r-*: fix depends, use metadata checks for several packages

BioArchLinux/r-batchqc/PKGBUILD

@@ -1,45 +1,63 @@
-# system requirements: pandoc (http://pandoc.org/installing.html) forgenerating reports from markdown files.
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=BatchQC
-_pkgver=1.30.0
+_pkgver=2.0.0
 pkgname=r-${_pkgname,,}
-pkgver=1.30.0
-pkgrel=2
-pkgdesc='Batch Effects Quality Control Software'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Batch Effects Quality Control Software"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('MIT')
 depends=(
-  r
-  r-corpcor
-  r-ggvis
-  r-gplots
-  r-heatmaply
-  r-knitr
+  r-data.table
+  r-deseq2
+  r-dplyr
+  r-ebseq
+  r-ggdendro
+  r-ggnewscale
+  r-ggplot2
   r-limma
   r-matrixstats
-  r-mcmcpack
-  r-moments
-  r-pander
+  r-pheatmap
+  r-rcolorbrewer
+  r-reader
   r-reshape2
-  r-rmarkdown
+  r-scran
   r-shiny
+  r-summarizedexperiment
   r-sva
-  pandoc
+  r-tibble
+  r-tidyr
+  r-tidyverse
 )
 optdepends=(
+  r-biocmanager
+  r-biocstyle
+  r-bladderbatch
+  r-dendextend
+  r-devtools
+  r-knitr
+  r-lintr
+  r-plotly
+  r-rmarkdown
+  r-shinythemes
+  r-spelling
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d89b36b950e87c4c7ae7e28d91fa997497b07a500eec85a8907f9f25c623caf5')
+md5sums=('775f7f746c2ada89c20ff78bb6faa103')
+b2sums=('3efff6f48d3a655cb32c4341d6cbb0a10b73560692bfaf6d2a5def765822a480a66be54d734d0c7702a4b430673e9b886e881851c7a4f7fde306917fc71f3d33')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$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:

BioArchLinux/r-batchqc/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-batchqc/lilac.yaml

@@ -3,22 +3,29 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-corpcor
-- r-ggvis
-- r-gplots
-- r-heatmaply
-- r-knitr
+- r-data.table
+- r-deseq2
+- r-dplyr
+- r-ebseq
+- r-ggdendro
+- r-ggnewscale
+- r-ggplot2
 - r-limma
 - r-matrixstats
-- r-mcmcpack
-- r-moments
-- r-pander
+- r-pheatmap
+- r-rcolorbrewer
+- r-reader
 - r-reshape2
-- r-rmarkdown
+- r-scran
 - r-shiny
+- r-summarizedexperiment
 - r-sva
+- r-tibble
+- r-tidyr
+- r-tidyverse
 update_on:
-- regex: BatchQC_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/BatchQC
+- source: rpkgs
+  pkgname: BatchQC
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-depecher/PKGBUILD

@@ -1,17 +1,17 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=DepecheR
-_pkgver=1.18.0
+_pkgver=1.20.0
 pkgname=r-${_pkgname,,}
-pkgver=1.18.0
-pkgrel=2
-pkgdesc='Determination of essential phenotypic elements of clusters in high-dimensional entities'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Determination of essential phenotypic elements of clusters in high-dimensional entities"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
 license=('MIT')
 depends=(
-  r
   r-beanplot
+  r-clusterr
   r-collapse
   r-dosnow
   r-dplyr
@@ -24,11 +24,13 @@ depends=(
   r-mixomics
   r-moments
   r-rcpp
-  r-rcppeigen
   r-reshape2
   r-robustbase
   r-viridis
 )
+makedepends=(
+  r-rcppeigen
+)
 optdepends=(
   r-biocstyle
   r-knitr
@@ -37,15 +39,18 @@ optdepends=(
   r-uwot
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5ce001eb0e4037d2cfc6f90d5f5ee81b5c6d8d344253c9da2210da5e1e0f6cac')
+md5sums=('5195d544797a0a5fc0eb9c0d712b9e68')
+b2sums=('aaa5c2ff15307613d25e925b6f3ae8d4d7c23954d84e93c3b7b41ff0b6b3ab67644a2c7a1da17599d54f679cd97190db2f63d267b7a2a9a360572ff748c22564')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 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:

