update dependencies and url for R pkgs.

2025-03-10 12:02:42 +00:00 · 2023-10-26 21:50:08 +08:00 · 2023-10-26 21:50:08 +08:00 · 93067ef334
commit 93067ef334
parent bc1211ce90
651 changed files with 1794 additions and 823 deletions
--- a/BioArchLinux/r-aer/PKGBUILD
+++ b/BioArchLinux/r-aer/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=AER
 _pkgver=1.2-10
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=3
 pkgdesc="Applied Econometrics with R"
 arch=(any)
 url="https://cran.r-project.org/package=${_pkgname}"
@ -17,13 +17,20 @@ depends=(
  r-zoo
 )
 optdepends=(
+  r-boot
  r-dynlm
  r-effects
  r-fgarch
  r-forecast
+  r-foreign
  r-ineq
+  r-kernsmooth
+  r-lattice
  r-longmemo
+  r-mass
  r-mlogit
+  r-nlme
+  r-nnet
  r-np
  r-plm
  r-pscl
--- a/BioArchLinux/r-affy/PKGBUILD
+++ b/BioArchLinux/r-affy/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=affy
 _pkgver=1.80.0
 pkgname=r-${_pkgname,,}
 pkgver=1.80.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Methods for Affymetrix Oligonucleotide Arrays'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -20,6 +20,7 @@ depends=(
 )
 optdepends=(
  r-affydata
+  r-hgu95av2cdf
  r-tkwidgets
  r-widgettools
 )
--- a/BioArchLinux/r-affyplm/PKGBUILD
+++ b/BioArchLinux/r-affyplm/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=affyPLM
 _pkgver=1.78.0
 pkgname=r-${_pkgname,,}
 pkgver=1.78.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Methods for fitting probe-level models'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -20,6 +20,7 @@ depends=(
 )
 optdepends=(
  r-affydata
+  r-hgu95av2cdf
  r-mass
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
--- a/BioArchLinux/r-affyrnadegradation/PKGBUILD
+++ b/BioArchLinux/r-affyrnadegradation/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=AffyRNADegradation
 _pkgver=1.48.0
 pkgname=r-${_pkgname,,}
 pkgver=1.48.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Analyze and correct probe positional bias in microarray data due to RNA degradation'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -15,6 +15,7 @@ depends=(
 )
 optdepends=(
  r-ampaffyexample
+  r-hgu133acdf
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('0e7eb53d71df494ecd04dbf5db1643a40244467949981676407d6dec5912e944')
--- a/BioArchLinux/r-ahmassbank/PKGBUILD
+++ b/BioArchLinux/r-ahmassbank/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=AHMassBank
 _pkgver=1.0.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=3
 pkgdesc="MassBank Annotation Resources for AnnotationHub"
 arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
@ -17,6 +17,7 @@ optdepends=(
  r-biocstyle
  r-compounddb
  r-knitr
+  r-methods
  r-rmarkdown
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
--- a/BioArchLinux/r-alabaster.base/PKGBUILD
+++ b/BioArchLinux/r-alabaster.base/PKGBUILD
@ -4,19 +4,20 @@ _pkgname=alabaster.base
 _pkgver=1.0.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=3
 pkgdesc="Save Bioconductor Objects To File"
 arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
 license=(MIT)
 depends=(
+  zlib
  r-alabaster.schemas
  r-jsonlite
  r-jsonvalidate
  r-rcpp
  r-rhdf5
+  r-rhdf5lib
  r-s4vectors
-  zlib
 )
 makedepends=(
  r-rhdf5lib
@ -28,6 +29,7 @@ optdepends=(
  r-biocstyle
  r-digest
  r-knitr
+  r-matrix
  r-rmarkdown
  r-testthat
 )
--- a/BioArchLinux/r-alabaster.base/lilac.yaml
+++ b/BioArchLinux/r-alabaster.base/lilac.yaml
@ -8,6 +8,7 @@ repo_depends:
 - r-jsonvalidate
 - r-rcpp
 - r-rhdf5
+- r-rhdf5lib
 - r-s4vectors
 repo_makedepends:
 - r-rhdf5lib
--- a/BioArchLinux/r-alabaster.matrix/PKGBUILD
+++ b/BioArchLinux/r-alabaster.matrix/PKGBUILD
@ -4,27 +4,28 @@ _pkgname=alabaster.matrix
 _pkgver=1.0.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=3
 pkgdesc="Load and Save Artifacts from File"
 arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
 license=(MIT)
 depends=(
  r-alabaster.base
+  r-biocgenerics
  r-delayedarray
  r-hdf5array
  r-rhdf5
+  r-s4vectors
+  r-sparsearray
 )
 checkdepends=(
  r-chihaya
  r-testthat
 )
 optdepends=(
-  r-biocgenerics
  r-biocstyle
  r-chihaya
  r-knitr
-  r-s4vectors
  r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
--- a/BioArchLinux/r-alabaster.matrix/lilac.yaml
+++ b/BioArchLinux/r-alabaster.matrix/lilac.yaml
@ -4,9 +4,12 @@ maintainers:
  email: pekkarr@protonmail.com
 repo_depends:
 - r-alabaster.base
+- r-biocgenerics
 - r-delayedarray
 - r-hdf5array
 - r-rhdf5
+- r-s4vectors
+- r-sparsearray
 repo_makedepends:
 - r-chihaya
 - r-testthat
--- a/BioArchLinux/r-alabaster.spatial/PKGBUILD
+++ b/BioArchLinux/r-alabaster.spatial/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=alabaster.spatial
 _pkgver=1.0.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=3
 pkgdesc="Save and Load Spatial 'Omics Data to/from File"
 arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
@ -24,6 +24,7 @@ checkdepends=(
 optdepends=(
  r-biocstyle
  r-digest
+  r-dropletutils
  r-knitr
  r-magick
  r-png
--- a/BioArchLinux/r-aldex2/PKGBUILD
+++ b/BioArchLinux/r-aldex2/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=ALDEx2
 _pkgver=1.32.0
 pkgname=r-${_pkgname,,}
 pkgver=1.32.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Analysis Of Differential Abundance Taking Sample Variation Into Account'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -12,8 +12,10 @@ license=('custom')
 depends=(
  r
  r-biocparallel
+  r-directlabels
  r-genomicranges
  r-iranges
+  r-latticeextra
  r-multtest
  r-rfast
  r-s4vectors
