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| author | BioArchLinuxBot | 2023-11-04 12:10:36 +0000 |
|---|---|---|
| committer | BioArchLinuxBot | 2023-11-04 12:10:36 +0000 |
| commit | b0c9c810bf5d9d437beeb30518a78d98cb225f8d (patch) | |
| tree | 94498048bae987f539bfe21419c30999cbd7ec2b | |
| parent | 10a58c5330cd9b697fc1540a39c18d84ecb239e2 (diff) | |
| download | aur-b0c9c810bf5d9d437beeb30518a78d98cb225f8d.tar.gz | |
[lilac] updated to 5.0.0-1
| -rw-r--r-- | .SRCINFO | 26 | ||||
| -rw-r--r-- | PKGBUILD | 62 |
2 files changed, 67 insertions, 21 deletions
@@ -1,15 +1,23 @@ pkgbase = r-seurat pkgdesc = Tools for Single Cell Genomics - pkgver = 4.4.0 + pkgver = 5.0.0 pkgrel = 1 url = https://cran.r-project.org/package=Seurat arch = x86_64 license = MIT - depends = r + checkdepends = r-glmgampoi + checkdepends = r-harmony + checkdepends = r-limma + checkdepends = r-singlecellexperiment + checkdepends = r-testthat + makedepends = r-rcppeigen + makedepends = r-rcppprogress depends = r-cowplot + depends = r-fastdummies depends = r-fitdistrplus depends = r-future depends = r-future.apply + depends = r-generics depends = r-ggplot2 depends = r-ggrepel depends = r-ggridges @@ -19,6 +27,7 @@ pkgbase = r-seurat depends = r-irlba depends = r-jsonlite depends = r-leiden + depends = r-lifecycle depends = r-lmtest depends = r-matrixstats depends = r-miniui @@ -32,11 +41,11 @@ pkgbase = r-seurat depends = r-rcolorbrewer depends = r-rcpp depends = r-rcppannoy - depends = r-rcppeigen - depends = r-rcppprogress + depends = r-rcpphnsw depends = r-reticulate depends = r-rlang depends = r-rocr + depends = r-rspectra depends = r-rtsne depends = r-scales depends = r-scattermore @@ -50,12 +59,15 @@ pkgbase = r-seurat optdepends = r-ape optdepends = r-biobase optdepends = r-biocgenerics + optdepends = r-bpcells optdepends = r-data.table + optdepends = r-delayedarray optdepends = r-deseq2 optdepends = r-enrichr optdepends = r-genomeinfodb optdepends = r-genomicranges optdepends = r-ggrastr + optdepends = r-harmony optdepends = r-hdf5r optdepends = r-iranges optdepends = r-limma @@ -63,6 +75,7 @@ pkgbase = r-seurat optdepends = r-metap optdepends = r-mixtools optdepends = r-monocle + optdepends = r-presto optdepends = r-r.utils optdepends = r-rfast2 optdepends = r-rsvd @@ -72,7 +85,8 @@ pkgbase = r-seurat optdepends = r-summarizedexperiment optdepends = r-testthat optdepends = r-vgam - source = https://cran.r-project.org/src/contrib/Seurat_4.4.0.tar.gz - sha256sums = 0f17df9597642cfc1db4d8718f0b59ebab9fbed328b1f885f42ee85ea0dcb4dd + source = https://cran.r-project.org/src/contrib/Seurat_5.0.0.tar.gz + md5sums = 0815d7d51e297bf1f4975cefb60e2b6d + sha256sums = bb8c91610f58753aa57f38bf2ef1c97c9c85fbfe89c1c47a33805f3eb5eb78c3 pkgname = r-seurat @@ -1,20 +1,22 @@ -# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net> +# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com> +# Contributor: Guoyi Zhang <guoyizhang at malacology dot net> _pkgname=Seurat -_pkgver=4.4.0 +_pkgver=5.0.0 pkgname=r-${_pkgname,,} -pkgver=4.4.0 +pkgver=${_pkgver//-/.} pkgrel=1 -pkgdesc='Tools for Single Cell Genomics' -arch=('x86_64') +pkgdesc="Tools for Single Cell Genomics" +arch=(x86_64) url="https://cran.r-project.org/package=${_pkgname}" -license=('MIT') +license=(MIT) depends=( - r r-cowplot + r-fastdummies r-fitdistrplus r-future r-future.apply + r-generics r-ggplot2 r-ggrepel r-ggridges @@ -24,6 +26,7 @@ depends=( r-irlba r-jsonlite r-leiden + r-lifecycle r-lmtest r-matrixstats r-miniui @@ -37,11 +40,11 @@ depends=( r-rcolorbrewer r-rcpp r-rcppannoy - r-rcppeigen - r-rcppprogress + r-rcpphnsw r-reticulate r-rlang r-rocr + r-rspectra r-rtsne r-scales r-scattermore @@ -53,16 +56,30 @@ depends=( r-tibble r-uwot ) +makedepends=( + r-rcppeigen + r-rcppprogress +) +checkdepends=( + r-glmgampoi + r-harmony + r-limma + r-singlecellexperiment + r-testthat +) optdepends=( r-ape r-biobase r-biocgenerics + r-bpcells r-data.table + r-delayedarray r-deseq2 r-enrichr r-genomeinfodb r-genomicranges r-ggrastr + r-harmony r-hdf5r r-iranges r-limma @@ -70,6 +87,7 @@ optdepends=( r-metap r-mixtools r-monocle + r-presto r-r.utils r-rfast2 r-rsvd @@ -81,15 +99,29 @@ optdepends=( r-vgam ) source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('0f17df9597642cfc1db4d8718f0b59ebab9fbed328b1f885f42ee85ea0dcb4dd') +md5sums=('0815d7d51e297bf1f4975cefb60e2b6d') +sha256sums=('bb8c91610f58753aa57f38bf2ef1c97c9c85fbfe89c1c47a33805f3eb5eb78c3') + +prepare() { + # skip test that requires BPCells + sed -i '/"pca is equivalent for BPCells"/a\ \ skip_if_not_installed("BPCells")' \ + "$_pkgname/tests/testthat/test_dimensional_reduction.R" +} build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" - install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" + + install -d "$pkgdir/usr/share/licenses/$pkgname" + ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname" } -# vim:set ts=2 sw=2 et: |