
+  r-knitr
   r-restfulse
   r-rmarkdown
   r-testthat

BioArchLinux/r-biocsklearn/lilac.yaml

@@ -4,8 +4,7 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-basilisk
-- r-knitr
-- r-rcpp
+- r-basilisk.utils
 - r-reticulate
 - r-summarizedexperiment
 update_on:

BioArchLinux/r-biocviews/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=biocViews
 _pkgver=1.66.0
 pkgname=r-${_pkgname,,}
 pkgver=1.66.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Categorized views of R package repositories'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -21,6 +21,7 @@ depends=(
 )
 optdepends=(
   r-biocgenerics
+  r-biocstyle
   r-commonmark
   r-knitr
 )

BioArchLinux/r-biomart/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=biomaRt
 _pkgver=2.54.0
 pkgname=r-${_pkgname,,}
 pkgver=2.54.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Interface to BioMart databases (i.e. Ensembl)'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -27,6 +27,7 @@ optdepends=(
   r-mockery
   r-rmarkdown
   r-testthat
+  r-webmockr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('989a1ac3c9f99833c277892dfc868f0aebc8ac106ce4d038766e4d514c7cca30')

BioArchLinux/r-biomartr/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=biomartr
 _pkgver=1.0.2
 pkgname=r-${_pkgname,,}
 pkgver=1.0.2
-pkgrel=4
+pkgrel=5
 pkgdesc='Genomic Data Retrieval'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -27,6 +27,7 @@ depends=(
   r-readr
   r-stringr
   r-tibble
+  r-withr
   r-xml
 )
 optdepends=(

BioArchLinux/r-biomartr/lilac.yaml

@@ -19,6 +19,7 @@ repo_depends:
 - r-readr
 - r-stringr
 - r-tibble
+- r-withr
 - r-xml
 update_on:
 - regex: biomartr_([\d._-]+).tar.gz

BioArchLinux/r-bionero/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=BioNERO
 _pkgver=1.6.0
 pkgname=r-${_pkgname,,}
 pkgver=1.6.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Biological Network Reconstruction Omnibus'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -13,29 +13,29 @@ depends=(
   r
   r-biocparallel
   r-complexheatmap
-  r-deseq2
   r-dynamictreecut
   r-genie3
   r-ggnetwork
   r-ggnewscale
   r-ggplot2
-  r-ggpubr
+  r-ggrepel
   r-igraph
   r-intergraph
   r-matrixstats
   r-minet
   r-netrep
   r-networkd3
+  r-patchwork
   r-rcolorbrewer
   r-reshape2
   r-summarizedexperiment
   r-sva
   r-wgcna
-  r-patchwork
 )
 optdepends=(
   r-biocstyle
   r-covr
+  r-deseq2
   r-knitr
   r-rmarkdown
   r-testthat

BioArchLinux/r-bionero/lilac.yaml

@@ -5,25 +5,24 @@ maintainers:
 repo_depends:
 - r-biocparallel
 - r-complexheatmap
-- r-deseq2
 - r-dynamictreecut
 - r-genie3
 - r-ggnetwork
 - r-ggnewscale
 - r-ggplot2
-- r-ggpubr
+- r-ggrepel
 - r-igraph
 - r-intergraph
 - r-matrixstats
 - r-minet
 - r-netrep
 - r-networkd3
+- r-patchwork
 - r-rcolorbrewer
 - r-reshape2
 - r-summarizedexperiment
 - r-sva
 - r-wgcna
-- r-patchwork
 update_on:
 - regex: BioNERO_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-biotip/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=BioTIP
 _pkgver=1.12.0
 pkgname=r-${_pkgname,,}
 pkgver=1.12.0
-pkgrel=1
+pkgrel=2
 pkgdesc='BioTIP: An R package for characterization of Biological Tipping-Point'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -12,11 +12,10 @@ license=('GPL')
 depends=(
   r
   r-genomicranges
-  r-hmisc
   r-igraph
   r-psych
-  r-stringr
   r-scran
+  r-stringr
 )
 optdepends=(
   r-base

