r-*: use old Bioconductor sources for some packages

These packages don't have a source archive in the latest Bioconductor release.
2025-03-10 12:02:42 +00:00 · 2024-02-12 18:50:23 +02:00 · 2024-02-12 18:50:23 +02:00 · 402eee338e
commit 402eee338e
parent 1058174b43
24 changed files with 174 additions and 161 deletions
--- a/BioArchLinux/r-deco/PKGBUILD
+++ b/BioArchLinux/r-deco/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=deco
 _pkgver=1.13.0
 pkgname=r-${_pkgname,,}
-pkgver=1.13.0
+pkgver=${_pkgver//-/.}
 pkgrel=2
-pkgdesc='Decomposing Heterogeneous Cohorts using Omic Data Profiling'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Decomposing Heterogeneous Cohorts using Omic Data Profiling"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
  r-ade4
  r-annotationdbi
  r-biobase
@ -36,15 +35,16 @@ optdepends=(
  r-multiassayexperiment
  r-rmarkdown
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('dc2e473826e54f53599ae6a8aced81304a841177f75068b45a4c983d5c5c8a34')
+source=("https://bioconductor.org/packages/3.16/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('2a6fcb887712cc6591e2800ed5b6f953')
+b2sums=('ff6427893e0be97660c3a729c18786fada53c61405cf23b3a37659287effaefafed2d4f35fbe87df6e43f689334568ea77051f8621cd45319d43cd7a9d0e0066')

 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:
--- a/BioArchLinux/r-deco/lilac.py
+++ b/BioArchLinux/r-deco/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)",
+    )

 def post_build():
    git_pkgbuild_commit()
--- a/BioArchLinux/r-deco/lilac.yaml
+++ b/BioArchLinux/r-deco/lilac.yaml
@ -21,7 +21,6 @@ repo_depends:
 - r-sfsmisc
 - r-summarizedexperiment
 update_on:
- regex: deco_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/deco
+- source: manual
+  manual: 1.13.0#2a6fcb887712cc6591e2800ed5b6f953
 - alias: r
--- a/BioArchLinux/r-dpeak/PKGBUILD
+++ b/BioArchLinux/r-dpeak/PKGBUILD
@ -1,17 +1,15 @@
-# system requirements: GNU make, meme, fimo
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>

 _pkgname=dpeak
 _pkgver=1.12.0
 pkgname=r-${_pkgname,,}
-pkgver=1.12.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='dPeak (Deconvolution of Peaks in ChIP-seq Analysis)'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="dPeak (Deconvolution of Peaks in ChIP-seq Analysis)"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
  r-bsgenome
  r-iranges
  r-rcpp
@ -19,15 +17,16 @@ depends=(
 optdepends=(
  r-bsgenome.ecoli.ncbi.20080805
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('850f40e7d6b47ed44ac2c614a711136ba4119629cad531679993c98a59cea2bb')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('7295c2b08b272b157f9345ef6c5a86d3')
+b2sums=('c604c9d09b919c0ef46f07e3ef327aaa050b304f60da5da1695783b6b3ecdb406b8ce7baca3e0133d6294df9d7c4e184feaf19ea07b9edfa482927f075bb5b7e')

 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:
--- a/BioArchLinux/r-dpeak/lilac.py
+++ b/BioArchLinux/r-dpeak/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, meme, fimo",
+    )

 def post_build():
    git_pkgbuild_commit()
--- a/BioArchLinux/r-dpeak/lilac.yaml
+++ b/BioArchLinux/r-dpeak/lilac.yaml
@ -7,7 +7,6 @@ repo_depends:
 - r-iranges
 - r-rcpp
 update_on:
- regex: dpeak_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/dpeak
+- source: manual
+  manual: 1.12.0#7295c2b08b272b157f9345ef6c5a86d3
 - alias: r
--- a/BioArchLinux/r-gcsscore/PKGBUILD
+++ b/BioArchLinux/r-gcsscore/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=GCSscore
 _pkgver=1.14.0
 pkgname=r-${_pkgname,,}
-pkgver=1.14.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='GCSscore: an R package for microarray analysis for Affymetrix/Thermo Fisher arrays'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="an R package for microarray analysis for Affymetrix/Thermo Fisher arrays"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
  r-affxparser
  r-biobase
  r-biocmanager
@ -25,15 +24,16 @@ optdepends=(
  r-r.utils
  r-siggenes
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('e33e180488ea2faaf49f735f214c204a625b79bd0ec5c7f76d735d7a9f06193b')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('80b3d2f6dfd1ff31fc433b40443e13b0')
+b2sums=('0e90d6b87e296ea36889831c7a0c602f9e24a8ee4cd80a2577c60fcdfe10ee4dd8d37a55d90c7970aff3fa2897d832c79a6ce92753023f20a21a48fdfdfffdd2')