BioArchLinux/r-depecher/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-depecher/lilac.yaml

@@ -4,6 +4,7 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-beanplot
+- r-clusterr
 - r-collapse
 - r-dosnow
 - r-dplyr
@@ -16,12 +17,14 @@ repo_depends:
 - r-mixomics
 - r-moments
 - r-rcpp
-- r-rcppeigen
 - r-reshape2
 - r-robustbase
 - r-viridis
+repo_makedepends:
+- r-rcppeigen
 update_on:
-- regex: DepecheR_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/DepecheR
+- source: rpkgs
+  pkgname: DepecheR
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-glmsparsenet/PKGBUILD

@@ -1,54 +1,54 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=glmSparseNet
-_pkgver=1.20.1
+_pkgver=1.22.0
 pkgname=r-${_pkgname,,}
-pkgver=1.20.1
-pkgrel=2
-pkgdesc='Network Centrality Metrics for Elastic-Net Regularized Models'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Network Centrality Metrics for Elastic-Net Regularized Models"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-biomart
-  r-digest
+  r-checkmate
   r-dplyr
   r-forcats
   r-futile.logger
-  r-futile.options
   r-ggplot2
   r-glmnet
   r-glue
   r-httr
+  r-lifecycle
   r-multiassayexperiment
   r-readr
-  r-reshape2
-  r-stringr
+  r-rlang
   r-summarizedexperiment
   r-survminer
+  r-tcgautils
 )
 optdepends=(
   r-biocstyle
   r-curatedtcgadata
   r-knitr
+  r-magrittr
   r-proc
+  r-reshape2
   r-rmarkdown
-  r-survcomp
-  r-survival
-  r-tcgautils
   r-testthat
   r-venndiagram
+  r-withr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('34d13f31513386993fb5b88433c2b48e6f7ee457498a7a477b9727c984519525')
+md5sums=('e36eea2e7603e3ae720b683d36e9c54a')
+b2sums=('5270ddcdf22fbec1cc179114369622268d1965624818fc47f4e9535d4360e85950136f65535227b6cef26b8736a0f1fe74f19a8106fcd7e7a25db4c39cd62cff')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-glmsparsenet/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-glmsparsenet/lilac.yaml

@@ -4,23 +4,24 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biomart
-- r-digest
+- r-checkmate
 - r-dplyr
 - r-forcats
 - r-futile.logger
-- r-futile.options
 - r-ggplot2
 - r-glmnet
 - r-glue
 - r-httr
+- r-lifecycle
 - r-multiassayexperiment
 - r-readr
-- r-reshape2
-- r-stringr
+- r-rlang
 - r-summarizedexperiment
 - r-survminer
+- r-tcgautils
 update_on:
-- regex: glmSparseNet_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/glmSparseNet
+- source: rpkgs
+  pkgname: glmSparseNet
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-imman/PKGBUILD

@@ -1,18 +1,17 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=IMMAN
-_pkgver=1.22.0
+_pkgver=1.24.0
 pkgname=r-${_pkgname,,}
-pkgver=1.22.0
-pkgrel=2
-pkgdesc='Interlog protein network reconstruction by Mapping and Mining ANalysis'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Interlog protein network reconstruction by Mapping and Mining ANalysis"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
-  r-biostrings
   r-igraph
+  r-pwalign
   r-seqinr
   r-stringdb
 )
@@ -22,14 +21,15 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5a5369e6c2d1a6a07017db76993dd625bd2568c6112388af1dd535bd19245b73')
+md5sums=('5d7082b60e3a0e4fc20e8c0ed492cf34')
+b2sums=('8b689831bd426977e1f4ecb21aa9c70852b23a565c9717a270642c723a33420e91382470ed757eedf55b3fb34ea102828a3951c96ff33e97ca5c083be86851a0')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-imman/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-imman/lilac.yaml