BioArchLinux/r-biotip/lilac.yaml

@@ -4,11 +4,10 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-genomicranges
-- r-hmisc
 - r-igraph
 - r-psych
-- r-stringr
 - r-scran
+- r-stringr
 update_on:
 - regex: BioTIP_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-birewire/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=BiRewire
 _pkgver=3.30.0
 pkgname=r-${_pkgname,,}
 pkgver=3.30.0
-pkgrel=1
+pkgrel=2
 pkgdesc='High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -12,9 +12,8 @@ license=('GPL')
 depends=(
   r
   r-igraph
-  r-slam
-  r-tsne
   r-rtsne
+  r-slam
 )
 optdepends=(
   r-biocgenerics

BioArchLinux/r-birewire/lilac.yaml

@@ -4,9 +4,8 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-igraph
-- r-slam
-- r-tsne
 - r-rtsne
+- r-slam
 update_on:
 - regex: BiRewire_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-biwt/PKGBUILD

@@ -4,14 +4,14 @@ _pkgname=biwt
 _pkgver=1.0.1
 pkgname=r-${_pkgname,,}
 pkgver=1.0.1
-pkgrel=2
+pkgrel=3
 pkgdesc='Functions to compute the biweight mean vector and covariance & correlation matrices'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
 license=('GPL')
 depends=(
   r
-  r-rrcov
+  r-robustbase
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('9c3528c5a4d2982d992f15086bad6bc8de291fe3c77ab0119b80350e6540e33d')

BioArchLinux/r-biwt/lilac.yaml

@@ -3,7 +3,7 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-rrcov
+- r-robustbase
 update_on:
 - regex: biwt_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-brew/PKGBUILD

@@ -7,7 +7,7 @@ _pkgname=brew
 _pkgver=1.0-8
 pkgname=r-${_pkgname,,}
 pkgver=1.0.8
-pkgrel=3
+pkgrel=4
 pkgdesc='Templating Framework for Report Generation'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -15,6 +15,9 @@ license=('GPL')
 depends=(
   r
 )
+optdepends=(
+  r-testthat
+)
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('11652d5a7042d645cc5be5f9f97ff4d46083cea7d3ad2dd6ad1570b52c097826')
 

BioArchLinux/r-brobdingnag/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=Brobdingnag
 _pkgver=1.2-9
 pkgname=r-${_pkgname,,}
 pkgver=1.2.9
-pkgrel=1
+pkgrel=2
 pkgdesc='Very Large Numbers in R'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -14,6 +14,7 @@ depends=(
 )
 optdepends=(
   r-cubature
+  r-testthat
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('f9012d250bc2a0f47815d6a7c06df2d4ddf3d8bab2d3b75e8cdefd964d20e91e')

BioArchLinux/r-brobdingnag/lilac.yaml

@@ -1,8 +1,8 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: sukanka
+- github: sukanka
 update_on:
-  - regex: Brobdingnag_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=Brobdingnag
-  - alias: r
+- regex: Brobdingnag_([\d._-]+).tar.gz
+  source: regex
+  url: https://cran.r-project.org/package=Brobdingnag
+- alias: r

BioArchLinux/r-broom.mixed/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=broom.mixed
 _pkgver=0.2.9.4
 pkgname=r-${_pkgname,,}
 pkgver=0.2.9.4
-pkgrel=8
+pkgrel=9
 pkgdesc='Tidying Methods for Mixed Models'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -42,6 +42,7 @@ optdepends=(
   r-rmarkdown
   r-rstan
   r-rstanarm
+  r-rstantools
   r-testthat
   r-tmb
 )