@ -22,9 +24,15 @@ depends=(
 )
 optdepends=(
  r-biocstyle
+  r-cowplot
+  r-ggpattern
+  r-ggplot2
  r-knitr
+  r-magick
+  r-purrr
  r-rmarkdown
  r-testthat
+  r-tidyverse
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('6851a6513775996dd204e907f3e33d68bef35476d4fe046299778fce3162b33d')
--- a/BioArchLinux/r-aldex2/lilac.yaml
+++ b/BioArchLinux/r-aldex2/lilac.yaml
@ -4,8 +4,10 @@ maintainers:
  email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biocparallel
+- r-directlabels
 - r-genomicranges
 - r-iranges
+- r-latticeextra
 - r-multtest
 - r-rfast
 - r-s4vectors
--- a/BioArchLinux/r-alpine/PKGBUILD
+++ b/BioArchLinux/r-alpine/PKGBUILD
@ -4,10 +4,10 @@ _pkgname=alpine
 _pkgver=1.26.0
 pkgname=r-${_pkgname,,}
 pkgver=1.26.0
-pkgrel=1
+pkgrel=2
 pkgdesc='alpine'
 arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/3.17/${_pkgname}"
 license=('GPL')
 depends=(
  r
@ -35,7 +35,7 @@ optdepends=(
  r-rtracklayer
  r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('6be1cbe591d858f1e70bf3bb64718c3b7f12bdd4561e28da71fdd66069aaa4d5')

 build() {
--- a/BioArchLinux/r-alpine/lilac.yaml
+++ b/BioArchLinux/r-alpine/lilac.yaml
@ -19,5 +19,5 @@ repo_depends:
 update_on:
 - regex: alpine_([\d._-]+).tar.gz
  source: regex
-  url: https://bioconductor.org/packages/alpine
+  url: https://bioconductor.org/packages/3.17/alpine
 - alias: r
--- a/BioArchLinux/r-annotationdbi/PKGBUILD
+++ b/BioArchLinux/r-annotationdbi/PKGBUILD
@ -6,7 +6,7 @@ _pkgname=AnnotationDbi
 _pkgver=1.64.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=1
+pkgrel=2
 pkgdesc="Manipulation of SQLite-based annotations in Bioconductor"
 arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
@ -34,6 +34,7 @@ optdepends=(
  r-reactome.db
  r-runit
  r-txdb.hsapiens.ucsc.hg19.knowngene
+  r-utils
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 md5sums=('8fc5d588e8ad00911d07990484a9cff6')
--- a/BioArchLinux/r-annotationhub/PKGBUILD
+++ b/BioArchLinux/r-annotationhub/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=AnnotationHub
 _pkgver=3.10.0
 pkgname=r-${_pkgname,,}
 pkgver=3.10.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Client to access AnnotationHub resources'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -30,6 +30,8 @@ optdepends=(
  r-annotationhubdata
  r-biocstyle
  r-biostrings
+  r-compounddb
+  r-ensembldb
  r-experimenthub
  r-gdsfmt
  r-genomeinfodb
@ -37,6 +39,7 @@ optdepends=(
  r-genomicranges
  r-hubpub
  r-iranges
+  r-keras
  r-knitr
  r-msnbase
  r-mzr
--- a/BioArchLinux/r-anytime/PKGBUILD
+++ b/BioArchLinux/r-anytime/PKGBUILD
@ -6,12 +6,13 @@ _pkgname=anytime
 _pkgver=0.3.9
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=4
+pkgrel=5
 pkgdesc="Anything to 'POSIXct' or 'Date' Converter"
 arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
 license=(GPL)
 depends=(
+  r-bh
  r-rcpp
 )
 makedepends=(
--- a/BioArchLinux/r-anytime/lilac.yaml
+++ b/BioArchLinux/r-anytime/lilac.yaml
@ -3,6 +3,7 @@ maintainers:
 - github: pekkarr
  email: pekkarr@protonmail.com
 repo_depends:
+- r-bh
 - r-rcpp
 repo_makedepends:
 - r-bh
--- a/BioArchLinux/r-archive/PKGBUILD
+++ b/BioArchLinux/r-archive/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=archive
 _pkgver=1.1.6
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=3
 pkgdesc="Multi-Format Archive and Compression Support"
 arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
@ -12,6 +12,7 @@ license=(MIT)
 depends=(
  libarchive
  r-cli
+  r-cpp11
  r-glue
  r-rlang
  r-tibble
--- a/BioArchLinux/r-archive/lilac.yaml
+++ b/BioArchLinux/r-archive/lilac.yaml
@ -4,6 +4,7 @@ maintainers:
  email: pekkarr@protonmail.com
 repo_depends:
 - r-cli
+- r-cpp11
 - r-glue
 - r-rlang
 - r-tibble
--- a/BioArchLinux/r-arrow/PKGBUILD
+++ b/BioArchLinux/r-arrow/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=arrow
 _pkgver=13.0.0.1
 pkgname=r-${_pkgname,,}
 pkgver=13.0.0.1
-pkgrel=1
+pkgrel=2
 pkgdesc="Integration to 'Apache' 'Arrow'"
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -35,6 +35,7 @@ optdepends=(
  r-dplyr
  r-duckdb
  r-hms
+  r-jsonlite
  r-knitr
  r-lubridate
  r-pillar
--- a/BioArchLinux/r-aspediafi/PKGBUILD
+++ b/BioArchLinux/r-aspediafi/PKGBUILD
@ -4,10 +4,10 @@ _pkgname=ASpediaFI
 _pkgver=1.11.0
 pkgname=r-${_pkgname,,}
 pkgver=1.11.0
-pkgrel=2
+pkgrel=3
 pkgdesc='ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events'
 arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/3.17/${_pkgname}"
 license=('GPL')
 depends=(
  r
@ -39,7 +39,7 @@ depends=(
 optdepends=(
  r-knitr
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('bada73c70b81c82b88bd2a014b01d05a1eedde536a9df19311ae41a498f1568e')

 build() {
--- a/BioArchLinux/r-aspediafi/lilac.yaml
+++ b/BioArchLinux/r-aspediafi/lilac.yaml
@ -30,5 +30,5 @@ repo_depends:
 update_on:
 - regex: ASpediaFI_([\d._-]+).tar.gz
  source: regex
-  url: https://bioconductor.org/packages/ASpediaFI
+  url: https://bioconductor.org/packages/3.17/ASpediaFI
 - alias: r
--- a/BioArchLinux/r-assertive.code/PKGBUILD
+++ b/BioArchLinux/r-assertive.code/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=assertive.code
 _pkgver=0.0-4
 pkgname=r-${_pkgname,,}
 pkgver=0.0.4
-pkgrel=1
+pkgrel=2
 pkgdesc='Assertions to Check Properties of Code'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -18,7 +18,7 @@ depends=(
 optdepends=(
  r-testthat
 )
-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=('2f820474ed20e06f65b284962c87cd1e85220a11cc7fcde09716f0eee5821387')

 build() {
