R package guidelines

This document covers standards and guidelines on writing PKGBUILDs for R packages. Most information can be obtained by looking at the package's DESCRIPTION file. You can get most of this from inside R by running tools::CRAN_package_db(). You could also visit CRAN, Bioconductor link1, and Bioconductor link2 for all the R packages' information.

Package naming

Packages should be named r-pkgname, where pkgname is taken from the Package field from the DESCRIPTION file. The package name should be lowercase.

Package Version

Take it from the Version field. R allows packages to have colons and hyphens in their version, this is disallowed in PKGBUILDs. Convert these to a period or underscore.

Arch

See PKGBUILD#arch. If the package's CRAN webpage has NeedsCompilation: yes it is likely architecture-specific. Otherwise, it is likely not.

Dependencies

R packages listed in Depends, Imports, or the LinkingTo fields in a package's DESCRIPTION file should be listed under depends.

R packages listed in Suggests should be listed as optdepends.

Some packages require external tools, these are listed under SystemRequirements.

gcc-fortran is needed as depends for some packages but is not always listed in the DESCRIPTION file.

Source

All R packages available on CRAN are available at the website https://cran.r-project.org/src/contrib/cranname_cranversion.tar.gz where cranname is the name of the package on CRAN and cranversion the cran version.

R packages avalable on Bioconductor are available at the website https://bioconductor.org/packages/release/bioc/src/contrib/bcname_bcname.tar.gz or https://bioconductor.org/packages/release/data/annotation/src/contrib/bcname_bcname.tar.gz where bcname is the name of the package on Bioconductor and bcver the version.

Build and Package

R has built-in support for building packages. Here are three templates of PKGBUILDs for three repositories: MRAN, CRAN and Bioconductor. MRAN is a snapshot mirror of CRAN, using this template will allow the package to build even when out-of-date.

MRAN

_cranname=
_cranver=
_updatedate=YYYY-MM-DD
pkgname=r-${_cranname,,}
pkgver=${_cranver//[:-]/.}
pkgrel=1
pkgdesc=""
arch=()
url="https://cran.r-project.org/package=${_cranname}"
license=()
depends=(r)
makedepends=()
optdepends=()
source=("https://cran.microsoft.com/snapshot/${_updatedate}/src/contrib/${_cranname}_${_cranver}.tar.gz")
sha256sums=()

build() {
  R CMD INSTALL ${_cranname}_${_cranver}.tar.gz -l "${srcdir}"
}

package() {
  install -dm0755 "${pkgdir}/usr/lib/R/library"

  cp -a --no-preserve=ownership "${_cranname}" "${pkgdir}/usr/lib/R/library"
}

CRAN

_cranname=
_cranver=
pkgname=r-${_cranname,,}
pkgver=${_cranver//[:-]/.}
pkgrel=1
pkgdesc=""
arch=()
url="https://cran.r-project.org/package=${_cranname}"
license=()
depends=(r)
makedepends=()
optdepends=()
source=("https://cran.r-project.org/src/contrib/${_cranname}_${_cranver}.tar.gz")
sha256sums=()

build() {
  R CMD INSTALL ${_cranname}_${_cranver}.tar.gz -l "${srcdir}"
}

package() {
  install -dm0755 "${pkgdir}/usr/lib/R/library"

  cp -a --no-preserve=ownership "${_cranname}" "${pkgdir}/usr/lib/R/library"
}

Bioconductor

_bcname=
_bcver=
pkgname=r-${_bcname,,}
pkgver=${_bcver//[:-]/.}
pkgrel=1
pkgdesc=""
arch=()
url="https://bioconductor.org/packages/${_bcname}"
license=()
depends=(r)
makedepends=()
optdepends=()
source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_bcname}_${_bcver}.tar.gz")
# or
# source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_bcname}_${_bcver}.tar.gz")
sha256sums=()

build() {
  R CMD INSTALL ${_bcname}_${_bcver}.tar.gz -l "${srcdir}"
}

package() {
  install -dm0755 "${pkgdir}/usr/lib/R/library"
  
  cp -a --no-preserve=ownership "${_bcname}" "${pkgdir}/usr/lib/R/library"
}

Tips and tricks

Bioconductor repository

To access the bioconductor packages easily, you can add the bioarchlinux repository.