BioArchLinux/r-broom.mixed/lilac.yaml

@@ -6,12 +6,12 @@ repo_depends:
 - r-broom
 - r-coda
 - r-dplyr
+- r-forcats
+- r-furrr
 - r-purrr
 - r-stringr
 - r-tibble
 - r-tidyr
-- r-forcats
-- r-furrr
 update_on:
 - regex: broom.mixed_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-broom/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=broom
 _pkgver=1.0.1
 pkgname=r-${_pkgname,,}
 pkgver=1.0.1
-pkgrel=1
+pkgrel=2
 pkgdesc='Convert Statistical Objects into Tidy Tibbles'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -25,7 +25,6 @@ depends=(
 )
 optdepends=(
   r-aer
-  r-akima
   r-auc
   r-bbmle
   r-betareg
@@ -34,6 +33,7 @@ optdepends=(
   r-boot
   r-btergm
   r-car
+  r-cardata
   r-caret
   r-cluster
   r-cmprsk
@@ -52,6 +52,7 @@ optdepends=(
   r-glmnetutils
   r-gmm
   r-hmisc
+  r-interp
   r-irlba
   r-joinerml
   r-kendall
@@ -70,7 +71,6 @@ optdepends=(
   r-maptools
   r-margins
   r-mass
-  r-matrix
   r-mclust
   r-mediation
   r-metafor

BioArchLinux/r-bs4dash/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=bs4Dash
 _pkgver=2.1.0
 pkgname=r-${_pkgname,,}
 pkgver=2.1.0
-pkgrel=2
+pkgrel=3
 pkgdesc="A 'Bootstrap 4' Version of 'shinydashboard'"
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -24,7 +24,6 @@ depends=(
 optdepends=(
   r-covr
   r-dt
-  r-echarts4r
   r-golem
   r-knitr
   r-rmarkdown

BioArchLinux/r-bugsigdbr/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=bugsigdbr
 _pkgver=1.4.0
 pkgname=r-${_pkgname,,}
 pkgver=1.4.0
-pkgrel=1
+pkgrel=2
 pkgdesc='R-side access to published microbial signatures from BugSigDB'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -17,6 +17,7 @@ depends=(
 optdepends=(
   r-biocstyle
   r-knitr
+  r-ontologyindex
   r-rmarkdown
   r-testthat
 )

BioArchLinux/r-cageminer/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=cageminer
 _pkgver=1.4.0
 pkgname=r-${_pkgname,,}
 pkgver=1.4.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Candidate Gene Miner'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -22,8 +22,10 @@ depends=(
 )
 optdepends=(
   r-biocstyle
+  r-covr
   r-knitr
   r-rmarkdown
+  r-sessioninfo
   r-summarizedexperiment
   r-testthat
 )

BioArchLinux/r-callr/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=callr
 _pkgver=3.7.3
 pkgname=r-${_pkgname,,}
 pkgver=3.7.3
-pkgrel=1
+pkgrel=2
 pkgdesc='Call R from R'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -15,8 +15,10 @@ depends=(
   r-r6
 )
 optdepends=(
+  r-asciicast
   r-cli
   r-covr
+  r-mockery
   r-ps
   r-rprojroot
   r-spelling

BioArchLinux/r-cancer/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=canceR
 _pkgver=1.32.0
 pkgname=r-${_pkgname,,}
 pkgver=1.32.0
-pkgrel=1
+pkgrel=2
 pkgdesc='A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -12,19 +12,22 @@ license=('GPL')
 depends=(
   r
   r-biobase
-  r-cgdsr
   r-circlize
   r-formula
   r-genetclassifier
   r-gseabase
+  r-httr
   r-phenotest
   r-plyr
+  r-r.methodss3
+  r-r.oo
   r-runit
-  r-tcltk2
   r-tkrplot
 )
 optdepends=(
-  r-r.rsp
+  r-biocstyle
+  r-knitr
+  r-rmarkdown
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-cancer/lilac.yaml

@@ -4,15 +4,16 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biobase
-- r-cgdsr
 - r-circlize
 - r-formula
 - r-genetclassifier
 - r-gseabase
+- r-httr
 - r-phenotest
 - r-plyr
+- r-r.methodss3
+- r-r.oo
 - r-runit
-- r-tcltk2
 - r-tkrplot
 update_on:
 - regex: canceR_([\d._-]+).tar.gz