@@ -3,12 +3,13 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-biostrings
 - r-igraph
+- r-pwalign
 - r-seqinr
 - r-stringdb
 update_on:
-- regex: IMMAN_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/IMMAN
+- source: rpkgs
+  pkgname: IMMAN
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-methtargetedngs/PKGBUILD

@@ -1,32 +1,32 @@
-# system requirements: HMMER3
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=MethTargetedNGS
-_pkgver=1.34.0
+_pkgver=1.36.0
 pkgname=r-${_pkgname,,}
-pkgver=1.34.0
-pkgrel=2
-pkgdesc='Perform Methylation Analysis on Next Generation Sequencing Data'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Perform Methylation Analysis on Next Generation Sequencing Data"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
+  hmmer
   r-biostrings
   r-gplots
+  r-pwalign
   r-seqinr
   r-stringr
-  hmmer
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('8cef3643e99f5f79706f68d542e73be6a964649f7b382c66e9b8f08be3fd4817')
+md5sums=('69ab4e5fae7355ad1393b9d2a70595d4')
+b2sums=('bebcfebce2b3a1a6220c8021590314763b1ca671d709f2e65dd81b06aeb166b20c385ade514da8d005d36e39225c14e9d5e756dfdcda8016236077ab9e220692')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-methtargetedngs/lilac.py

@@ -1,12 +1,16 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(
+        _G,
+        expect_systemrequirements = "HMMER3",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-methtargetedngs/lilac.yaml

@@ -3,13 +3,15 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- hmmer
 - r-biostrings
 - r-gplots
+- r-pwalign
 - r-seqinr
 - r-stringr
-- hmmer
 update_on:
-- regex: MethTargetedNGS_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/MethTargetedNGS
+- source: rpkgs
+  pkgname: MethTargetedNGS
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-milor/PKGBUILD

@@ -1,16 +1,17 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=miloR
-_pkgver=1.10.0
+_pkgver=2.0.0
 pkgname=r-${_pkgname,,}
-pkgver=1.10.0
-pkgrel=2
-pkgdesc='Differential neighbourhood abundance testing on a graph'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Differential neighbourhood abundance testing on a graph"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
+  blas
+  lapack
   r-biocgenerics
   r-biocneighbors
   r-biocparallel
@@ -26,9 +27,12 @@ depends=(
   r-igraph
   r-irlba
   r-limma
+  r-matrixgenerics
   r-matrixstats
+  r-numderiv
   r-patchwork
   r-rcolorbrewer
+  r-rcpp
   r-s4vectors
   r-singlecellexperiment
   r-stringr
@@ -36,14 +40,15 @@ depends=(
   r-tibble
   r-tidyr
 )
+makedepends=(
+  r-rcpparmadillo
+)
 optdepends=(
   r-biocstyle
   r-covr
   r-curl
-  r-graphics
   r-knitr
   r-magick
-  r-mass
   r-mousegastrulationdata
   r-mousethymusageing
   r-mvtnorm
@@ -51,19 +56,21 @@ optdepends=(
   r-rmarkdown
   r-scater
   r-scran
+  r-scrnaseq
   r-scuttle
   r-testthat
   r-uwot
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('926df31d90058416b3449c553ee4b8a86e3b8efdf36f4ff2024bf20e7ae2dbc2')
+md5sums=('f02be1539df5c6cfd31ae8042f78f274')
+b2sums=('2a01b1ed954a83da6b5640145b41d25c3f67343a28307291f8bfe66f8ecb0462d024361e83882066409b2735fa824630d9903c28d857daf6655bc1dcc5f2e8a5')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-milor/lilac.py

@@ -1,12 +1,16 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(
+        _G,
+        expect_license = "GPL-3 + file LICENSE",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-milor/lilac.yaml

