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

BioArchLinux/r-aspli/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=ASpli
-_pkgver=2.12.0
+_pkgver=2.14.0
 pkgname=r-${_pkgname,,}
-pkgver=2.12.0
-pkgrel=2
-pkgdesc='Analysis of Alternative Splicing Using RNA-Seq'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Analysis of Alternative Splicing Using RNA-Seq"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-annotationdbi
   r-biocgenerics
   r-biocstyle
@@ -29,17 +28,19 @@ depends=(
   r-rsamtools
   r-s4vectors
   r-tidyr
+  r-txdbmaker
   r-upsetr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5e9ec698127d453cde27310b815b047da4114e0c89a00032104c38b7f7004166')
+md5sums=('0c318ecaa7d695b92852277fb46a2c05')
+b2sums=('fba656c6321a757e9575e53aa57b499f0b40e60ade6e9014b27cd12bb02e9b9260eff3f74395a0b1d56babf37d3a98277f5b2ca0cafc468fa394fefd222cbb50')
 
 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-aspli/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-aspli/lilac.yaml

@@ -21,9 +21,11 @@ repo_depends:
 - r-rsamtools
 - r-s4vectors
 - r-tidyr
+- r-txdbmaker
 - r-upsetr
 update_on:
-- regex: ASpli_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/ASpli
+- source: rpkgs
+  pkgname: ASpli
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-customprodb/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=customProDB
-_pkgver=1.42.1
+_pkgver=1.44.0
 pkgname=r-${_pkgname,,}
-pkgver=1.42.1
-pkgrel=2
-pkgdesc='Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-ahocorasicktrie
   r-annotationdbi
   r-biomart
@@ -28,6 +27,7 @@ depends=(
   r-rtracklayer
   r-s4vectors
   r-stringr
+  r-txdbmaker
   r-variantannotation
 )
 optdepends=(
@@ -35,14 +35,15 @@ optdepends=(
   r-rmariadb
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('28be9c341aa2bc3e2c89560f041c5c3c23e6018de4591949f91a22043b3b51fc')
+md5sums=('fbeece69015d5687c3cc2ff4cd0b6544')
+b2sums=('2191f16d8759b32453cc923b72d7c1af4340b12c75f54604e07e7217b0759cdfa61a47ad85d1c46202d9f458d93159f2284c78b106b0a98e25f7b3cfb754a5f4')
 
 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-customprodb/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-customprodb/lilac.yaml

@@ -20,9 +20,11 @@ repo_depends:
 - r-rtracklayer
 - r-s4vectors
 - r-stringr
+- r-txdbmaker
 - r-variantannotation
 update_on:
-- regex: customProDB_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/customProDB
+- source: rpkgs
+  pkgname: customProDB
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-dominoeffect/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=DominoEffect
-_pkgver=1.22.0
+_pkgver=1.24.0
 pkgname=r-${_pkgname,,}
-pkgver=1.22.0
-pkgrel=2
-pkgdesc='Identification and Annotation of Protein Hotspot Residues'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Identification and Annotation of Protein Hotspot Residues"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
   r-annotationdbi
   r-biomart
   r-biostrings
@@ -18,6 +17,7 @@ depends=(
   r-genomeinfodb
   r-genomicranges
   r-iranges
+  r-pwalign
   r-summarizedexperiment
   r-variantannotation
 )
@@ -27,14 +27,15 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('f06fecfec8481f8eb6a049e4f28a23a49e957c362ecc55ac1166de8007cb4701')
+md5sums=('75738ae6c59cfed0643a3bb2da6cd8cc')
+b2sums=('12a601b4463ddaf4ab6e95eda0a274a5cdd8af2f0749011dc7455c72476e4517c7b6b59c7b96e9c182451fa1f1bc6e85a6b7bbf0978e85fa633aa942ff2d17e1')
 
 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-dominoeffect/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-dominoeffect/lilac.yaml

@@ -10,10 +10,12 @@ repo_depends:
 - r-genomeinfodb
 - r-genomicranges
 - r-iranges
+- r-pwalign
 - r-summarizedexperiment
 - r-variantannotation
 update_on:
-- regex: DominoEffect_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/DominoEffect
+- source: rpkgs
+  pkgname: DominoEffect
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-escape/PKGBUILD

