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

BioArchLinux/r-atena/PKGBUILD

@@ -1,23 +1,25 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=atena
-_pkgver=1.8.0
+_pkgver=1.10.0
 pkgname=r-${_pkgname,,}
-pkgver=1.8.0
-pkgrel=2
-pkgdesc='Analysis of Transposable Elements'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Analysis of Transposable Elements"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-annotationhub
   r-biocgenerics
   r-biocparallel
+  r-cli
   r-genomeinfodb
   r-genomicalignments
+  r-genomicfeatures
   r-genomicranges
   r-iranges
+  r-matrixgenerics
   r-matrixstats
   r-rsamtools
   r-s4vectors
@@ -35,14 +37,15 @@ optdepends=(
   r-txdb.dmelanogaster.ucsc.dm6.ensgene
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('cffe3ee62e8564012ec6cfa5e514a37eab1d2c10ce07eec4e80b16d3ccf1cfe1')
+md5sums=('1af6f43fd617b2c4d2d8ea14a71f7ced')
+b2sums=('cffe0fd0f4a20da45591339ab7a3ec1b6a7a1ab432518f7862ee626fd32d4df9bf8ba67b6f530ec4680a52ec32734efb983419aa43a8fa6e3ff74f941f2556af')
 
 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-atena/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-atena/lilac.yaml

@@ -6,10 +6,13 @@ repo_depends:
 - r-annotationhub
 - r-biocgenerics
 - r-biocparallel
+- r-cli
 - r-genomeinfodb
 - r-genomicalignments
+- r-genomicfeatures
 - r-genomicranges
 - r-iranges
+- r-matrixgenerics
 - r-matrixstats
 - r-rsamtools
 - r-s4vectors
@@ -17,7 +20,8 @@ repo_depends:
 - r-squarem
 - r-summarizedexperiment
 update_on:
-- regex: atena_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/atena
+- source: rpkgs
+  pkgname: atena
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-clustifyr/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=clustifyr
-_pkgver=1.14.0
+_pkgver=1.16.0
 pkgname=r-${_pkgname,,}
-pkgver=1.14.0
-pkgrel=2
-pkgdesc='Classifier for Single-cell RNA-seq Using Cell Clusters'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Classifier for Single-cell RNA-seq Using Cell Clusters"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
 license=('MIT')
 depends=(
-  r
   r-cowplot
   r-dplyr
   r-entropy
@@ -22,6 +21,7 @@ depends=(
   r-rlang
   r-s4vectors
   r-scales
+  r-seuratobject
   r-singlecellexperiment
   r-stringr
   r-summarizedexperiment
@@ -41,20 +41,22 @@ optdepends=(
   r-r.utils
   r-remotes
   r-rmarkdown
-  r-seurat
   r-shiny
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('f6ea4930a9179e9ea79423361d2841b027c58785a84c7ee2e29a9da51497d731')
+md5sums=('e636ea159b4fe186b37a723f523395d0')
+b2sums=('f8d280fb46591d82825ad306c3aee5c54d33af416c0c842f44d13cb10b34de69b9acaf441a8662ec7964a2fb6433672fc21e89c2afcd315ddf5b76b81b05076a')
 
 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-clustifyr/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-clustifyr/lilac.yaml

@@ -14,13 +14,15 @@ repo_depends:
 - r-rlang
 - r-s4vectors
 - r-scales
+- r-seuratobject
 - r-singlecellexperiment
 - r-stringr
 - r-summarizedexperiment
 - r-tibble
 - r-tidyr
 update_on:
-- regex: clustifyr_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/clustifyr
+- source: rpkgs
+  pkgname: clustifyr
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-degnorm/PKGBUILD

@@ -1,16 +1,16 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=DegNorm
-_pkgver=1.12.0
+_pkgver=1.14.0
 pkgname=r-${_pkgname,,}
-pkgver=1.12.0
-pkgrel=2
-pkgdesc='DegNorm: degradation normalization for RNA-seq data'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('LGPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="degradation normalization for RNA-seq data"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('LGPL-3.0-or-later')
 depends=(
-  r
+  blas
   r-data.table
   r-doparallel
   r-foreach
@@ -23,25 +23,29 @@ depends=(
   r-plotly
   r-plyr
   r-rcpp
-  r-rcpparmadillo
   r-rsamtools
   r-s4vectors
+  r-txdbmaker
   r-viridis
 )
+makedepends=(
+  r-rcpparmadillo
+)
 optdepends=(
   r-formatr
   r-knitr
   r-rmarkdown
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('dfde2d06f0dfd30f748f20a400390aa7dfd07407b90cc68a082445f21d6b57b4')
+md5sums=('ddec837f11060052bab42f70ca20d9ec')
+b2sums=('7c0949f8ab49e35495a2738ab0538db7e8c03f63faf8d39a27e4a68ca5c891901c3e5b8ec3720c8a4b3ef847a7f7ba8a01a543b52583905d7db997eb471e31cf')
 