@@ -18,17 +18,31 @@ repo_depends:
 - r-igraph
 - r-irlba
 - r-limma
+- r-matrixgenerics
 - r-matrixstats
+- r-numderiv
 - r-patchwork
 - r-rcolorbrewer
+- r-rcpp
 - r-s4vectors
 - r-singlecellexperiment
 - r-stringr
 - r-summarizedexperiment
 - r-tibble
 - r-tidyr
+repo_makedepends:
+- r-rcpparmadillo
 update_on:
-- regex: miloR_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/miloR
+- source: rpkgs
+  pkgname: miloR
+  repo: bioc
+  md5: true
 - alias: r
+- source: alpmfiles
+  pkgname: blas
+  filename: usr/lib/libblas\.so\.([^.]+)
+  repo: extra
+- source: alpmfiles
+  pkgname: lapack
+  filename: usr/lib/liblapack\.so\.([^.]+)
+  repo: extra

BioArchLinux/r-mosim/PKGBUILD

@@ -1,48 +1,64 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=MOSim
-_pkgver=1.16.0
+_pkgver=2.0.0
 pkgname=r-${_pkgname,,}
-pkgver=1.16.0
-pkgrel=2
-pkgdesc='Multi-Omics Simulation (MOSim)'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Multi-Omics Simulation (MOSim)"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
-  r-biobase
   r-dplyr
+  r-edger
   r-ggplot2
   r-hiddenmarkov
   r-iranges
   r-lazyeval
   r-matrixstats
-  r-purrr
+  r-rcpp
   r-rlang
   r-s4vectors
-  r-scales
+  r-scran
+  r-seurat
+  r-signac
   r-stringi
   r-stringr
-  r-tibble
-  r-tidyr
   r-zoo
 )
+makedepends=(
+  r-cpp11
+)
 optdepends=(
+  r-biobase
   r-biocstyle
+  r-bluster
+  r-decor
+  r-igraph
   r-knitr
+  r-leiden
+  r-markdown
+  r-purrr
   r-rmarkdown
+  r-rsamtools
+  r-scales
+  r-scater
+  r-singlecellexperiment
   r-testthat
+  r-tibble
+  r-tidyr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('49152fdac7d284e3a2c5c8fc19960e813157fb78911a71bb20a118bee69c9d5f')
+md5sums=('f6de9c73396f84ca3dea595207c5186f')
+b2sums=('fe7fffaf7c8c2ae6e4e233bf530442f9c3f02716d446738e56e8de1e2962ea3b6332ec2764638ef2e00bf1cb939b8a81b40913232ddc7d4e4d6f27d51343a983')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-mosim/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-mosim/lilac.yaml

@@ -3,24 +3,27 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-biobase
 - r-dplyr
+- r-edger
 - r-ggplot2
 - r-hiddenmarkov
 - r-iranges
 - r-lazyeval
 - r-matrixstats
-- r-purrr
+- r-rcpp
 - r-rlang
 - r-s4vectors
-- r-scales
+- r-scran
+- r-seurat
+- r-signac
 - r-stringi
 - r-stringr
-- r-tibble
-- r-tidyr
 - r-zoo
+repo_makedepends:
+- r-cpp11
 update_on:
-- regex: MOSim_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/MOSim
+- source: rpkgs
+  pkgname: MOSim
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-ngsreports/PKGBUILD

@@ -1,31 +1,27 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=ngsReports
-_pkgver=2.4.0
+_pkgver=2.6.0
 pkgname=r-${_pkgname,,}
-pkgver=2.4.0
-pkgrel=2
-pkgdesc='Load FastqQC reports and other NGS related files'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('custom')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Load FastqQC reports and other NGS related files"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('LGPL-3.0-only')
 depends=(
-  r
   r-biocgenerics
   r-biostrings
   r-checkmate
   r-dplyr
-  r-dt
   r-forcats
   r-ggdendro
   r-ggplot2
   r-jsonlite
   r-lifecycle
   r-lubridate
-  r-pander
   r-patchwork
   r-plotly
-  r-readr
   r-reshape2
   r-rlang
   r-rmarkdown
@@ -39,20 +35,23 @@ depends=(
 optdepends=(
   r-biocstyle
   r-cairo
+  r-dt
   r-knitr
+  r-pander
+  r-readr
   r-testthat
   r-truncnorm
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('abc115a8dd01244ce57952cfbee1d09b675d40c8141d53c4fc33b4adb1a9145e')
+md5sums=('c080f808fd3a26fe71440f9c2051bab2')
+b2sums=('09daa5fa3d5cba8fae8cdabde776ae88bc9cd803a20fdae49a8c1fb0a1a946adcbeb954c39ee12541aafcb87eb887b522316fedf6f217963bf7d4065aa7871d4')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 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"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-ngsreports/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-ngsreports/lilac.yaml