--- a/BioArchLinux/r-assertive.code/lilac.yaml
+++ b/BioArchLinux/r-assertive.code/lilac.yaml
@ -9,5 +9,5 @@ repo_depends:
 update_on:
 - regex: assertive.code_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=assertive.code
+  url: https://cran.r-project.org/src/contrib/Archive/assertive.code
 - alias: r
--- a/BioArchLinux/r-assertive.data.uk/PKGBUILD
+++ b/BioArchLinux/r-assertive.data.uk/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=assertive.data.uk
 _pkgver=0.0-2
 pkgname=r-${_pkgname,,}
 pkgver=0.0.2
-pkgrel=6
+pkgrel=7
 pkgdesc='Assertions to Check Properties of Strings'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -17,7 +17,7 @@ depends=(
 optdepends=(
  r-testthat
 )
-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=('ab48dab6977e8f43d6fffb33228d158865f68dde7026d123c693d77339dcf2bb')

 build() {
--- a/BioArchLinux/r-assertive.data.uk/lilac.yaml
+++ b/BioArchLinux/r-assertive.data.uk/lilac.yaml
@ -8,5 +8,5 @@ repo_depends:
 update_on:
 - regex: assertive.data.uk_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=assertive.data.uk
+  url: https://cran.r-project.org/src/contrib/Archive/assertive.data.uk
 - alias: r
--- a/BioArchLinux/r-assertive.data.us/PKGBUILD
+++ b/BioArchLinux/r-assertive.data.us/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=assertive.data.us
 _pkgver=0.0-2
 pkgname=r-${_pkgname,,}
 pkgver=0.0.2
-pkgrel=6
+pkgrel=7
 pkgdesc='Assertions to Check Properties of Strings'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -18,7 +18,7 @@ optdepends=(
  r-devtools
  r-testthat
 )
-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=('180e64dfe6339d25dd27d7fe9e77619ef697ef6e5bb6a3cf4fb732a681bdfaad')

 build() {
--- a/BioArchLinux/r-assertive.data.us/lilac.yaml
+++ b/BioArchLinux/r-assertive.data.us/lilac.yaml
@ -8,5 +8,5 @@ repo_depends:
 update_on:
 - regex: assertive.data.us_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=assertive.data.us
+  url: https://cran.r-project.org/src/contrib/Archive/assertive.data.us
 - alias: r
--- a/BioArchLinux/r-assertive.data/PKGBUILD
+++ b/BioArchLinux/r-assertive.data/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=assertive.data
 _pkgver=0.0-3
 pkgname=r-${_pkgname,,}
 pkgver=0.0.3
-pkgrel=6
+pkgrel=7
 pkgdesc='Assertions to Check Properties of Data'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -17,7 +17,7 @@ depends=(
 optdepends=(
  r-testthat
 )
-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=('5a00fb48ad870d9b3c872ce3d6aa20a7948687a980f49fe945b455339e789b01')

 build() {
--- a/BioArchLinux/r-assertive.data/lilac.yaml
+++ b/BioArchLinux/r-assertive.data/lilac.yaml
@ -8,5 +8,5 @@ repo_depends:
 update_on:
 - regex: assertive.data_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=assertive.data
+  url: https://cran.r-project.org/src/contrib/Archive/assertive.data
 - alias: r
--- a/BioArchLinux/r-assertive.datetimes/PKGBUILD
+++ b/BioArchLinux/r-assertive.datetimes/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=assertive.datetimes
 _pkgver=0.0-3
 pkgname=r-${_pkgname,,}
 pkgver=0.0.3
-pkgrel=6
+pkgrel=7
 pkgdesc='Assertions to Check Properties of Dates and Times'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -17,7 +17,7 @@ depends=(
 optdepends=(
  r-testthat
 )
-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=('014e2162f5a8d95138ed8330f7477e71c908a29341697c09a1b7198b7e012d94')

 build() {
--- a/BioArchLinux/r-assertive.datetimes/lilac.yaml
+++ b/BioArchLinux/r-assertive.datetimes/lilac.yaml
@ -8,5 +8,5 @@ repo_depends:
 update_on:
 - regex: assertive.datetimes_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=assertive.datetimes
+  url: https://cran.r-project.org/src/contrib/Archive/assertive.datetimes
 - alias: r
--- a/BioArchLinux/r-assertive.properties/PKGBUILD
+++ b/BioArchLinux/r-assertive.properties/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=assertive.properties
 _pkgver=0.0-5
 pkgname=r-${_pkgname,,}
 pkgver=0.0.5
-pkgrel=5
+pkgrel=6
 pkgdesc='Assertions to Check Properties of Variables'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -16,7 +16,7 @@ depends=(
 optdepends=(
  r-testthat
 )
-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=('b68954f53082561f0242682611bf3373e0bf30d8ac2256d82474edc5f992f4dd')

 build() {
--- a/BioArchLinux/r-assertive.properties/lilac.yaml
+++ b/BioArchLinux/r-assertive.properties/lilac.yaml
@ -7,5 +7,5 @@ repo_depends:
 update_on:
 - regex: assertive.properties_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=assertive.properties
+  url: https://cran.r-project.org/src/contrib/Archive/assertive.properties
 - alias: r
--- a/BioArchLinux/r-assertive.strings/PKGBUILD
+++ b/BioArchLinux/r-assertive.strings/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=assertive.strings
 _pkgver=0.0-3
 pkgname=r-${_pkgname,,}
 pkgver=0.0.3
-pkgrel=6
+pkgrel=7
 pkgdesc='Assertions to Check Properties of Strings'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -18,7 +18,7 @@ depends=(
 optdepends=(
  r-testthat
 )
-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=('d541d608a01640347d661cc9a67af8202904142031a20caa270f1c83d0ccd258')

 build() {
--- a/BioArchLinux/r-assertive.strings/lilac.yaml
+++ b/BioArchLinux/r-assertive.strings/lilac.yaml
@ -9,5 +9,5 @@ repo_depends:
 update_on:
 - regex: assertive.strings_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=assertive.strings
+  url: https://cran.r-project.org/src/contrib/Archive/assertive.strings
 - alias: r
--- a/BioArchLinux/r-assertive.types/PKGBUILD