BioArchLinux/r-cancersubtypes/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=CancerSubtypes
 _pkgver=1.24.0
 pkgname=r-${_pkgname,,}
 pkgver=1.24.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Cancer subtypes identification, validation and visualization based on multiple genomic data sets'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -12,7 +12,6 @@ license=('GPL')
 depends=(
   r
   r-consensusclusterplus
-  r-icluster
   r-impute
   r-limma
   r-nmf

BioArchLinux/r-cancersubtypes/lilac.yaml

@@ -4,7 +4,6 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-consensusclusterplus
-- r-icluster
 - r-impute
 - r-limma
 - r-nmf

BioArchLinux/r-car/PKGBUILD

@@ -6,7 +6,7 @@ _pkgname=car
 _pkgver=3.1-1
 pkgname=r-${_pkgname,,}
 pkgver=3.1.1
-pkgrel=1
+pkgrel=2
 pkgdesc='Companion to Applied Regression'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -16,9 +16,9 @@ depends=(
   r-abind
   r-cardata
   r-lme4
-  r-maptools
   r-pbkrtest
   r-quantreg
+  r-scales
 )
 optdepends=(
   r-alr4
@@ -30,6 +30,7 @@ optdepends=(
   r-lmtest
   r-matrix
   r-matrixmodels
+  r-mvtnorm
   r-rgl
   r-rio
   r-sandwich

BioArchLinux/r-car/lilac.yaml

@@ -6,9 +6,9 @@ repo_depends:
 - r-abind
 - r-cardata
 - r-lme4
-- r-maptools
 - r-pbkrtest
 - r-quantreg
+- r-scales
 update_on:
 - regex: car_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-cardinal/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=Cardinal
 _pkgver=3.0.1
 pkgname=r-${_pkgname,,}
 pkgver=3.0.1
-pkgrel=1
+pkgrel=2
 pkgdesc='A mass spectrometry imaging toolbox for statistical analysis'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -14,7 +14,6 @@ depends=(
   r-biobase
   r-biocgenerics
   r-biocparallel
-  r-dplyr
   r-ebimage
   r-irlba
   r-magrittr

BioArchLinux/r-cardinal/lilac.yaml

@@ -6,7 +6,6 @@ repo_depends:
 - r-biobase
 - r-biocgenerics
 - r-biocparallel
-- r-dplyr
 - r-ebimage
 - r-irlba
 - r-magrittr

BioArchLinux/r-caret/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=caret
 _pkgver=6.0-93
 pkgname=r-${_pkgname,,}
 pkgver=6.0.93
-pkgrel=2
+pkgrel=3
 pkgdesc='Classification and Regression Training'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -20,7 +20,6 @@ depends=(
   r-recipes
   r-reshape2
   r-withr
-  r-stringi
 )
 optdepends=(
   r-bradleyterry2

BioArchLinux/r-caret/lilac.yaml

@@ -12,7 +12,6 @@ repo_depends:
 - r-recipes
 - r-reshape2
 - r-withr
-- r-stringi
 update_on:
 - regex: caret_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-carnival/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=CARNIVAL
 _pkgver=2.8.0
 pkgname=r-${_pkgname,,}
 pkgver=2.8.0
-pkgrel=1
+pkgrel=2
 pkgdesc='A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -18,10 +18,15 @@ depends=(
   r-rjson
   r-rmarkdown
   r-stringr
+  r-tibble
   r-tidyr
 )
 optdepends=(
+  r-biocstyle
+  r-covr
   r-knitr
+  r-refmanager
+  r-sessioninfo
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")

BioArchLinux/r-carnival/lilac.yaml

@@ -10,6 +10,7 @@ repo_depends:
 - r-rjson
 - r-rmarkdown
 - r-stringr
+- r-tibble
 - r-tidyr
 update_on:
 - regex: CARNIVAL_([\d._-]+).tar.gz