@@ -7,17 +7,14 @@ repo_depends:
 - r-biostrings
 - r-checkmate
 - r-dplyr
-- r-dt
 - r-forcats
 - r-ggdendro
 - r-ggplot2
 - r-jsonlite
 - r-lifecycle
 - r-lubridate
-- r-pander
 - r-patchwork
 - r-plotly
-- r-readr
 - r-reshape2
 - r-rlang
 - r-rmarkdown
@@ -28,7 +25,8 @@ repo_depends:
 - r-tidyselect
 - r-zoo
 update_on:
-- regex: ngsReports_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/ngsReports
+- source: rpkgs
+  pkgname: ngsReports
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-poma/PKGBUILD

@@ -1,34 +1,36 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=POMA
-_pkgver=1.12.0
+_pkgver=1.14.0
 pkgname=r-${_pkgname,,}
-pkgver=1.12.0
-pkgrel=2
-pkgdesc='User-friendly Workflow for Metabolomics and Proteomics Data Analysis'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Tools for Omics Data Analysis"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-broom
   r-caret
   r-complexheatmap
   r-dbscan
   r-deseq2
   r-dplyr
+  r-fsa
   r-ggplot2
   r-ggrepel
-  r-glasso
   r-glmnet
   r-impute
+  r-janitor
   r-limma
+  r-lme4
   r-magrittr
   r-mixomics
   r-randomforest
   r-rankprod
-  r-rmarkdown
+  r-rlang
   r-summarizedexperiment
+  r-sva
   r-tibble
   r-tidyr
   r-uwot
@@ -38,6 +40,7 @@ optdepends=(
   r-biocstyle
   r-covr
   r-ggraph
+  r-ggtext
   r-knitr
   r-patchwork
   r-plotly
@@ -45,14 +48,15 @@ optdepends=(
   r-tidyverse
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('83f550759c222e7aa4a640a6bdb0ce8e66445d5389d96f7487d8ac624b7db921')
+md5sums=('2319e020f51efe618ec87124847cfbc4')
+b2sums=('992e5eafcebcc30a9d52249b86008f28b47d01925a1ffd396cbc204f12a34006f29c4e1139af44fdc7bd924a7853bd84528df4e24d58c76af03a8df47cfa4437')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-poma/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-poma/lilac.yaml

