r-*: fresh depends

2025-03-10 12:02:42 +00:00 · 2023-05-08 19:54:26 +08:00 · 2023-05-08 19:54:26 +08:00 · 9e5af0c394
commit 9e5af0c394
parent e2b3323125
31 changed files with 125 additions and 34 deletions
--- a/BioArchLinux/r-amplican/PKGBUILD
+++ b/BioArchLinux/r-amplican/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=amplican
 _pkgver=1.21.0
 pkgname=r-${_pkgname,,}
 pkgver=1.21.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Automated analysis of CRISPR experiments'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -14,7 +14,6 @@ depends=(
  r-biocgenerics
  r-biocparallel
  r-biostrings
-  r-clustercrit
  r-data.table
  r-dplyr
  r-genomeinfodb
--- a/BioArchLinux/r-amplican/lilac.yaml
+++ b/BioArchLinux/r-amplican/lilac.yaml
@ -6,7 +6,6 @@ repo_depends:
 - r-biocgenerics
 - r-biocparallel
 - r-biostrings
- r-clustercrit
 - r-data.table
 - r-dplyr
 - r-genomeinfodb
--- a/BioArchLinux/r-annotationdbi/PKGBUILD
+++ b/BioArchLinux/r-annotationdbi/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=AnnotationDbi
 _pkgver=1.62.1
 pkgname=r-${_pkgname,,}
 pkgver=1.62.1
-pkgrel=1
+pkgrel=2
 pkgdesc='Manipulation of SQLite-based annotations in Bioconductor'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -33,6 +33,7 @@ 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")
 sha256sums=('6187e6b4b26b92ef79d91cef94c9b963ff9aa3f579cfb3909ee082009acbab28')
--- a/BioArchLinux/r-bench/PKGBUILD
+++ b/BioArchLinux/r-bench/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=bench
 _pkgver=1.1.3
 pkgname=r-${_pkgname,,}
 pkgver=1.1.3
-pkgrel=1
+pkgrel=2
 pkgdesc='High Precision Timing of R Expressions'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -24,8 +24,6 @@ optdepends=(
  r-ggbeeswarm
  r-ggplot2
  r-ggridges
-  r-jsonlite
-  r-mockery
  r-parallel
  r-scales
  r-testthat
--- a/BioArchLinux/r-delayedarray/PKGBUILD
+++ b/BioArchLinux/r-delayedarray/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=DelayedArray
 _pkgver=0.25.0
 pkgname=r-${_pkgname,,}
 pkgver=0.25.0
-pkgrel=1
+pkgrel=2
 pkgdesc='A unified framework for working transparently with on-disk and in-memory array-like datasets'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -14,6 +14,7 @@ depends=(
  r-biocgenerics
  r-iranges
  r-matrixgenerics
+  r-s4arrays
  r-s4vectors
 )
 optdepends=(
--- a/BioArchLinux/r-delayedarray/lilac.yaml
+++ b/BioArchLinux/r-delayedarray/lilac.yaml
@ -6,6 +6,7 @@ repo_depends:
 - r-biocgenerics
 - r-iranges
 - r-matrixgenerics
+- r-s4arrays
 - r-s4vectors
 update_on:
 - regex: DelayedArray_([\d._-]+).tar.gz
--- a/BioArchLinux/r-distr/PKGBUILD
+++ b/BioArchLinux/r-distr/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=distr
 _pkgver=2.9.1
 pkgname=r-${_pkgname,,}
 pkgver=2.9.1
-pkgrel=4
+pkgrel=5
 pkgdesc='Object Oriented Implementation of Distributions'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -18,6 +18,7 @@ optdepends=(
  r-distrex
  r-distrmod
  r-knitr
+  r-robastbase
  r-roptest
  r-svunit
 )
--- a/BioArchLinux/r-evaluate/PKGBUILD
+++ b/BioArchLinux/r-evaluate/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=evaluate
 _pkgver=0.21
 pkgname=r-${_pkgname,,}
 pkgver=0.21
-pkgrel=1
+pkgrel=2
 pkgdesc='Parsing and Evaluation Tools that Provide More Details than the Default'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -16,7 +16,9 @@ optdepends=(