@@ -1,21 +1,21 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=escape
-_pkgver=1.12.0
+_pkgver=2.0.0
 pkgname=r-${_pkgname,,}
-pkgver=1.12.0
-pkgrel=2
-pkgdesc='Easy single cell analysis platform for enrichment'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Apache')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Easy single cell analysis platform for enrichment"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('MIT')
 depends=(
-  r
+  r-aucell
   r-biocparallel
-  r-broom
-  r-data.table
   r-dplyr
+  r-ggdist
   r-ggplot2
+  r-ggpointdensity
   r-ggridges
   r-gseabase
   r-gsva
@@ -23,7 +23,7 @@ depends=(
   r-msigdbr
   r-patchwork
   r-reshape2
-  r-rlang
+  r-seuratobject
   r-singlecellexperiment
   r-stringr
   r-summarizedexperiment
@@ -31,23 +31,31 @@ depends=(
 )
 optdepends=(
   r-biocstyle
-  r-dittoseq
+  r-hexbin
   r-knitr
   r-markdown
+  r-rcolorbrewer
+  r-rlang
   r-rmarkdown
+  r-scran
   r-seurat
-  r-seuratobject
+  r-spelling
   r-testthat
+  r-vdiffr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d69dda267e9346b1d3f10274fb0985409d23060abba609d4e8859eae92b1b12e')
+md5sums=('7b3c16032574ae1639cf3d8b0f4eda1a')
+b2sums=('85b0342930e2971515787fbd0739062c8a8faecb6a8bb7a73b93c9fe8c79994c90a4b8fa3f3cf0919e155f3cd316d6afc15f5e55335cd49b93cbd7ebadacc5bd')
 
 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-escape/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-escape/lilac.yaml

@@ -3,11 +3,12 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
+- r-aucell
 - r-biocparallel
-- r-broom
-- r-data.table
 - r-dplyr
+- r-ggdist
 - r-ggplot2
+- r-ggpointdensity
 - r-ggridges
 - r-gseabase
 - r-gsva
@@ -15,13 +16,14 @@ repo_depends:
 - r-msigdbr
 - r-patchwork
 - r-reshape2
-- r-rlang
+- r-seuratobject
 - r-singlecellexperiment
 - r-stringr
 - r-summarizedexperiment
 - r-ucell
 update_on:
-- regex: escape_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/escape
+- source: rpkgs
+  pkgname: escape
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-flames/PKGBUILD

@@ -1,17 +1,17 @@
-# system requirements: GNU make, C++11
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=FLAMES
-_pkgver=1.8.0
+_pkgver=1.10.0
 pkgname=r-${_pkgname,,}
-pkgver=1.8.0
-pkgrel=2
-pkgdesc='FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Full Length Analysis of Mutations and Splicing in long read RNA-seq data"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
+  bzip2
+  curl
   r-bambu
   r-basilisk
   r-biocgenerics
@@ -30,13 +30,12 @@ depends=(
   r-ggplot2
   r-gridextra
   r-igraph
+  r-iranges
   r-jsonlite
   r-magrittr
   r-multiassayexperiment
   r-rcolorbrewer
-  r-rcpp
   r-reticulate
-  r-rhtslib
   r-rsamtools
   r-rtracklayer
   r-s4vectors
@@ -46,9 +45,19 @@ depends=(
   r-singlecellexperiment
   r-stringr
   r-summarizedexperiment
+  r-tibble
   r-tidyr
+  r-tidyselect
+  r-txdbmaker
   r-withr
   r-zlibbioc
+  xz
+  zlib
+)
+makedepends=(
+  r-rcpp
+  r-rhtslib
+  r-testthat
 )
 optdepends=(
   r-biocfilecache
@@ -61,16 +70,18 @@ optdepends=(
   r-shortread
   r-testthat
   r-uwot
+  r-xml2
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('da12030c47ad7d766a7a76ed97e5fb089af15fd1c78846afba7b11089efa6724')
+md5sums=('b4f8a2b352544fb940fcf3718956872f')
+b2sums=('dfd4f5cc647abf971173b45968ab8862322bbe5b9d5322315abebedc44a748e6cc3e19291ecccda09adf1fe82107a323b697d662543378b78888198a767eaa03')
 
 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-flames/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 = "GNU make, C++17, samtools (>= 1.19), minimap2 (>= 2.17)",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-flames/lilac.yaml