@@ -9,24 +9,28 @@ repo_depends:
 - r-dbscan
 - r-deseq2
 - r-dplyr
+- r-fsa
 - r-ggplot2
 - r-ggrepel
-- r-glasso
 - r-glmnet
 - r-impute
+- r-janitor
 - r-limma
+- r-lme4
 - r-magrittr
 - r-mixomics
 - r-randomforest
 - r-rankprod
-- r-rmarkdown
+- r-rlang
 - r-summarizedexperiment
+- r-sva
 - r-tibble
 - r-tidyr
 - r-uwot
 - r-vegan
 update_on:
-- regex: POMA_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/POMA
+- source: rpkgs
+  pkgname: POMA
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-qfeatures/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=QFeatures
-_pkgver=1.14.0
+_pkgver=1.14.1
 pkgname=r-${_pkgname,,}
-pkgver=1.14.0
-pkgrel=1
-pkgdesc='Quantitative features for mass spectrometry data'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Quantitative features for mass spectrometry data"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-annotationfilter
   r-biobase
   r-biocgenerics
@@ -21,8 +20,11 @@ depends=(
   r-multiassayexperiment
   r-plotly
   r-protgenerics
+  r-reshape2
   r-s4vectors
   r-summarizedexperiment
+  r-tidyr
+  r-tidyselect
 )
 optdepends=(
   r-biocstyle
@@ -36,9 +38,9 @@ optdepends=(
   r-imputelcmd
   r-knitr
   r-limma
-  r-matrix
   r-matrixstats
   r-msdata
+  r-msdatahub
   r-norm
   r-pcamethods
   r-preprocesscore
@@ -50,14 +52,15 @@ optdepends=(
   r-vsn
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('8569179537e59b6d68e4a5cc1780e877b71a59bbc390212b9968d23cdf5d6b62')
+md5sums=('406acbe6cc86562cc5126e35894b6531')
+b2sums=('a8f179c6d3d66b377aaf3ed28889d182c4857a48041f2fd17a99a8de495553cace112d906d22567af63a82f4b076f7d391daf6e95cd7a466374a878732b6a2ce')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-qfeatures/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-qfeatures/lilac.yaml

@@ -13,10 +13,14 @@ repo_depends:
 - r-multiassayexperiment
 - r-plotly
 - r-protgenerics
+- r-reshape2
 - r-s4vectors
 - r-summarizedexperiment
+- r-tidyr
+- r-tidyselect
 update_on:
-- regex: QFeatures_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/QFeatures
+- source: rpkgs
+  pkgname: QFeatures
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-qsutils/PKGBUILD

@@ -1,20 +1,20 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=QSutils
-_pkgver=1.20.0
+_pkgver=1.22.0
 pkgname=r-${_pkgname,,}
-pkgver=1.20.0
-pkgrel=2
-pkgdesc='Quasispecies Diversity'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('custom')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Quasispecies Diversity"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
-  r
   r-ape
   r-biocgenerics
   r-biostrings
   r-psych
+  r-pwalign
 )
 optdepends=(
   r-biocstyle
@@ -23,15 +23,15 @@ optdepends=(
   r-rmarkdown
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d964b12cf00cdf9ca665bddc2e56083b3a5e6a2751e5605790c7ce7894ac238c')
+md5sums=('e22810c5de4ffad732597e641c47b875')
+b2sums=('f3dfd16562db0643d532e67df559131caa6afee60cfca44fdd185b72b95fe782a850a1ce594c823556a1ccbce4654caa57c2d9d593a755a931c73b41a6b5a3c1')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 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"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-qsutils/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-qsutils/lilac.yaml

@@ -7,8 +7,10 @@ repo_depends:
 - r-biocgenerics
 - r-biostrings
 - r-psych
+- r-pwalign
 update_on:
-- regex: QSutils_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/QSutils
+- source: rpkgs
+  pkgname: QSutils
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-rrdp/PKGBUILD

@@ -1,31 +1,34 @@
-# system requirements: Java
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=rRDP
-_pkgver=1.36.0
+_pkgver=1.38.0
 pkgname=r-${_pkgname,,}
-pkgver=1.36.0
-pkgrel=2
-pkgdesc='Interface to the RDP Classifier'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Interface to the RDP Classifier"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only AND Apache-2.0 AND LGPL-2.1-only')
 depends=(
-  r
+  java-runtime
   r-biostrings
+  r-rjava
 )
 optdepends=(
+  r-knitr
+  r-rmarkdown
   r-rrdpdata
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('2c57d6b282c48d92b0362ab6f8e35293532ca3733ba1b679a2c33aac3126f478')
+md5sums=('c5a717da1389a34ff60abbaafe0c2e95')
+b2sums=('d789e17be4dc87fe772643c0f33ecd2dbb7a452883cd4a5662d2446281e8df9c35ea9525e070f166c8b61962a1bbe66cd0bf80c80e235edaafde161905915833')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-rrdp/lilac.py

@@ -1,12 +1,17 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(
+        _G,
+        expect_license = "GPL-2 + file LICENSE",
+        expect_systemrequirements = "Java JDK 1.4 or higher",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-rrdp/lilac.yaml