+++ b/BioArchLinux/r-assertive.types/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=assertive.types
 _pkgver=0.0-3
 pkgname=r-${_pkgname,,}
 pkgver=0.0.3
-pkgrel=6
+pkgrel=7
 pkgdesc='Assertions to Check Types of Variables'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -20,7 +20,7 @@ optdepends=(
  r-testthat
  r-xml2
 )
-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=('ab6db2eb926e7bc885f2043fab679330aa336d07755375282d89bf9f9d0cb87f')

 build() {
--- a/BioArchLinux/r-assertive.types/lilac.yaml
+++ b/BioArchLinux/r-assertive.types/lilac.yaml
@ -8,5 +8,5 @@ repo_depends:
 update_on:
 - regex: assertive.types_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=assertive.types
+  url: https://cran.r-project.org/src/contrib/Archive/assertive.types
 - alias: r
--- a/BioArchLinux/r-assertive/PKGBUILD
+++ b/BioArchLinux/r-assertive/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=assertive
 _pkgver=0.3-6
 pkgname=r-${_pkgname,,}
 pkgver=0.3.6
-pkgrel=6
+pkgrel=7
 pkgdesc='Readable Check Functions to Ensure Code Integrity'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -32,7 +32,7 @@ optdepends=(
  r-markdown
  r-testthat
 )
-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=('c403169e83c433b65e911f7fd640b378e2a4a4765a36063584b8458168a4ea0a')

 build() {
--- a/BioArchLinux/r-assertive/lilac.yaml
+++ b/BioArchLinux/r-assertive/lilac.yaml
@ -22,5 +22,5 @@ repo_depends:
 update_on:
 - regex: assertive_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=assertive
+  url: https://cran.r-project.org/src/contrib/Archive/assertive
 - alias: r
--- a/BioArchLinux/r-bamlss/PKGBUILD
+++ b/BioArchLinux/r-bamlss/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=bamlss
 _pkgver=1.2-1
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-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=${_pkgname}"
@ -35,6 +35,8 @@ optdepends=(
  r-knitr
  r-mapdata
  r-maps
+  r-mass
+  r-nnet
  r-rjags
  r-rmarkdown
  r-scoringrules
--- a/BioArchLinux/r-base64enc/PKGBUILD
+++ b/BioArchLinux/r-base64enc/PKGBUILD
@ -8,7 +8,7 @@ _pkgname=base64enc
 _pkgver=0.1-3
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=10
+pkgrel=11
 pkgdesc="Tools for base64 encoding"
 arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
@ -16,6 +16,9 @@ license=(GPL)
 depends=(
  r
 )
+optdepends=(
+  r-png
+)
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 md5sums=('0f476dacdd11a3e0ad56d13f5bc2f190')
 sha256sums=('6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d')
--- a/BioArchLinux/r-bayesfactor/PKGBUILD
+++ b/BioArchLinux/r-bayesfactor/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=BayesFactor
 _pkgver=0.9.12-4.5
 pkgname=r-${_pkgname,,}
 pkgver=0.9.12.4.5
-pkgrel=1
+pkgrel=2
 pkgdesc='Computation of Bayes Factors for Common Designs'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -28,6 +28,7 @@ optdepends=(
  r-languager
  r-lme4
  r-markdown
+  r-rmarkdown
  r-testthat
  r-xtable
 )
--- a/BioArchLinux/r-bayesm/PKGBUILD
+++ b/BioArchLinux/r-bayesm/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=bayesm
 _pkgver=3.1-6
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=3
 pkgdesc="Bayesian Inference for Marketing/Micro-Econometrics"
 arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
@ -14,6 +14,7 @@ depends=(
  blas
  lapack
  r-rcpp
+  r-rcpparmadillo
 )
 makedepends=(
  r-rcpparmadillo
--- a/BioArchLinux/r-bayesm/lilac.yaml
+++ b/BioArchLinux/r-bayesm/lilac.yaml
@ -4,6 +4,7 @@ maintainers:
  email: pekkarr@protonmail.com
 repo_depends:
 - r-rcpp
+- r-rcpparmadillo
 repo_makedepends:
 - r-rcpparmadillo
 update_on:
--- a/BioArchLinux/r-bayesrel/PKGBUILD
+++ b/BioArchLinux/r-bayesrel/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=Bayesrel
 _pkgver=0.7.7
 pkgname=r-${_pkgname,,}
 pkgver=0.7.7
-pkgrel=1
+pkgrel=2
 pkgdesc='Bayesian Reliability Estimation'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -21,7 +21,7 @@ depends=(
 optdepends=(
  r-knitr
  r-rmarkdown
-  r-testthat
+  r-tinytest
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('ed41d6dcf3adf55fc65dad7aec91fec2dfedfc2340bcc0bbfd4d4728e9bcdb30')
--- a/BioArchLinux/r-bayesrel/lilac.yaml
+++ b/BioArchLinux/r-bayesrel/lilac.yaml
@ -1,15 +1,15 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: sukanka
+- github: sukanka
 repo_depends:
-  - r-coda
-  - r-laplacesdemon
-  - r-lavaan
-  - r-rcpp
-  - r-rcpparmadillo
-  - r-rdpack
+- r-coda
+- r-laplacesdemon
+- r-lavaan
+- r-rcpp
+- r-rcpparmadillo
+- r-rdpack
 update_on:
-  - regex: Bayesrel_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=Bayesrel/
-  - alias: r
+- regex: Bayesrel_([\d._-]+).tar.gz
+  source: regex
+  url: https://cran.r-project.org/package=Bayesrel
+- alias: r
--- a/BioArchLinux/r-bayestools/PKGBUILD
+++ b/BioArchLinux/r-bayestools/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=BayesTools
 _pkgver=0.2.16
 pkgname=r-${_pkgname,,}
 pkgver=0.2.16
-pkgrel=1
+pkgrel=2
 pkgdesc='Tools for Bayesian Analyses'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -19,6 +19,7 @@ depends=(
  r-ggplot2
  r-mvtnorm
  r-rdpack
+  r-rlang
 )
 optdepends=(
  r-bayesfactor
--- a/BioArchLinux/r-bayestools/lilac.yaml
+++ b/BioArchLinux/r-bayestools/lilac.yaml
@ -9,6 +9,7 @@ repo_depends:
 - r-ggplot2
 - r-mvtnorm
 - r-rdpack
+- r-rlang
 update_on:
 - regex: BayesTools_([\d._-]+).tar.gz
  source: regex
--- a/BioArchLinux/r-beachmat/PKGBUILD
+++ b/BioArchLinux/r-beachmat/PKGBUILD
@ -5,17 +5,18 @@ _pkgname=beachmat