BioArchLinux/r-catnet/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=catnet
 _pkgver=1.16.1
 pkgname=r-${_pkgname,,}
 pkgver=1.16.1
-pkgrel=1
+pkgrel=2
 pkgdesc='Categorical Bayesian Network Inference'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -12,7 +12,7 @@ license=('GPL')
 depends=(
   r
 )
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+source=("https://cran.r-project.org/src/contrib/Archive/${_pkgname}/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('fb0f055cd862d10533fa6c2d099bc54b42c1e3078c21a21bab98a7393962d5e1')
 
 build() {

BioArchLinux/r-catnet/lilac.yaml

@@ -5,5 +5,5 @@ maintainers:
 update_on:
 - regex: catnet_([\d._-]+).tar.gz
   source: regex
-  url: https://cran.r-project.org/package=catnet
+  url: https://cran.r-project.org/src/contrib/Archive/catnet
 - alias: r

BioArchLinux/r-cellarepertorium/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=CellaRepertorium
 _pkgver=1.8.0
 pkgname=r-${_pkgname,,}
 pkgver=1.8.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -15,6 +15,8 @@ depends=(
   r-biostrings
   r-dplyr
   r-forcats
+  r-generics
+  r-glue
   r-progress
   r-purrr
   r-rcpp

BioArchLinux/r-cellarepertorium/lilac.yaml

@@ -7,6 +7,8 @@ repo_depends:
 - r-biostrings
 - r-dplyr
 - r-forcats
+- r-generics
+- r-glue
 - r-progress
 - r-purrr
 - r-rcpp

BioArchLinux/r-cellnoptr/PKGBUILD

@@ -5,7 +5,7 @@ _pkgname=CellNOptR
 _pkgver=1.44.0
 pkgname=r-${_pkgname,,}
 pkgver=1.44.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -30,7 +30,7 @@ optdepends=(
   r-doparallel
   r-dplyr
   r-foreach
-  r-plyr
+  r-knitr
   r-readr
   r-runit
   r-tidyr

BioArchLinux/r-cgen/PKGBUILD

@@ -5,7 +5,7 @@ _pkgname=CGEN
 _pkgver=3.34.0
 pkgname=r-${_pkgname,,}
 pkgver=3.34.0
-pkgrel=1
+pkgrel=2
 pkgdesc="An R package for analysis of case-control studies in genetic epidemiology"
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -14,6 +14,9 @@ depends=(
   'r>=4.0'
    r-mvtnorm
 )
+optdepends=(
+  r-cluster
+)
 makedepends=(
   gcc-fortran
 )

BioArchLinux/r-changepoint/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=changepoint
 _pkgver=2.2.4
 pkgname=r-${_pkgname,,}
 pkgver=2.2.4
-pkgrel=1
+pkgrel=2
 pkgdesc='Methods for Changepoint Detection'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -15,6 +15,7 @@ depends=(
 )
 optdepends=(
   r-testthat
+  r-vdiffr
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('ac636fde7610137385dde1e3d8a22a2ff856a8d5c917c7ad1a5cc49f98b8649b')

BioArchLinux/r-chemminer/PKGBUILD

@@ -5,7 +5,7 @@ _pkgname=ChemmineR
 _pkgver=3.50.0
 pkgname=r-${_pkgname,,}
 pkgver=3.50.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Cheminformatics Toolkit for R'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -30,6 +30,7 @@ depends=(
   make
 )
 optdepends=(
+  r-bibtex
   r-biocmanager
   r-biocstyle
   r-chemminedrugs

BioArchLinux/r-chetah/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=CHETAH
 _pkgver=1.14.0
 pkgname=r-${_pkgname,,}
 pkgver=1.14.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Fast and accurate scRNA-seq cell type identification'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -16,7 +16,6 @@ depends=(
   r-cowplot
   r-dendextend
   r-ggplot2
-  r-gplots
   r-pheatmap
   r-plotly
   r-reshape2