@@ -4,8 +4,10 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-biostrings
+- r-rjava
 update_on:
-- regex: rRDP_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/rRDP
+- source: rpkgs
+  pkgname: rRDP
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-rvs/PKGBUILD

@@ -1,19 +1,19 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=RVS
-_pkgver=1.24.0
+_pkgver=1.26.0
 pkgname=r-${_pkgname,,}
-pkgver=1.24.0
-pkgrel=2
-pkgdesc='Computes estimates of the probability of related individuals sharing a rare variant'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Computes estimates of the probability of related individuals sharing a rare variant"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
-  r
   r-genlib
   r-grain
   r-kinship2
+  r-r.utils
   r-snpstats
 )
 optdepends=(
@@ -24,14 +24,15 @@ optdepends=(
   r-variantannotation
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('a538323370013882ccdc88e79009a08569de8fb37ce1337caf52bfb80100fd5d')
+md5sums=('febdd7a2cdb41bfcc9159ba32798f708')
+b2sums=('f7924e7bfeca7be2ca0c73714de6ee22505c4827d510ea477754a542969091ada9ce180b8026797f6e5e36cb8271b81048727cba842ea40b7bfb39ab4da1077f')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-rvs/lilac.py

@@ -1,12 +1,13 @@
 #!/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():
-    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('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-rvs/lilac.yaml

@@ -6,9 +6,11 @@ repo_depends:
 - r-genlib
 - r-grain
 - r-kinship2
+- r-r.utils
 - r-snpstats
 update_on:
-- regex: RVS_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/RVS
+- source: rpkgs
+  pkgname: RVS
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-signac/PKGBUILD

@@ -0,0 +1,81 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=Signac
+_pkgver=1.13.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Analysis of Single-Cell Chromatin Data"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('MIT')
+depends=(
+  r-biocgenerics
+  r-data.table
+  r-dplyr
+  r-fastmatch
+  r-future
+  r-future.apply
+  r-genomeinfodb
+  r-genomicranges
+  r-ggplot2
+  r-iranges
+  r-irlba
+  r-lifecycle
+  r-patchwork
+  r-pbapply
+  r-rcpp
+  r-rcpproll
+  r-rlang
+  r-rsamtools
+  r-s4vectors
+  r-scales
+  r-seuratobject
+  r-stringi
+  r-tidyr
+  r-tidyselect
+  r-vctrs
+  zlib
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biostrings
+  r-biovizbase
+  r-bsgenome
+  r-chromvar
+  r-ggforce
+  r-ggrepel
+  r-ggseqlogo
+  r-lsa
+  r-miniui
+  r-motifmatchr
+  r-rtracklayer
+  r-seurat
+  r-shiny
+  r-summarizedexperiment
+  r-testthat
+  r-tfbstools
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('a0cb5bebb0496441c31efa4d50ee90f4')
+b2sums=('006d618df85a9ebcba6117f65f4889ecbe60a28b1c56f559ebc43bc44158c77f43b6103342198f76931c5945fe796aa38f1d8165f445406b6fa37b6de74327f7')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+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" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}

BioArchLinux/r-signac/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-signac/lilac.yaml

@@ -0,0 +1,43 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocgenerics
+- r-data.table
+- r-dplyr
+- r-fastmatch
+- r-future
+- r-future.apply
+- r-genomeinfodb
+- r-genomicranges
+- r-ggplot2
+- r-iranges
+- r-irlba
+- r-lifecycle
+- r-patchwork
+- r-pbapply
+- r-rcpp
+- r-rcpproll
+- r-rlang
+- r-rsamtools
+- r-s4vectors
+- r-scales
+- r-seuratobject
+- r-stringi
+- r-tidyr
+- r-tidyselect
+- r-vctrs
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: Signac
+  repo: cran
+  md5: true
+- alias: r
+- source: alpm
+  alpm: zlib
+  repo: core
+  provided: libz.so
+  strip_release: true