 _pkgver=2.16.0
 pkgname=r-${_pkgname,,}
 pkgver=2.16.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Compiling Bioconductor to Handle Each Matrix Type'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('GPL')
 depends=(
+  gcc
  r
  r-biocgenerics
  r-delayedarray
  r-rcpp
-  gcc
+  r-sparsearray
 )
 optdepends=(
  r-biocparallel
--- a/BioArchLinux/r-beachmat/lilac.yaml
+++ b/BioArchLinux/r-beachmat/lilac.yaml
@ -6,6 +6,7 @@ repo_depends:
 - r-biocgenerics
 - r-delayedarray
 - r-rcpp
+- r-sparsearray
 update_on:
 - regex: beachmat_([\d._-]+).tar.gz
  source: regex
--- a/BioArchLinux/r-benchdamic/PKGBUILD
+++ b/BioArchLinux/r-benchdamic/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=benchdamic
 _pkgver=1.6.4
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=1
+pkgrel=2
 pkgdesc="Benchmark of differential abundance methods on microbiome data"
 arch=(any)
 url="https://bioconductor.org/packages/${_pkgname}"
@ -30,6 +30,7 @@ depends=(
  r-metagenomeseq
  r-mglm
  r-microbiomestat
+  r-mixomics
  r-noiseq
  r-phyloseq
  r-plyr
--- a/BioArchLinux/r-benchdamic/lilac.yaml
+++ b/BioArchLinux/r-benchdamic/lilac.yaml
@ -22,6 +22,7 @@ repo_depends:
 - r-metagenomeseq
 - r-mglm
 - r-microbiomestat
+- r-mixomics
 - r-noiseq
 - r-phyloseq
 - r-plyr
--- a/BioArchLinux/r-biganalytics/PKGBUILD
+++ b/BioArchLinux/r-biganalytics/PKGBUILD
@ -5,15 +5,20 @@ _pkgname=biganalytics
 _pkgver=1.1.21
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=7
+pkgrel=8
 pkgdesc="Utilities for 'big.matrix' Objects from Package 'bigmemory'"
 arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
 license=(Apache LGPL3)
 depends=(
+  r-bh
  r-biglm
  r-bigmemory
  r-foreach
+  r-rcpp
+)
+optdepends=(
+  r-methods
 )
 makedepends=(
  r-bh
--- a/BioArchLinux/r-biganalytics/lilac.yaml
+++ b/BioArchLinux/r-biganalytics/lilac.yaml
@ -3,9 +3,11 @@ maintainers:
 - github: pekkarr
  email: pekkarr@protonmail.com
 repo_depends:
+- r-bh
 - r-biglm
 - r-bigmemory
 - r-foreach
+- r-rcpp
 repo_makedepends:
 - r-bh
 - r-rcpp
--- a/BioArchLinux/r-bigmemory/PKGBUILD
+++ b/BioArchLinux/r-bigmemory/PKGBUILD
@ -5,12 +5,13 @@ _pkgname=bigmemory
 _pkgver=4.6.1
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=6
+pkgrel=7
 pkgdesc="Manage Massive Matrices with Shared Memory and Memory-Mapped Files"
 arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
 license=(Apache LGPL3)
 depends=(
+  r-bh
  r-bigmemory.sri
  r-rcpp
  r-uuid
@ -22,6 +23,8 @@ checkdepends=(
  r-testthat
 )
 optdepends=(
+  r-biganalytics
+  r-bigtabulate
  r-remotes
  r-testthat
 )
--- a/BioArchLinux/r-bigmemory/lilac.yaml
+++ b/BioArchLinux/r-bigmemory/lilac.yaml
@ -3,6 +3,7 @@ maintainers:
 - github: pekkarr
  email: pekkarr@protonmail.com
 repo_depends:
+- r-bh
 - r-bigmemory.sri
 - r-rcpp
 - r-uuid
--- a/BioArchLinux/r-bindingsitefinder/PKGBUILD
+++ b/BioArchLinux/r-bindingsitefinder/PKGBUILD
@ -4,35 +4,52 @@ _pkgname=BindingSiteFinder
 _pkgver=1.6.0
 pkgname=r-${_pkgname,,}
 pkgver=1.6.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Binding site defintion based on iCLIP data'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
  r
+  r-complexheatmap
  r-dplyr
+  r-forcats
  r-genomeinfodb
+  r-genomicfeatures
  r-genomicranges
+  r-ggdist
  r-ggforce
  r-ggplot2
-  r-gviz
+  r-iranges
+  r-kableextra
+  r-lifecycle
  r-matrixstats
  r-plyr
+  r-rcolorbrewer
+  r-rlang
  r-rtracklayer
  r-s4vectors
  r-tibble
  r-tidyr
 )
 optdepends=(
+  r-ashr
  r-biocstyle
-  r-complexheatmap
-  r-forcats
+  r-deseq2
  r-genomicalignments
+  r-ggally
+  r-ggplotify
+  r-ggpointdensity
+  r-ggrastr
+  r-gviz
  r-knitr
+  r-patchwork
  r-rmarkdown
  r-scales
+  r-summarizedexperiment
  r-testthat
+  r-viridis
+  r-xlsx
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('e648fc497ecaabd9de283a7f58d773924a7edaa94a02d9c339c19e2c6b8ba998')
--- a/BioArchLinux/r-bindingsitefinder/lilac.yaml
+++ b/BioArchLinux/r-bindingsitefinder/lilac.yaml
@ -3,14 +3,22 @@ maintainers:
 - github: starsareintherose
  email: kuoi@bioarchlinux.org
 repo_depends:
+- r-complexheatmap
 - r-dplyr
+- r-forcats
 - r-genomeinfodb
+- r-genomicfeatures
 - r-genomicranges
+- r-ggdist
 - r-ggforce
 - r-ggplot2
- r-gviz
+- r-iranges
+- r-kableextra
+- r-lifecycle
 - r-matrixstats
 - r-plyr
+- r-rcolorbrewer
+- r-rlang
 - r-rtracklayer
 - r-s4vectors
 - r-tibble
--- a/BioArchLinux/r-bioccheck/PKGBUILD
+++ b/BioArchLinux/r-bioccheck/PKGBUILD
@ -4,16 +4,18 @@ _pkgname=BiocCheck
 _pkgver=1.36.1
 pkgname=r-${_pkgname,,}
 pkgver=1.36.1
-pkgrel=1
+pkgrel=2
 pkgdesc='Bioconductor-specific package checks'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
  r
+  r-biocbaseutils
  r-biocfilecache
  r-biocmanager
  r-biocviews
+  r-callr
  r-graph
  r-httr
  r-knitr
@ -23,9 +25,10 @@ optdepends=(
  r-biobase
  r-biocgenerics
  r-biocstyle
-  r-callr
  r-devtools
  r-downloader
+  r-genomicranges
+  r-gert
  r-jsonlite
  r-rmarkdown
  r-runit
--- a/BioArchLinux/r-bioccheck/lilac.yaml
+++ b/BioArchLinux/r-bioccheck/lilac.yaml
@ -3,9 +3,11 @@ maintainers:
 - github: starsareintherose
  email: kuoi@bioarchlinux.org
 repo_depends:
+- r-biocbaseutils
 - r-biocfilecache
 - r-biocmanager
 - r-biocviews
+- r-callr
 - r-graph
 - r-httr
 - r-knitr
--- a/BioArchLinux/r-biocdockermanager/PKGBUILD
+++ b/BioArchLinux/r-biocdockermanager/PKGBUILD
@ -5,10 +5,10 @@ _pkgname=BiocDockerManager
 _pkgver=1.11.0
 pkgname=r-${_pkgname,,}
 pkgver=1.11.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Access Bioconductor docker images'
 arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/3.17/${_pkgname}"
 license=('Artistic2.0')
 depends=(
  r
@ -25,7 +25,7 @@ optdepends=(
  r-rmarkdown
  r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('d3cbab0f6ccad2ac50163d56d938d4ddb2f24864c27d09a6bda38848821b6970')

 build() {
--- a/BioArchLinux/r-biocdockermanager/lilac.yaml
+++ b/BioArchLinux/r-biocdockermanager/lilac.yaml
@ -11,5 +11,5 @@ repo_depends:
 update_on:
 - regex: BiocDockerManager_([\d._-]+).tar.gz
  source: regex
-  url: https://bioconductor.org/packages/BiocDockerManager
+  url: https://bioconductor.org/packages/3.17/BiocDockerManager
 - alias: r
--- a/BioArchLinux/r-biocor/PKGBUILD
+++ b/BioArchLinux/r-biocor/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=BioCor
 _pkgver=1.26.0
 pkgname=r-${_pkgname,,}
 pkgver=1.26.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Functional similarities'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -19,6 +19,7 @@ optdepends=(
  r-biocstyle
  r-boot
  r-deseq2
+  r-ggplot2
  r-gosemsim
  r-hmisc
  r-knitr
--- a/BioArchLinux/r-biocparallel/PKGBUILD
+++ b/BioArchLinux/r-biocparallel/PKGBUILD
@ -8,12 +8,14 @@ _pkgname=BiocParallel
 _pkgver=1.36.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=1
+pkgrel=2
 pkgdesc="Bioconductor facilities for parallel evaluation"
 arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
 license=(GPL)
 depends=(
+  r-bh
+  r-cpp11
  r-futile.logger
  r-snow
 )
@ -32,10 +34,12 @@ optdepends=(
  r-genomicalignments
  r-genomicranges
  r-knitr
+  r-rmpi
  r-rnaseqdata.hnrnpc.bam.chr14
  r-rsamtools
  r-runit
  r-shortread
+  r-tools
  r-txdb.hsapiens.ucsc.hg19.knowngene
  r-variantannotation
 )
--- a/BioArchLinux/r-biocparallel/lilac.yaml
+++ b/BioArchLinux/r-biocparallel/lilac.yaml
@ -3,6 +3,8 @@ maintainers:
 - github: pekkarr
  email: pekkarr@protonmail.com
 repo_depends:
+- r-bh
+- r-cpp11
 - r-futile.logger
 - r-snow
 repo_makedepends:
--- a/BioArchLinux/r-biodb/PKGBUILD
+++ b/BioArchLinux/r-biodb/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=biodb
 _pkgver=1.10.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=1
+pkgrel=2
 pkgdesc="biodb, a library and a development framework for connecting to chemical and biological databases"
 arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
@ -26,6 +26,7 @@ depends=(
  r-rcurl
  r-rsqlite
  r-stringr
+  r-testthat
  r-withr
  r-xml
  r-yaml
--- a/BioArchLinux/r-biodb/lilac.yaml
+++ b/BioArchLinux/r-biodb/lilac.yaml
@ -18,6 +18,7 @@ repo_depends:
 - r-rcurl
 - r-rsqlite
 - r-stringr
+- r-testthat
 - r-withr
 - r-xml
 - r-yaml
--- a/BioArchLinux/r-biodbhmdb/PKGBUILD
+++ b/BioArchLinux/r-biodbhmdb/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=biodbHmdb
 _pkgver=1.8.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=1
+pkgrel=2
 pkgdesc="biodbHmdb, a library for connecting to the HMDB Database"
 arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
@ -14,6 +14,7 @@ depends=(
  r-biodb
  r-r6
  r-rcpp
+  r-testthat
  r-zip
 )
 makedepends=(
--- a/BioArchLinux/r-biodbhmdb/lilac.yaml
+++ b/BioArchLinux/r-biodbhmdb/lilac.yaml
@ -6,6 +6,7 @@ repo_depends:
 - r-biodb
 - r-r6
 - r-rcpp
+- r-testthat
 - r-zip
 repo_makedepends:
 - r-testthat
--- a/BioArchLinux/r-biostrings/PKGBUILD
+++ b/BioArchLinux/r-biostrings/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=Biostrings
 _pkgver=2.70.0
 pkgname=r-${_pkgname,,}
 pkgver=2.70.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Efficient manipulation of biological strings'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -21,6 +21,7 @@ depends=(
 optdepends=(
  r-affy
  r-affydata
+  r-biocstyle
  r-bsgenome
  r-bsgenome.celegans.ucsc.ce2
  r-bsgenome.dmelanogaster.ucsc.dm3
@ -30,6 +31,7 @@ optdepends=(
  r-hgu133aprobe
  r-hgu95av2cdf
  r-hgu95av2probe
+  r-knitr
  r-rmpi
  r-runit
 )
--- a/BioArchLinux/r-bluster/PKGBUILD
+++ b/BioArchLinux/r-bluster/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=bluster
 _pkgver=1.12.0
 pkgname=r-${_pkgname,,}
 pkgver=1.12.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Clustering Algorithms for Bioconductor'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -22,7 +22,9 @@ depends=(
 optdepends=(
  r-apcluster
  r-biocstyle
+  r-dirichletmultinomial
  r-dynamictreecut
+  r-fastcluster
  r-knitr
  r-kohonen
  r-mbkmeans
@ -33,6 +35,7 @@ optdepends=(
  r-scrnaseq
  r-scuttle
  r-testthat
+  r-vegan
  r-viridis
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
--- a/BioArchLinux/r-bnem/PKGBUILD
+++ b/BioArchLinux/r-bnem/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=bnem
 _pkgver=1.10.0
 pkgname=r-${_pkgname,,}
 pkgver=1.10.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Training of logical models from indirect measurements of perturbation experiments'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -33,6 +33,7 @@ optdepends=(
  r-biocstyle
  r-knitr
  r-matrixgenerics
+  r-runit
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('ba3014cf2a72af41a66cc61a1cb35c7b755bf3c69205d866b0258cd697c98572')
--- a/BioArchLinux/r-bnlearn/PKGBUILD
+++ b/BioArchLinux/r-bnlearn/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=bnlearn
 _pkgver=4.9
 pkgname=r-${_pkgname,,}
 pkgver=4.9
-pkgrel=1
+pkgrel=2
 pkgdesc='Bayesian Network Structure Learning, Parameter Learning and Inference'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -16,6 +16,7 @@ optdepends=(
  r-gmp
  r-grain
  r-graph
+  r-grbase
  r-igraph
  r-lattice
  r-parallel