 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-degnorm/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 = "LGPL (>= 3)",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-degnorm/lilac.yaml

@@ -15,12 +15,19 @@ repo_depends:
 - r-plotly
 - r-plyr
 - r-rcpp
-- r-rcpparmadillo
 - r-rsamtools
 - r-s4vectors
+- r-txdbmaker
 - r-viridis
+repo_makedepends:
+- r-rcpparmadillo
 update_on:
-- regex: DegNorm_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/DegNorm
+- source: rpkgs
+  pkgname: DegNorm
+  repo: bioc
+  md5: true
 - alias: r
+- source: alpmfiles
+  pkgname: blas
+  filename: usr/lib/libblas\.so\.([^.]+)
+  repo: extra

BioArchLinux/r-epitxdb/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=EpiTxDb
-_pkgver=1.14.1
+_pkgver=1.16.0
 pkgname=r-${_pkgname,,}
-pkgver=1.14.1
-pkgrel=2
-pkgdesc='Storing and accessing epitranscriptomic information using the AnnotationDbi interface'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Storing and accessing epitranscriptomic information using the AnnotationDbi interface"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-annotationdbi
   r-biocfilecache
   r-biocgenerics
@@ -23,9 +22,11 @@ depends=(
   r-httr
   r-iranges
   r-modstrings
+  r-rex
   r-rsqlite
   r-s4vectors
   r-trnadbimport
+  r-txdbmaker
   r-xml2
 )
 optdepends=(
@@ -43,14 +44,15 @@ optdepends=(
   r-txdb.hsapiens.ucsc.hg38.knowngene
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('ad425f358f3cd7b31efb8c29069b204bd9b83d90cf13638dd92f704826c78762')
+md5sums=('20e35a30fee32809fda75ba666f36a8c')
+b2sums=('ba8bf305321b12954444d77c2f46b35b1bccfb6e5f7da515192c9dde0fcecee8b2f8055f6dc4b9dcec8ee29f4a9a4472b4a9d82867135c600832ca7e7fc66b5d')
 
 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-epitxdb/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-epitxdb/lilac.yaml

@@ -15,12 +15,15 @@ repo_depends:
 - r-httr
 - r-iranges
 - r-modstrings
+- r-rex
 - r-rsqlite
 - r-s4vectors
 - r-trnadbimport
+- r-txdbmaker
 - r-xml2
 update_on:
-- regex: EpiTxDb_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/EpiTxDb
+- source: rpkgs
+  pkgname: EpiTxDb
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-peakpanther/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=peakPantheR
-_pkgver=1.16.1
+_pkgver=1.18.0
 pkgname=r-${_pkgname,,}
-pkgver=1.16.1
-pkgrel=2
-pkgdesc='Peak Picking and Annotation of High Resolution Experiments'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Peak Picking and Annotation of High Resolution Experiments"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-bslib
   r-doparallel
   r-dt
@@ -26,6 +25,7 @@ depends=(
   r-shiny
   r-shinycssloaders
   r-stringr
+  r-svglite
   r-xml
 )
 optdepends=(
@@ -39,14 +39,15 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('f91d3a7f3ae883d09cfd7b134a95b884c6be8df3f94b1b07209a9dfdeb21f120')
+md5sums=('fbe12ab960e941136d434a1a65a7f9f8')
+b2sums=('d5d3913cfef01d017256f89dcb1c7e4d992405d222e11ca1a4a8f2ce4313bbea62393f71af91cfd7964bd41ab2c56944e4f759ef21520de4f2ee97905882736e')
 
 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-peakpanther/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-peakpanther/lilac.yaml

@@ -18,9 +18,11 @@ repo_depends:
 - r-shiny
 - r-shinycssloaders
 - r-stringr
+- r-svglite
 - r-xml
 update_on:
-- regex: peakPantheR_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/peakPantheR
+- source: rpkgs
+  pkgname: peakPantheR
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-phantasus/PKGBUILD