  r-covr
  r-ggplot2
  r-lattice
+  r-rlang
  r-testthat
+  r-withr
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('3178c99cee8917d7d128806d064d4fecce7845ed07f42e759dcc0adda89c22b9')
--- a/BioArchLinux/r-ggbeeswarm/PKGBUILD
+++ b/BioArchLinux/r-ggbeeswarm/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=ggbeeswarm
 _pkgver=0.7.2
 pkgname=r-${_pkgname,,}
 pkgver=0.7.2
-pkgrel=1
+pkgrel=2
 pkgdesc='Categorical Scatter (Violin Point) Plots'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -12,6 +12,7 @@ license=('GPL')
 depends=(
  r
  r-beeswarm
+  r-cli
  r-ggplot2
  r-lifecycle
  r-vipor
--- a/BioArchLinux/r-ggbeeswarm/lilac.yaml
+++ b/BioArchLinux/r-ggbeeswarm/lilac.yaml
@ -4,6 +4,7 @@ maintainers:
  email: kuoi@bioarchlinux.org
 repo_depends:
 - r-beeswarm
+- r-cli
 - r-ggplot2
 - r-lifecycle
 - r-vipor
--- a/BioArchLinux/r-hdf5array/PKGBUILD
+++ b/BioArchLinux/r-hdf5array/PKGBUILD
@ -5,12 +5,13 @@ _pkgname=HDF5Array
 _pkgver=1.28.0
 pkgname=r-${_pkgname,,}
 pkgver=1.28.0
-pkgrel=1
+pkgrel=2
 pkgdesc='HDF5 backend for DelayedArray objects'
 arch=('x86_64')
 url="https://bioconductor.org/packages/${_pkgname}"
 license=('Artistic2.0')
 depends=(
+  make
  r
  r-biocgenerics
  r-delayedarray
@ -18,8 +19,8 @@ depends=(
  r-rhdf5
  r-rhdf5filters
  r-rhdf5lib
+  r-s4arrays
  r-s4vectors
-  make
 )
 optdepends=(
  r-biocparallel
--- a/BioArchLinux/r-hdf5array/lilac.yaml
+++ b/BioArchLinux/r-hdf5array/lilac.yaml
@ -9,6 +9,7 @@ repo_depends:
 - r-rhdf5
 - r-rhdf5filters
 - r-rhdf5lib
+- r-s4arrays
 - r-s4vectors
 update_on:
 - regex: HDF5Array_([\d._-]+).tar.gz
--- a/BioArchLinux/r-hmisc/PKGBUILD
+++ b/BioArchLinux/r-hmisc/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=Hmisc
 _pkgver=5.0-1
 pkgname=r-${_pkgname,,}
 pkgver=5.0.1
-pkgrel=4
+pkgrel=5
 pkgdesc='Harrell Miscellaneous'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -29,6 +29,9 @@ optdepends=(
  r-acepack
  r-chron
  r-digest
+  r-gt
+  r-htmlwidgets
+  r-jsonlite
  r-kableextra
  r-lattice
  r-latticeextra
@ -44,6 +47,7 @@ optdepends=(
  r-rlang
  r-rms
  r-rstudioapi
+  r-sparkline
  r-survival
  r-tables
  r-vgam
--- a/BioArchLinux/r-logistf/PKGBUILD
+++ b/BioArchLinux/r-logistf/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=logistf
 _pkgver=1.25.0
 pkgname=r-${_pkgname,,}
 pkgver=1.25.0
-pkgrel=1
+pkgrel=2
 pkgdesc="Firth's Bias-Reduced Logistic Regression"
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -14,6 +14,10 @@ depends=(
  r-formula.tools
  r-mice
 )
+optdepends=(
+  r-emmeans
+  r-estimability
+)
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('3d3ed3ce30a8b2afb82ccbf2dff3dbf119f533d252eb91131d50166ebd96e870')

--- a/BioArchLinux/r-primme/PKGBUILD
+++ b/BioArchLinux/r-primme/PKGBUILD
@ -5,7 +5,7 @@ _pkgname=PRIMME
 _pkgver=3.2-3
 pkgname=r-${_pkgname,,}
 pkgver=3.2.3
-pkgrel=2
+pkgrel=3
 pkgdesc='Eigenvalues and Singular Values and Vectors from Large Matrices'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -18,7 +18,7 @@ depends=(
 optdepends=(
  r-matrix
 )
-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=('052c606d7648a4de5b94836e2c410a52cd1562f5cf660cb9351bd9e7b1643705')

 build() {
--- a/BioArchLinux/r-primme/lilac.yaml
+++ b/BioArchLinux/r-primme/lilac.yaml
@ -7,5 +7,5 @@ repo_depends:
 update_on:
 - regex: PRIMME_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=PRIMME
