r-*: update depends

BioArchLinux/r-hardhat/PKGBUILD

@@ -4,13 +4,14 @@ _pkgname=hardhat
 _pkgver=1.3.0
 pkgname=r-${_pkgname,,}
 pkgver=1.3.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Construct Modeling Packages'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
 license=('MIT')
 depends=(
   r
+  r-cli
   r-glue
   r-rlang
   r-tibble

BioArchLinux/r-hardhat/lilac.yaml

@@ -3,6 +3,7 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-cli
 - r-glue
 - r-rlang
 - r-tibble

BioArchLinux/r-loo/PKGBUILD

@@ -8,7 +8,7 @@ _pkgname=loo
 _pkgver=2.5.1
 pkgname=r-${_pkgname,,}
 pkgver=2.5.1
-pkgrel=6
+pkgrel=7
 pkgdesc='Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian Models'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@@ -25,6 +25,7 @@ optdepends=(
   r-ggplot2
   r-graphics
   r-knitr
+  r-posterior
   r-rmarkdown
   r-rstan
   r-rstanarm

BioArchLinux/r-msstats/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=MSstats
 _pkgver=4.6.3
 pkgname=r-${_pkgname,,}
 pkgver=4.6.3
-pkgrel=1
+pkgrel=2
 pkgdesc='Protein Significance Analysis in DDA, SRM and DIA for Label-free or Label-based Proteomics Experiments'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -23,6 +23,7 @@ depends=(
   r-preprocesscore
   r-rcpp
   r-rcpparmadillo
+  r-statmod
 )
 optdepends=(
   r-biocstyle

BioArchLinux/r-msstats/lilac.yaml

@@ -15,6 +15,7 @@ repo_depends:
 - r-preprocesscore
 - r-rcpp
 - r-rcpparmadillo
+- r-statmod
 update_on:
 - regex: MSstats_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-recountmethylation/PKGBUILD

@@ -4,21 +4,23 @@ _pkgname=recountmethylation
 _pkgver=1.8.3
 pkgname=r-${_pkgname,,}
 pkgver=1.8.3
-pkgrel=1
+pkgrel=2
 pkgdesc='Access and analyze DNA methylation database compilations'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
   r
+  r-basilisk
   r-biocfilecache
+  r-delayedmatrixstats
   r-hdf5array
   r-minfi
   r-r.utils
   r-rcurl
+  r-reticulate
   r-rhdf5
   r-s4vectors
-  r-illuminahumanmethylation450kmanifest
 )
 optdepends=(
   r-annotationhub
@@ -29,6 +31,7 @@ optdepends=(
   r-gridextra
   r-knitr
   r-limma
+  r-minfidata
   r-rmarkdown
   r-testthat
 )

BioArchLinux/r-recountmethylation/lilac.yaml

@@ -3,14 +3,16 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-basilisk
 - r-biocfilecache
+- r-delayedmatrixstats
 - r-hdf5array
 - r-minfi
 - r-r.utils
 - r-rcurl
+- r-reticulate
 - r-rhdf5
 - r-s4vectors
-- r-illuminahumanmethylation450kmanifest
 update_on:
 - regex: recountmethylation_([\d._-]+).tar.gz
   source: regex

BioArchLinux/r-scfa/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=SCFA
 _pkgver=1.8.1
 pkgname=r-${_pkgname,,}
 pkgver=1.8.1
-pkgrel=1
+pkgrel=2
 pkgdesc='SCFA: Subtyping via Consensus Factor Analysis'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@@ -12,7 +12,6 @@ license=('LGPL')
 depends=(
   r
   r-biocparallel
-  r-clustercrit
   r-coro
   r-glmnet
   r-igraph

BioArchLinux/r-scfa/lilac.yaml

@@ -4,7 +4,6 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biocparallel
-- r-clustercrit
 - r-coro
 - r-glmnet
 - r-igraph