@@ -21,13 +21,12 @@ repo_depends:
 - r-ggplot2
 - r-gridextra
 - r-igraph
+- r-iranges
 - r-jsonlite
 - r-magrittr
 - r-multiassayexperiment
 - r-rcolorbrewer
-- r-rcpp
 - r-reticulate
-- r-rhtslib
 - r-rsamtools
 - r-rtracklayer
 - r-s4vectors
@@ -37,11 +36,39 @@ repo_depends:
 - r-singlecellexperiment
 - r-stringr
 - r-summarizedexperiment
+- r-tibble
 - r-tidyr
+- r-tidyselect
+- r-txdbmaker
 - r-withr
 - r-zlibbioc
+repo_makedepends:
+- r-rcpp
+- r-rhtslib
+- r-testthat
 update_on:
-- regex: FLAMES_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/FLAMES
+- source: rpkgs
+  pkgname: FLAMES
+  repo: bioc
+  md5: true
 - alias: r
+- source: alpm
+  alpm: bzip2
+  repo: core
+  provided: libbz2.so
+  strip_release: true
+- source: alpm
+  alpm: curl
+  repo: core
+  provided: libcurl.so
+  strip_release: true
+- source: alpm
+  alpm: xz
+  repo: core
+  provided: liblzma.so
+  strip_release: true
+- source: alpm
+  alpm: zlib
+  repo: core
+  provided: libz.so
+  strip_release: true

BioArchLinux/r-ggspavis/PKGBUILD

@@ -1,18 +1,20 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=ggspavis
-_pkgver=1.8.1
+_pkgver=1.9.10
 pkgname=r-${_pkgname,,}
-pkgver=1.8.1
-pkgrel=2
-pkgdesc='Visualization functions for spatially resolved transcriptomics data'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Visualization functions for spatial transcriptomics data"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
 license=('MIT')
 depends=(
-  r
   r-ggplot2
+  r-ggrepel
   r-ggside
+  r-rcolorbrewer
+  r-scales
   r-singlecellexperiment
   r-spatialexperiment
   r-summarizedexperiment
@@ -21,6 +23,7 @@ optdepends=(
   r-biocstyle
   r-bumpymatrix
   r-knitr
+  r-patchwork
   r-rmarkdown
   r-scater
   r-scran
@@ -29,15 +32,18 @@ optdepends=(
   r-uwot
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('3d77170f633c44140baf45b7051ff7ce2f770d184877818ebb6e88464e3e1d18')
+md5sums=('8ae0e48cac33cc32aa212747aaf43a16')
+b2sums=('c5e8f86f6dd734605737c40198bda606adcdadfcb60489909d96dbd704061537df4939099ef4b77884dcb290a6eb79b76cca6203c0c5f71570044bb04874bfad')
 
 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-ggspavis/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-ggspavis/lilac.yaml

@@ -4,12 +4,16 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-ggplot2
+- r-ggrepel
 - r-ggside
+- r-rcolorbrewer
+- r-scales
 - r-singlecellexperiment
 - r-spatialexperiment
 - r-summarizedexperiment
 update_on:
-- regex: ggspavis_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/ggspavis
+- source: rpkgs
+  pkgname: ggspavis
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-hireadsprocessor/PKGBUILD

@@ -1,17 +1,15 @@
-# system requirements: BLAT, UCSC hg18 in 2bit format for BLAT
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=hiReadsProcessor
-_pkgver=1.38.0
+_pkgver=1.40.0
 pkgname=r-${_pkgname,,}
-pkgver=1.38.0
-pkgrel=2
-pkgdesc='Functions to process LM-PCR reads from 454/Illumina data'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Functions to process LM-PCR reads from 454/Illumina data"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-biocgenerics
   r-biocparallel
   r-biostrings
@@ -19,6 +17,7 @@ depends=(
   r-genomicalignments
   r-genomicranges
   r-hiannotator
+  r-pwalign
   r-readxl
   r-soniclength
 )
@@ -28,14 +27,15 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('ba8924a92f80f6aefa9f64070d5806428c15bd8430410ffdc94de54130246f36')
+md5sums=('a77515300961f592ea26eb818b1b6a32')
+b2sums=('86c4fde4bee6e9fa5b2b5f349d38a53de47ef1c6172ee9030ca0ae03dc0a8303e7e3d5ae0140d9b53ab2cd423af6e0113f52b63a9b86aa6196950c58bea10906')
 
 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-hireadsprocessor/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 = "BLAT, UCSC hg18 in 2bit format for BLAT",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-hireadsprocessor/lilac.yaml