+  url: https://cran.r-project.org/src/contrib/Archive/PRIMME
 - alias: r
--- a/BioArchLinux/r-profvis/PKGBUILD
+++ b/BioArchLinux/r-profvis/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=profvis
 _pkgver=0.3.7
 pkgname=r-${_pkgname,,}
 pkgver=0.3.7
-pkgrel=3
+pkgrel=4
 pkgdesc='Interactive Visualizations for Profiling R Code'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -12,7 +12,10 @@ license=('GPL')
 depends=(
  r
  r-htmlwidgets
+  r-purrr
+  r-rlang
  r-stringr
+  r-vctrs
 )
 optdepends=(
  r-devtools
--- a/BioArchLinux/r-profvis/lilac.yaml
+++ b/BioArchLinux/r-profvis/lilac.yaml
@ -3,7 +3,10 @@ maintainers:
  - github: sukanka
 repo_depends:
  - r-htmlwidgets
+  - r-purrr
+  - r-rlang
  - r-stringr
+  - r-vctrs
 update_on:
  - regex: profvis_([\d._-]+).tar.gz
    source: regex
--- a/BioArchLinux/r-qdaptools/PKGBUILD
+++ b/BioArchLinux/r-qdaptools/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=qdapTools
 _pkgver=1.3.5
 pkgname=r-${_pkgname,,}
 pkgver=1.3.5
-pkgrel=6
+pkgrel=7
 pkgdesc="Tools for the 'qdap' Package"
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -19,7 +19,7 @@ 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=('8c8828877ab63ad705b69e187c01d7c7098a88989bdde9e956ac559cc6de7e25')

 build() {
--- a/BioArchLinux/r-qdaptools/lilac.yaml
+++ b/BioArchLinux/r-qdaptools/lilac.yaml
@ -10,5 +10,5 @@ repo_depends:
 update_on:
 - regex: qdapTools_([\d._-]+).tar.gz
  source: regex
-  url: https://cran.r-project.org/package=qdapTools
+  url: https://cran.r-project.org/src/contrib/Archive/qdapTools
 - alias: r
--- a/BioArchLinux/r-s4arrays/PKGBUILD
+++ b/BioArchLinux/r-s4arrays/PKGBUILD
@ -0,0 +1,39 @@
+# Maintainer: sukanka <su975853527@gmail.com>
+
+_pkgname=S4Arrays
+_pkgver=1.0.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//[:-]/.}
+pkgrel=1
+pkgdesc='Foundation of array-like containers in Bioconductor'
+arch=('x86_64')
+url="https://bioconductor.org/packages/${_pkgname}"
+license=('Artistic2.0')
+depends=(
+  r
+  r-biocgenerics
+  r-crayon
+  r-iranges
+  r-s4vectors
+)
+optdepends=(
+  r-biocparallel
+  r-biocstyle
+  r-delayedarray
+  r-knitr
+  r-rmarkdown
+  r-sparsearray
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('5a0e9d7bdf9fecc2408c8a2c3b90cc40acb617714c15bba85bd361c1d06fcb16')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et:
--- a/BioArchLinux/r-s4arrays/lilac.yaml
+++ b/BioArchLinux/r-s4arrays/lilac.yaml
@ -0,0 +1,22 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: sukanka
+post_build_script: |
+  git_pkgbuild_commit()
+  update_aur_repo()
+pre_build_script: |
+  for line in edit_file('PKGBUILD'):
+    if line.startswith('_pkgver='):
+      line = f'_pkgver={_G.newver}'
+    print(line)
+  update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+repo_depends:
+  - r-biocgenerics
+  - r-crayon
+  - r-iranges
+  - r-s4vectors
+update_on:
+  - regex: S4Arrays_([\d._-]+).tar.gz
+    source: regex
+    url: https://bioconductor.org/packages/S4Arrays
+  - alias: r
--- a/BioArchLinux/r-scattermore/PKGBUILD
+++ b/BioArchLinux/r-scattermore/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=scattermore
 _pkgver=1.0
 pkgname=r-${_pkgname,,}
 pkgver=1.0
-pkgrel=1
+pkgrel=2
 pkgdesc='Scatterplots with More Points'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -14,6 +14,12 @@ depends=(