--- a/BioArchLinux/r-broom/PKGBUILD
+++ b/BioArchLinux/r-broom/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=broom
 _pkgver=1.0.5
 pkgname=r-${_pkgname,,}
 pkgver=1.0.5
-pkgrel=1
+pkgrel=2
 pkgdesc='Convert Statistical Objects into Tidy Tibbles'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -69,7 +69,6 @@ optdepends=(
  r-lmtest
  r-lsmeans
  r-maps
-  r-maptools
  r-margins
  r-mass
  r-mclust
@ -90,7 +89,6 @@ optdepends=(
  r-polca
  r-psych
  r-quantreg
-  r-rgeos
  r-rmarkdown
  r-robust
  r-robustbase
--- a/BioArchLinux/r-bsgenome/PKGBUILD
+++ b/BioArchLinux/r-bsgenome/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=BSgenome
 _pkgver=1.68.0
 pkgname=r-${_pkgname,,}
 pkgver=1.68.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Software infrastructure for efficient representation of full genomes and their SNPs'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -12,6 +12,7 @@ license=('Artistic2.0')
 depends=(
  r
  r-biocgenerics
+  r-biocio
  r-biostrings
  r-genomeinfodb
  r-genomicranges
@ -32,6 +33,7 @@ optdepends=(
  r-bsgenome.mmusculus.ucsc.mm10
  r-bsgenome.rnorvegicus.ucsc.rn5
  r-bsgenome.scerevisiae.ucsc.saccer1
+  r-bsgenomeforge
  r-hgu95av2probe
  r-runit
  r-snplocs.hsapiens.dbsnp144.grch38
--- a/BioArchLinux/r-bsgenome/lilac.yaml
+++ b/BioArchLinux/r-bsgenome/lilac.yaml
@ -4,6 +4,7 @@ maintainers:
  email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biocgenerics
+- r-biocio
 - r-biostrings
 - r-genomeinfodb
 - r-genomicranges
--- a/BioArchLinux/r-busparse/PKGBUILD
+++ b/BioArchLinux/r-busparse/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=BUSpaRse
 _pkgver=1.14.1
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=3
 pkgdesc="kallisto | bustools R utilities"
 arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
@ -13,6 +13,7 @@ license=(BSD)
 depends=(
  r-annotationdbi
  r-annotationfilter
+  r-bh
  r-biocgenerics
  r-biomart
  r-biostrings
@ -27,6 +28,8 @@ depends=(
  r-magrittr
  r-plyranges
  r-rcpp
+  r-rcpparmadillo
+  r-rcppprogress
  r-s4vectors
  r-stringr
  r-tibble
--- a/BioArchLinux/r-busparse/lilac.yaml
+++ b/BioArchLinux/r-busparse/lilac.yaml
@ -5,6 +5,7 @@ maintainers:
 repo_depends:
 - r-annotationdbi
 - r-annotationfilter
+- r-bh
 - r-biocgenerics
 - r-biomart
 - r-biostrings
@ -19,6 +20,8 @@ repo_depends:
 - r-magrittr
 - r-plyranges
 - r-rcpp
+- r-rcpparmadillo
+- r-rcppprogress
 - r-s4vectors
 - r-stringr
 - r-tibble
--- a/BioArchLinux/r-butcher/PKGBUILD
+++ b/BioArchLinux/r-butcher/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=butcher
 _pkgver=0.3.3
 pkgname=r-${_pkgname,,}
 pkgver=0.3.3
-pkgrel=1
+pkgrel=2
 pkgdesc='Model Butcher'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -42,6 +42,7 @@ optdepends=(
  r-mda
  r-mgcv
  r-modeldata
+  r-nestedmodels
  r-nnet
  r-parsnip
  r-pkgload
@ -59,6 +60,7 @@ optdepends=(
  r-survival
  r-testthat
  r-th.data
+  r-tidyr
  r-usethis
  r-xgboost
  r-xrf
--- a/BioArchLinux/r-butcher/lilac.yaml
+++ b/BioArchLinux/r-butcher/lilac.yaml
@ -1,17 +1,17 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: sukanka
+- github: sukanka
 repo_depends:
-  - r-cli
-  - r-lobstr
-  - r-purrr
-  - r-rlang
-  - r-tibble
-  - r-vctrs
+- r-cli
+- r-lobstr
+- r-purrr
+- r-rlang
+- r-tibble
+- r-vctrs
 post_build_script: |
  git_pkgbuild_commit()
  update_aur_repo()
 update_on:
-  - regex: butcher_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=butcher
+- regex: butcher_([\d._-]+).tar.gz
+  source: regex
+  url: https://cran.r-project.org/package=butcher
--- a/BioArchLinux/r-cageminer/PKGBUILD
+++ b/BioArchLinux/r-cageminer/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=cageminer
 _pkgver=1.6.2
 pkgname=r-${_pkgname,,}
 pkgver=1.6.2
-pkgrel=1
+pkgrel=2
 pkgdesc='Candidate Gene Miner'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -19,6 +19,7 @@ depends=(
  r-ggtext
  r-iranges
  r-reshape2
+  r-rlang
 )
 optdepends=(
  r-biocstyle
--- a/BioArchLinux/r-cageminer/lilac.yaml
+++ b/BioArchLinux/r-cageminer/lilac.yaml
@ -11,6 +11,7 @@ repo_depends:
 - r-ggtext
 - r-iranges
 - r-reshape2
+- r-rlang
 update_on:
 - regex: cageminer_([\d._-]+).tar.gz
  source: regex
--- a/BioArchLinux/r-cairo/PKGBUILD
+++ b/BioArchLinux/r-cairo/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=Cairo
 _pkgver=1.6-1
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=3
+pkgrel=4
 pkgdesc="R Graphics Device using Cairo Graphics Library for Creating High-Quality Bitmap (PNG, JPEG, TIFF), Vector (PDF, SVG, PostScript) and Display (X11 and Win32) Output"
 arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
@ -22,6 +22,7 @@ depends=(
  r
 )
 optdepends=(
+  r-fastrweb
  r-png
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
--- a/BioArchLinux/r-car/PKGBUILD
+++ b/BioArchLinux/r-car/PKGBUILD
@ -9,7 +9,7 @@ _pkgname=car
 _pkgver=3.1-2
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=3
+pkgrel=4
 pkgdesc="Companion to Applied Regression"
 arch=(any)
 url="https://cran.r-project.org/package=${_pkgname}"
@ -24,11 +24,13 @@ depends=(
 )
 optdepends=(
  r-alr4
+  r-boot
  r-coxme
  r-effects
  r-knitr
  r-leaps
  r-lmtest
+  r-matrix
  r-matrixmodels
  r-mvtnorm
  r-rgl
@ -36,6 +38,7 @@ optdepends=(
  r-sandwich
  r-sparsem
  r-survey
+  r-survival
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 md5sums=('f8be85a665aa367951aacf80d89eb5e9')
--- a/BioArchLinux/r-cardinal/PKGBUILD
+++ b/BioArchLinux/r-cardinal/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=Cardinal
 _pkgver=3.2.1
