r-ccimpute: init

BioArchLinux/r-ccimpute/PKGBUILD

@@ -0,0 +1,52 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=ccImpute
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)"
+arch=(x86_64)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-biocparallel
+  r-matrixstats
+  r-rcpp
+  r-simlr
+)
+makedepends=(
+  r-rcppeigen
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-knitr
+  r-mclust
+  r-rmarkdown
+  r-scater
+  r-scrnaseq
+  r-sessioninfo
+  r-singlecellexperiment
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('f402177e3fc7bbbcac504c956889dfa9')
+sha256sums=('12728b12c2f470112c7a3108a6f999d798d67e07f892c75f08571c6462f2476c')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-ccimpute/lilac.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-ccimpute/lilac.yaml

@@ -0,0 +1,18 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocparallel
+- r-matrixstats
+- r-rcpp
+- r-simlr
+repo_makedepends:
+- r-rcppeigen
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: ccImpute
+  repo: bioc
+  md5: true
+- alias: r