  r-ggplot2
  r-scales
 )
+optdepends=(
+  r-covr
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
 sha256sums=('a71d5d1ae06bc6b7d9a446293e3c12a5ce970754c24a0cc6f31ad0ea52cbaf91')

--- a/BioArchLinux/r-speedglm/PKGBUILD
+++ b/BioArchLinux/r-speedglm/PKGBUILD
@ -3,13 +3,14 @@
 _pkgname=speedglm
 pkgname=r-${_pkgname,,}
 pkgver=0.3_4
-pkgrel=10
+pkgrel=11
 pkgdesc='Fitting Linear and Generalized Linear Models to Large Data Sets'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
 license=('GPL')
 depends=(
  r
+  r-biglm
 )
 source=("${_pkgname}-${pkgver}.tar.gz::https://github.com/cran/${_pkgname}/archive/refs/tags/${pkgver//_/-}.tar.gz")
 sha256sums=('f1f38689d562babbd9d701631608509476c0ff2a34384478c6512b29f00fa767')
--- a/BioArchLinux/r-speedglm/lilac.yaml
+++ b/BioArchLinux/r-speedglm/lilac.yaml
@ -12,6 +12,8 @@ update_on:
  - source: github
    github: cran/speedglm
    use_max_tag: true
-    from_pattern: '([\d.]+)-(\d+)'
-    to_pattern: '\1_\2'
+    from_pattern: ([\d.]+)-(\d+)
+    to_pattern: \1_\2
  - alias: r
+repo_depends:
+  - r-biglm
--- a/BioArchLinux/r-summarizedexperiment/PKGBUILD
+++ b/BioArchLinux/r-summarizedexperiment/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=SummarizedExperiment
 _pkgver=1.30.0
 pkgname=r-${_pkgname,,}
 pkgver=1.30.0
-pkgrel=1
+pkgrel=2
 pkgdesc='SummarizedExperiment container'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
@ -18,6 +18,7 @@ depends=(
  r-genomicranges
  r-iranges
  r-matrixgenerics
+  r-s4arrays
  r-s4vectors
 )
 optdepends=(
--- a/BioArchLinux/r-summarizedexperiment/lilac.yaml
+++ b/BioArchLinux/r-summarizedexperiment/lilac.yaml
@ -10,6 +10,7 @@ repo_depends:
 - r-genomicranges
 - r-iranges
 - r-matrixgenerics
+- r-s4arrays
 - r-s4vectors
 update_on:
 - regex: SummarizedExperiment_([\d._-]+).tar.gz
--- a/BioArchLinux/r-testthat/PKGBUILD
+++ b/BioArchLinux/r-testthat/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=testthat
 _pkgver=3.1.8
 pkgname=r-${_pkgname,,}
 pkgver=3.1.8
-pkgrel=1
+pkgrel=2
 pkgdesc='Unit Testing for R'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -35,7 +35,6 @@ optdepends=(
  r-curl
  r-diffviewer
  r-knitr
-  r-mockery
  r-rmarkdown
  r-rstudioapi
  r-shiny
--- a/BioArchLinux/r-tseries/PKGBUILD
+++ b/BioArchLinux/r-tseries/PKGBUILD
@ -4,13 +4,14 @@ _pkgname=tseries
 _pkgver=0.10-54
 pkgname=r-${_pkgname,,}
 pkgver=0.10.54
-pkgrel=1
+pkgrel=2
 pkgdesc='Time Series Analysis and Computational Finance'
 arch=('x86_64')
 url="https://cran.r-project.org/package=${_pkgname}"
 license=('GPL')
 depends=(
  r
+  r-jsonlite
  r-quadprog
  r-quantmod
  r-zoo
--- a/BioArchLinux/r-tseries/lilac.yaml
+++ b/BioArchLinux/r-tseries/lilac.yaml
@ -3,6 +3,7 @@ maintainers:
 - github: starsareintherose
  email: kuoi@bioarchlinux.org
 repo_depends:
+- r-jsonlite
 - r-quadprog
 - r-quantmod
 - r-zoo
--- a/BioArchLinux/r-viridis/PKGBUILD
+++ b/BioArchLinux/r-viridis/PKGBUILD
@ -4,7 +4,7 @@ _pkgname=viridis
 _pkgver=0.6.3
 pkgname=r-${_pkgname,,}
 pkgver=0.6.3
-pkgrel=1
+pkgrel=2
 pkgdesc='Colorblind-Friendly Color Maps for R'
 arch=('any')
 url="https://cran.r-project.org/package=${_pkgname}"
@ -25,12 +25,10 @@ optdepends=(
  r-mapproj
  r-maps
  r-mass
-  r-raster
-  r-rastervis
-  r-rgdal
  r-rmarkdown
  r-scales
  r-svglite
+  r-terra
  r-testthat
  r-vdiffr
 )