@@ -1,25 +1,26 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=phantasus
-_pkgver=1.22.2
+_pkgver=1.24.0
 pkgname=r-${_pkgname,,}
-pkgver=1.22.2
-pkgrel=2
-pkgdesc='Visual and interactive gene expression analysis'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Visual and interactive gene expression analysis"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
 license=('MIT')
 depends=(
-  r
   r-annotationdbi
   r-assertthat
   r-biobase
   r-ccapp
+  r-config
   r-curl
   r-data.table
   r-deseq2
   r-edger
   r-fgsea
+  r-fs
   r-geoquery
   r-ggplot2
   r-gtable
@@ -29,30 +30,39 @@ depends=(
   r-jsonlite
   r-limma
   r-opencpu
+  r-phantasuslite
   r-pheatmap
   r-protolite
   r-rhdf5
+  r-rhdf5client
   r-rook
   r-scales
   r-stringr
   r-svglite
+  r-xml
+  r-yaml
 )
 optdepends=(
   r-biocstyle
   r-knitr
+  r-org.hs.eg.db
+  r-org.mm.eg.db
   r-rmarkdown
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d6490abd7e41769582081f2b5dd0cbea65f5ebc37d92c8a0a93dc8bf56e8dcfa')
+md5sums=('2f928065c75c3581ae26e7129339f1bc')
+b2sums=('66b0cd827bc5b3b77654daa61898521ca97090d94843f0552614302edaac7599283fcf6442dcdd638526c58380fbe888c171a8f79b7b7de67fe94b1f94d75c11')
 
 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-phantasus/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-phantasus/lilac.yaml

@@ -7,11 +7,13 @@ repo_depends:
 - r-assertthat
 - r-biobase
 - r-ccapp
+- r-config
 - r-curl
 - r-data.table
 - r-deseq2
 - r-edger
 - r-fgsea
+- r-fs
 - r-geoquery
 - r-ggplot2
 - r-gtable
@@ -21,15 +23,20 @@ repo_depends:
 - r-jsonlite
 - r-limma
 - r-opencpu
+- r-phantasuslite
 - r-pheatmap
 - r-protolite
 - r-rhdf5
+- r-rhdf5client
 - r-rook
 - r-scales
 - r-stringr
 - r-svglite
+- r-xml
+- r-yaml
 update_on:
-- regex: phantasus_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/phantasus
+- source: rpkgs
+  pkgname: phantasus
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-proactiv/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=proActiv
-_pkgver=1.12.0
+_pkgver=1.14.0
 pkgname=r-${_pkgname,,}
-pkgver=1.12.0
-pkgrel=2
-pkgdesc='Estimate Promoter Activity from RNA-Seq data'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Estimate Promoter Activity from RNA-Seq data"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
 license=('MIT')
 depends=(
-  r
   r-annotationdbi
   r-biocparallel
   r-data.table
@@ -28,6 +27,7 @@ depends=(
   r-scales
   r-summarizedexperiment
   r-tibble
+  r-txdbmaker
 )
 optdepends=(
   r-gridextra
@@ -37,15 +37,18 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('12727aa216c2884a461a63222e9503bec5930536e0cddc836c3966f6604a9501')
+md5sums=('b41f3047e8eea9f19a7829524e190786')
+b2sums=('7d0cef54045b3686fb4a0bca705fba52f2553b7a6704b7f26924c95b3dd5547d414ed5737d52b800a3dba08d8c16e1ea5314a7c1ccff4804c04f4e233e7986e5')
 
 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-proactiv/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-proactiv/lilac.yaml

@@ -20,8 +20,10 @@ repo_depends:
 - r-scales
 - r-summarizedexperiment
 - r-tibble
+- r-txdbmaker
 update_on:
-- regex: proActiv_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/proActiv
+- source: rpkgs
+  pkgname: proActiv
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-probamr/PKGBUILD

@@ -1,36 +1,37 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=proBAMr
-_pkgver=1.36.0
+_pkgver=1.38.0
 pkgname=r-${_pkgname,,}
-pkgver=1.36.0
-pkgrel=2
-pkgdesc='Generating SAM file for PSMs in shotgun proteomics data'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Generating SAM file for PSMs in shotgun proteomics data"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-annotationdbi
   r-biostrings
   r-genomicfeatures
   r-genomicranges
   r-iranges
   r-rtracklayer
+  r-txdbmaker
 )
 optdepends=(
   r-biocgenerics
   r-runit
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('3984b967cc0b8e5a853b7a2029fc6a996ac7fb55edae5569f4d33b8bc866c04a')
+md5sums=('94d83f4f906106e1da12c9f9fdbb6485')
+b2sums=('63572fc9ddb06b7e835c156c1cce4f71e07d25cf0ddf72582f1faa46c418da02fb3fb362707ebb97cdd5ae61b85f718088faff53ec86903cb834f87b2dd10e2c')
 
 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-probamr/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-probamr/lilac.yaml