@@ -10,10 +10,12 @@ repo_depends:
 - r-genomicalignments
 - r-genomicranges
 - r-hiannotator
+- r-pwalign
 - r-readxl
 - r-soniclength
 update_on:
-- regex: hiReadsProcessor_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/hiReadsProcessor
+- source: rpkgs
+  pkgname: hiReadsProcessor
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-interest/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=IntEREst
-_pkgver=1.26.0
+_pkgver=1.28.0
 pkgname=r-${_pkgname,,}
-pkgver=1.26.0
-pkgrel=2
-pkgdesc='Intron-Exon Retention Estimator'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Intron-Exon Retention Estimator"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
-  r
   r-biocgenerics
   r-biocparallel
   r-biostrings
@@ -29,6 +28,7 @@ depends=(
   r-seqinr
   r-seqlogo
   r-summarizedexperiment
+  r-txdbmaker
 )
 optdepends=(
   r-bsgenome.hsapiens.ucsc.hg19
@@ -37,14 +37,15 @@ optdepends=(
   r-rmarkdown
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('ee1f9d05316744a28bd404f2041c0e63438e8453e5456e783781e9f9235b473f')
+md5sums=('34b2ef2a05b7c64d9ca8091957da686f')
+b2sums=('5ddc5e1e14b43223671c5a7452440a034033aa7983a66b4e08fb12c58f9e55f5f7339e61aaa2640148773703463450a6323d40492822eee550a4af53bbcb5a7d')
 
 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-interest/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-interest/lilac.yaml

@@ -21,8 +21,10 @@ repo_depends:
 - r-seqinr
 - r-seqlogo
 - r-summarizedexperiment
+- r-txdbmaker
 update_on:
-- regex: IntEREst_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/IntEREst
+- source: rpkgs
+  pkgname: IntEREst
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-jaspar2024/PKGBUILD

@@ -0,0 +1,33 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=JASPAR2024
+_pkgver=0.99.6
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Data package for JASPAR database (version 2024)"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
+depends=(
+  r-biocfilecache
+)
+optdepends=(
+  r-biocstyle
+  r-knitr
+  r-rmarkdown
+  r-rsqlite
+)
+source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('9c8144547873a36473a5f9cad793f578')
+b2sums=('5004a5b32dea164588389586376b0dd52303c989dfe1f72a2784490c7f328b697ef7adc2968601542f8ba80f860c87ad571693a2ae955c3fa361022493f39eb2')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-jaspar2024/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-jaspar2024/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocfilecache
+update_on:
+- source: rpkgs
+  pkgname: JASPAR2024
+  repo: bioc-data-annotation
+  md5: true
+- alias: r

BioArchLinux/r-magar/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=MAGAR
-_pkgver=1.10.0
+_pkgver=1.12.0
 pkgname=r-${_pkgname,,}
-pkgver=1.10.0
-pkgrel=2
-pkgdesc='MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-argparse
   r-bigstatsr
   r-crlmm
@@ -26,6 +25,7 @@ depends=(
   r-rjson
   r-rnbeads
   r-rnbeads.hg19
+  r-rnbeads.hg38
   r-snpstats
   r-upsetr
 )
@@ -46,14 +46,15 @@ optdepends=(
   r-venndiagram
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('ba32845894424388558fc9e5db7d6c199e656b79abc7ad89db7fed399f6063fa')
+md5sums=('8be03f80b6556ec3a2e79c29a0cbc114')
+b2sums=('7533aa381e4c74936a34311d67dfc662f298ed6bfb588b266c0bfaa904e0a31a32777a49211c01affdc1900217af7d48de1873b9f17afe60fe92a8b16ec98cee')
 
 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-magar/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-magar/lilac.yaml

@@ -18,10 +18,12 @@ repo_depends:
 - r-rjson
 - r-rnbeads
 - r-rnbeads.hg19
+- r-rnbeads.hg38
 - r-snpstats
 - r-upsetr
 update_on:
-- regex: MAGAR_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/MAGAR
+- source: rpkgs
+  pkgname: MAGAR
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-metaseqr2/PKGBUILD