 pkgname=r-${_pkgname,,}
 pkgver=3.2.1
-pkgrel=1
+pkgrel=2
 pkgdesc='A mass spectrometry imaging toolbox for statistical analysis'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -14,6 +14,7 @@ depends=(
  r-biobase
  r-biocgenerics
  r-biocparallel
+  r-cardinalio
  r-ebimage
  r-irlba
  r-magrittr
@ -22,7 +23,6 @@ depends=(
  r-protgenerics
  r-s4vectors
  r-signal
-  r-sp
  r-viridislite
 )
 optdepends=(
--- a/BioArchLinux/r-cardinal/lilac.yaml
+++ b/BioArchLinux/r-cardinal/lilac.yaml
@ -6,6 +6,7 @@ repo_depends:
 - r-biobase
 - r-biocgenerics
 - r-biocparallel
+- r-cardinalio
 - r-ebimage
 - r-irlba
 - r-magrittr
@ -14,7 +15,6 @@ repo_depends:
 - r-protgenerics
 - r-s4vectors
 - r-signal
- r-sp
 - r-viridislite
 update_on:
 - regex: Cardinal_([\d._-]+).tar.gz
--- a/BioArchLinux/r-caret/PKGBUILD
+++ b/BioArchLinux/r-caret/PKGBUILD
@ -9,7 +9,7 @@ _pkgname=caret
 _pkgver=6.0-94
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=3
+pkgrel=4
 pkgdesc="Classification and Regression Training"
 arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
@ -49,9 +49,13 @@ optdepends=(
  r-kernlab
  r-klar
  r-knitr
+  r-mass
+  r-matrix
  r-mda
+  r-mgcv
  r-mlbench
  r-mlmetrics
+  r-nnet
  r-pamr
  r-party
  r-pls
@ -59,6 +63,7 @@ optdepends=(
  r-randomforest
  r-rann
  r-rmarkdown
+  r-rpart
  r-spls
  r-subselect
  r-superpc
--- a/BioArchLinux/r-catalyst/PKGBUILD
+++ b/BioArchLinux/r-catalyst/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=CATALYST
 _pkgver=1.24.0
 pkgname=r-${_pkgname,,}
 pkgver=1.24.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Cytometry dATa anALYSis Tools'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -24,7 +24,6 @@ depends=(
  r-ggrepel
  r-ggridges
  r-gridextra
-  r-magrittr
  r-matrixstats
  r-nnls
  r-purrr
--- a/BioArchLinux/r-catalyst/lilac.yaml
+++ b/BioArchLinux/r-catalyst/lilac.yaml
@ -16,7 +16,6 @@ repo_depends:
 - r-ggrepel
 - r-ggridges
 - r-gridextra
- r-magrittr
 - r-matrixstats
 - r-nnls
 - r-purrr
--- a/BioArchLinux/r-catdata/PKGBUILD
+++ b/BioArchLinux/r-catdata/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=catdata
 _pkgver=1.2.3
 pkgname=r-${_pkgname,,}
 pkgver=1.2.3
-pkgrel=1
+pkgrel=2
 pkgdesc='Categorical Data'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -17,7 +17,6 @@ optdepends=(
  r-e1071
  r-ecdat
  r-flexmix
-  r-gamboost
  r-gee
  r-geepack
  r-glmmml
--- a/BioArchLinux/r-catools/PKGBUILD
+++ b/BioArchLinux/r-catools/PKGBUILD
@ -8,7 +8,7 @@ _pkgname=caTools
 _pkgver=1.18.2
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=9
+pkgrel=10
 pkgdesc="Tools: Moving Window Statistics, GIF, Base64, ROC AUC, etc"
 arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
@ -16,6 +16,10 @@ license=(GPL3)
 depends=(
  r-bitops
 )
+optdepends=(
+  r-mass
+  r-rpart
+)
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 md5sums=('c95edd3f71a8fe1ad2cfd0ae274ad9ab')
 sha256sums=('75d61115afec754b053ed1732cc034f2aeb27b13e6e1932aa0f26bf590cf0293')
--- a/BioArchLinux/r-cbpmanager/PKGBUILD
+++ b/BioArchLinux/r-cbpmanager/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=cbpManager
 _pkgver=1.10.0
 pkgname=r-${_pkgname,,}
 pkgver=1.10.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -22,6 +22,7 @@ depends=(
  r-rapportools
  r-reticulate
  r-rintrojs
+  r-rlang
  r-shiny
  r-shinybs
  r-shinycssloaders
--- a/BioArchLinux/r-cbpmanager/lilac.yaml
+++ b/BioArchLinux/r-cbpmanager/lilac.yaml
@ -14,6 +14,7 @@ repo_depends:
 - r-rapportools
 - r-reticulate
 - r-rintrojs
+- r-rlang
 - r-shiny
 - r-shinybs
 - r-shinycssloaders
--- a/BioArchLinux/r-cellbarcode/PKGBUILD
+++ b/BioArchLinux/r-cellbarcode/PKGBUILD
@ -5,12 +5,13 @@ _pkgname=CellBarcode
 _pkgver=1.6.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=3
 pkgdesc="Cellular DNA Barcode Analysis toolkit"
 arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
 license=(MIT)
 depends=(
+  r-bh
  r-biostrings
  r-ckmeans.1d.dp
  r-data.table
--- a/BioArchLinux/r-cellbarcode/lilac.yaml
+++ b/BioArchLinux/r-cellbarcode/lilac.yaml
@ -3,6 +3,7 @@ maintainers:
 - github: pekkarr
  email: pekkarr@protonmail.com
 repo_depends:
+- r-bh
 - r-biostrings
 - r-ckmeans.1d.dp
 - r-data.table
--- a/BioArchLinux/r-celldex/PKGBUILD
+++ b/BioArchLinux/r-celldex/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=celldex
 _pkgver=1.10.1
 pkgname=r-${_pkgname,,}
 pkgver=1.10.1
-pkgrel=1
+pkgrel=2
 pkgdesc='Reference Index for Cell Types'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -22,6 +22,7 @@ depends=(
 optdepends=(
  r-biocstyle
  r-dt
+  r-ensembldb
  r-knitr
  r-rmarkdown
  r-testthat
--- a/BioArchLinux/r-cellscore/PKGBUILD
+++ b/BioArchLinux/r-cellscore/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=CellScore
 _pkgver=1.20.0
 pkgname=r-${_pkgname,,}
 pkgver=1.20.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Tool for Evaluation of Cell Identity from Transcription Profiles'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -16,10 +16,12 @@ depends=(
  r-lsa
  r-rcolorbrewer
  r-squash
+  r-summarizedexperiment
 )
 optdepends=(
  r-hgu133plus2cellscore
  r-knitr
+  r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('19575619029881593bcf4a474c8e75abb8b78581ef7b17de86ce4277265bb485')
--- a/BioArchLinux/r-cellscore/lilac.yaml
+++ b/BioArchLinux/r-cellscore/lilac.yaml
@ -8,6 +8,7 @@ repo_depends:
 - r-lsa
 - r-rcolorbrewer
 - r-squash
+- r-summarizedexperiment
 update_on:
 - regex: CellScore_([\d._-]+).tar.gz
  source: regex
--- a/Show more
+++ b/Show more