@@ -9,8 +9,10 @@ repo_depends:
 - r-genomicranges
 - r-iranges
 - r-rtracklayer
+- r-txdbmaker
 update_on:
-- regex: proBAMr_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/proBAMr
+- source: rpkgs
+  pkgname: proBAMr
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-rcpi/PKGBUILD

@@ -1,20 +1,20 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=Rcpi
-_pkgver=1.38.0
+_pkgver=1.40.0
 pkgname=r-${_pkgname,,}
-pkgver=1.38.0
-pkgrel=4
-pkgdesc='Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-biostrings
   r-doparallel
   r-foreach
   r-gosemsim
+  r-pwalign
   r-rcurl
   r-rjson
   r-rlang
@@ -25,14 +25,15 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5a085bf6ee3b958a53a807ae558c8004f29adde466437edd92bc7984b7e0cbf2')
+md5sums=('a96804d0873834e384d594a6a0b87845')
+b2sums=('c79601c8cb2b028a93d73f0808647631833145922eceab6be786b7e407ac46dc37d6013293a918c3b865220d6668a538e40214714e0f5719b4b2595595430e3e')
 
 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-rcpi/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 = "Artistic-2.0 | file LICENSE",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-rcpi/lilac.yaml

@@ -7,11 +7,13 @@ repo_depends:
 - r-doparallel
 - r-foreach
 - r-gosemsim
+- r-pwalign
 - r-rcurl
 - r-rjson
 - r-rlang
 update_on:
-- regex: Rcpi_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/Rcpi
+- source: rpkgs
+  pkgname: Rcpi
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-recoup/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=recoup
-_pkgver=1.30.0
+_pkgver=1.32.0
 pkgname=r-${_pkgname,,}
-pkgver=1.30.0
-pkgrel=2
-pkgdesc='An R package for the creation of complex genomic profile plots'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="An R package for the creation of complex genomic profile plots"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
   r-biocgenerics
   r-biomart
   r-biostrings
@@ -28,12 +27,12 @@ depends=(
   r-rtracklayer
   r-s4vectors
   r-stringr
+  r-txdbmaker
 )
 optdepends=(
   r-biocmanager
   r-biocstyle
   r-bsgenome
-  r-grid
   r-knitr
   r-rmarkdown
   r-rmysql
@@ -41,14 +40,15 @@ optdepends=(
   r-zoo
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('7c26314ff1d0f12edab6f8773e6c0f30c98afd46bbd7d080ae3c74b517be53b0')
+md5sums=('8eed3be079e7850d78065e6faf64a07c')
+b2sums=('3c70f1054c63b501cc4b83be06f40cb982df1f62fb1886c7ed8387542f6ec319e194ac6a6d6dfcda7d4e44102957edcb1ba4aad3004a113f7cf53723755f8c12')
 
 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-recoup/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-recoup/lilac.yaml

@@ -20,8 +20,10 @@ repo_depends:
 - r-rtracklayer
 - r-s4vectors
 - r-stringr
+- r-txdbmaker
 update_on:
-- regex: recoup_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/recoup
+- source: rpkgs
+  pkgname: recoup
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-ribodipa/PKGBUILD

@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=RiboDiPA
-_pkgver=1.10.0
+_pkgver=1.12.0
 pkgname=r-${_pkgname,,}
-pkgver=1.10.0
-pkgrel=2
-pkgdesc='Differential pattern analysis for Ribo-seq data'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('LGPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Differential pattern analysis for Ribo-seq data"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('LGPL-3.0-or-later')
 depends=(
-  r
   r-biocfilecache
   r-biocgenerics
   r-data.table
@@ -29,20 +28,22 @@ depends=(
   r-reldist
   r-rsamtools
   r-s4vectors
+  r-txdbmaker
 )
 optdepends=(
   r-knitr
   r-rmarkdown
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('0fc423fe3ebd68e5f06da1f3a5316eb08f2d5db24733d6236ba1fa4712c0de00')
+md5sums=('d40e9c0d0b7ce710b4151487f7e5d855')
+b2sums=('e61ec6fe467c18bb102c285d754f022f2388b2e050098e8e1e1c24aa82c77fcb8ae9198c36547c07c1f96f99e98f6bffa74448ab3fc14b299fdd6c5680519e8e')
 
 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-ribodipa/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 = "LGPL (>= 3)",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-ribodipa/lilac.yaml

@@ -21,8 +21,10 @@ repo_depends:
 - r-reldist
 - r-rsamtools
 - r-s4vectors
+- r-txdbmaker
 update_on:
-- regex: RiboDiPA_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/RiboDiPA
+- source: rpkgs
+  pkgname: RiboDiPA
+  repo: bioc
+  md5: true
 - alias: r