@@ -1,18 +1,16 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=metaseqR2
-_pkgver=1.14.0
+_pkgver=1.16.0
 pkgname=r-${_pkgname,,}
-pkgver=1.14.0
-pkgrel=2
-pkgdesc='An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
   r-absseq
-  r-bayseq
   r-biobase
   r-biocgenerics
   r-biocparallel
@@ -52,6 +50,7 @@ depends=(
   r-stringr
   r-summarizedexperiment
   r-survcomp
+  r-txdbmaker
   r-venndiagram
   r-vsn
   r-yaml
@@ -59,21 +58,22 @@ depends=(
 )
 optdepends=(
   r-biocmanager
+  r-biocstyle
   r-bsgenome
   r-knitr
   r-rmysql
   r-runit
-  r-tcc
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('c590809d04fdcd8b7f3de13f531cfbc60b2aa47ab697926b1fcfc8683652e9e9')
+md5sums=('a406f8ff6d42c145b6b2bc0982d9faa4')
+b2sums=('1967c3caf3b366a9ec9f26a7e154a8313b7d809e6784179df3d9d230c15dadd3f1012873f3b7c49a20b11e4f11fa9a1be30f6aa12343bcb73aa5e36e18fc743f')
 
 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-metaseqr2/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-metaseqr2/lilac.yaml

@@ -4,7 +4,6 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-absseq
-- r-bayseq
 - r-biobase
 - r-biocgenerics
 - r-biocparallel
@@ -44,12 +43,14 @@ repo_depends:
 - r-stringr
 - r-summarizedexperiment
 - r-survcomp
+- r-txdbmaker
 - r-venndiagram
 - r-vsn
 - r-yaml
 - r-zoo
 update_on:
-- regex: metaseqR2_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/metaseqR2
+- source: rpkgs
+  pkgname: metaseqR2
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-methreg/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=MethReg
-_pkgver=1.12.0
+_pkgver=1.14.0
 pkgname=r-${_pkgname,,}
-pkgver=1.12.0
-pkgrel=2
-pkgdesc='Assessing the regulatory potential of DNA methylation regions or sites on gene transcription'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Assessing the regulatory potential of DNA methylation regions or sites on gene transcription"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-annotationhub
   r-delayedarray
   r-dplyr
@@ -19,17 +18,21 @@ depends=(
   r-ggplot2
   r-ggpubr
   r-iranges
+  r-jaspar2024
+  r-openxlsx
   r-plyr
   r-progress
   r-pscl
   r-readr
   r-rlang
+  r-rsqlite
   r-s4vectors
   r-sesame
   r-sesamedata
   r-sfsmisc
   r-stringr
   r-summarizedexperiment
+  r-tfbstools
   r-tibble
   r-tidyr
 )
@@ -43,33 +46,29 @@ optdepends=(
   r-doparallel
   r-dorothea
   r-downloader
-  r-downloader
   r-htmltools
-  r-jaspar2022
   r-jpeg
   r-knitr
   r-matrixstats
   r-motifmatchr
-  r-openxlsx
-  r-parallel
   r-png
   r-r.utils
   r-reshape2
   r-rmarkdown
   r-stager
   r-testthat
-  r-tfbstools
   r-viper
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('56d0158f27fca8c25a26aceeffb3de7ffcdb98aade3ffb8748eee44d5b1114c3')
+md5sums=('d0b31767857b067628875b92dfa6fa7d')
+b2sums=('e9a912a0f59b1163e51cc8b8ef53bacbb75b1dbf19999c4fbbf9d52f72d20c6756d9482b65a78ff349dc488f2db24e4cda3f172e0982d21abeb0e644d7501380')
 
 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-methreg/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-methreg/lilac.yaml

@@ -11,21 +11,26 @@ repo_depends:
 - r-ggplot2
 - r-ggpubr
 - r-iranges
+- r-jaspar2024
+- r-openxlsx
 - r-plyr
 - r-progress
 - r-pscl
 - r-readr
 - r-rlang
+- r-rsqlite
 - r-s4vectors
 - r-sesame
 - r-sesamedata
 - r-sfsmisc
 - r-stringr
 - r-summarizedexperiment
+- r-tfbstools
 - r-tibble
 - r-tidyr
 update_on:
-- regex: MethReg_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/MethReg
+- source: rpkgs
+  pkgname: MethReg
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-ribosomeprofilingqc/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=ribosomeProfilingQC
-_pkgver=1.14.1
+_pkgver=1.16.0
 pkgname=r-${_pkgname,,}
-pkgver=1.14.1
-pkgrel=2
-pkgdesc='Ribosome Profiling Quality Control'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Ribosome Profiling Quality Control"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
   r-annotationdbi
   r-biocgenerics
   r-biostrings
@@ -20,6 +19,7 @@ depends=(
   r-genomicalignments
   r-genomicfeatures
   r-genomicranges
+  r-ggextra
   r-ggfittext
   r-ggplot2
   r-ggrepel
@@ -31,27 +31,33 @@ depends=(
   r-ruvseq
   r-s4vectors
   r-scales
+  r-txdbmaker
   r-xvector
 )
 optdepends=(
+  r-ashr
+  r-biobase
   r-biocstyle
   r-bsgenome.drerio.ucsc.danrer10
+  r-deseq2
   r-edger
   r-knitr
   r-limma
   r-rmarkdown
   r-runit
   r-testthat
+  r-vsn
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('c7460cca1cc4a2a730670ba59f6a05659deef401075e0bc74aed98f3cf03214d')
+md5sums=('d633d56b98baef25b32f80e354eb9e8f')
+b2sums=('e2e0d0c504111989bb2805be01036f84f7e83c7bb8648d8b611822a4de69313d5c3cb6a0a9d8c794877c5bb2ad80589d32834fb3b9f6d3f777d1c8fbfb5d6b9b')
 
 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-ribosomeprofilingqc/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-ribosomeprofilingqc/lilac.yaml

@@ -12,6 +12,7 @@ repo_depends:
 - r-genomicalignments
 - r-genomicfeatures
 - r-genomicranges
+- r-ggextra
 - r-ggfittext
 - r-ggplot2
 - r-ggrepel
@@ -23,9 +24,11 @@ repo_depends:
 - r-ruvseq
 - r-s4vectors
 - r-scales
+- r-txdbmaker
 - r-xvector
 update_on:
-- regex: ribosomeProfilingQC_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/ribosomeProfilingQC
+- source: rpkgs
+  pkgname: ribosomeProfilingQC
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-rnbeads.hg38/PKGBUILD

@@ -0,0 +1,30 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=RnBeads.hg38
+_pkgver=1.36.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="RnBeads.hg38"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
+depends=(
+  r-genomicranges
+)
+optdepends=(
+  r-rnbeads
+)
+source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('bc0a6b6c9dae6663329d419b38112e0f')
+b2sums=('d1e4fc11a94abd231fbc3a39b432684184a3576e93d8283276dd52dc7aa9110944b50507ca19ef71e77f7a31610e5e1c3d7eb9e2b1751c4d68f0f7ef62f7f1cc')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-rnbeads.hg38/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-rnbeads.hg38/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-genomicranges
+update_on:
+- source: rpkgs
+  pkgname: RnBeads.hg38
+  repo: bioc-data-experiment
+  md5: true
+- alias: r

BioArchLinux/r-scanmirapp/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=scanMiRApp
-_pkgver=1.8.0
+_pkgver=1.10.0
 pkgname=r-${_pkgname,,}
-pkgver=1.8.0
-pkgrel=2
-pkgdesc='scanMiR shiny application'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="scanMiR shiny application"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-annotationdbi
   r-annotationfilter
   r-annotationhub
@@ -36,13 +35,15 @@ depends=(
   r-shiny
   r-shinycssloaders
   r-shinydashboard
-  r-waiter
   r-shinyjqui
+  r-txdbmaker
+  r-waiter
 )
 optdepends=(
   r-biocstyle
   r-bsgenome.hsapiens.ucsc.hg38
   r-bsgenome.mmusculus.ucsc.mm10
+  r-bsgenome.mmusculus.ucsc.mm39
   r-bsgenome.rnorvegicus.ucsc.rn6
   r-knitr
   r-rmarkdown
@@ -50,14 +51,15 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('c9b97ba39395ca75fd844b0cb9e397cb733115961697336df628bb5049dd36e6')
+md5sums=('ffd8892c002d452584bbf670cd293e25')
+b2sums=('07e30009918f36cc2d11680aa77f057f2baf2cbeaa6b31b4dcdcc7249764cd1cfd13e72aa0160a7ab24706e11c19237f5eb119392e82a6d1b20c936e7af6af9e')
 
 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-scanmirapp/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-scanmirapp/lilac.yaml

@@ -28,10 +28,12 @@ repo_depends:
 - r-shiny
 - r-shinycssloaders
 - r-shinydashboard
-- r-waiter
 - r-shinyjqui
+- r-txdbmaker
+- r-waiter
 update_on:
-- regex: scanMiRApp_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/scanMiRApp
+- source: rpkgs
+  pkgname: scanMiRApp
+  repo: bioc
+  md5: true
 - alias: r