 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:
--- a/BioArchLinux/r-gcsscore/lilac.py
+++ b/BioArchLinux/r-gcsscore/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)",
+    )

 def post_build():
    git_pkgbuild_commit()
--- a/BioArchLinux/r-gcsscore/lilac.yaml
+++ b/BioArchLinux/r-gcsscore/lilac.yaml
@ -12,7 +12,6 @@ repo_depends:
 - r-rsqlite
 - r-stringr
 update_on:
- regex: GCSscore_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/GCSscore
+- source: manual
+  manual: 1.14.0#80b3d2f6dfd1ff31fc433b40443e13b0
 - alias: r
--- a/BioArchLinux/r-grridge/PKGBUILD
+++ b/BioArchLinux/r-grridge/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=GRridge
 _pkgver=1.22.0
 pkgname=r-${_pkgname,,}
-pkgver=1.22.0
+pkgver=${_pkgver//-/.}
 pkgrel=2
-pkgdesc='Better prediction by use of co-data: Adaptive group-regularized ridge regression'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Better prediction by use of co-data: Adaptive group-regularized ridge regression"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
  r-glmnet
  r-graph
  r-iso
@ -20,15 +19,16 @@ depends=(
 optdepends=(
  r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('c3d99f251e8dc94fce4aa7d6eacaffdc63576f4c7003d2f1a8714cde40a9bc6e')
+source=("https://bioconductor.org/packages/3.16/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('5c7da0baf7039c0cf766a9b0f904c1dd')
+b2sums=('f9c08f51d87b9102f3295959b3da553780c3b4078ce07b2653dd856314f5cbe2eaaf1dda109f00fcab0bcd55172e4180c4fe7ef773a34ee896db6df7dad65dc6')

 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:
--- a/BioArchLinux/r-grridge/lilac.py
+++ b/BioArchLinux/r-grridge/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()
--- a/BioArchLinux/r-grridge/lilac.yaml
+++ b/BioArchLinux/r-grridge/lilac.yaml
@ -9,7 +9,6 @@ repo_depends:
 - r-mvtnorm
 - r-penalized
 update_on:
- regex: GRridge_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/GRridge
+- source: manual
+  manual: 1.22.0#5c7da0baf7039c0cf766a9b0f904c1dd
 - alias: r
--- a/BioArchLinux/r-neighbornet/PKGBUILD
+++ b/BioArchLinux/r-neighbornet/PKGBUILD
@ -3,25 +3,25 @@
 _pkgname=NeighborNet
 _pkgver=1.18.0
 pkgname=r-${_pkgname,,}
-pkgver=1.18.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Neighbor_net analysis'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('CCPL:by-nc-sa')
+pkgdesc="Neighbor_net analysis"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('CC-BY-NC-ND-4.0')
 depends=(
-  r
  r-graph
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('08cb505e613ec82e7d4404dde37f6d6718f1dd2d23392809e7e77c9ed209d310')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('d39375ac39ea34b0bd06ffd019eac6ee')
+b2sums=('895783555f8a431a8b0b7640c9b2d1dce32b14eb56616a770f2fef884a5643b252f038a72e8d47612f74ee91fd79f01559da1d6d38fa112204afd5f40ec0b314')

 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:
--- a/BioArchLinux/r-neighbornet/lilac.py
+++ b/BioArchLinux/r-neighbornet/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 = "CC BY-NC-ND 4.0",
+    )

 def post_build():
    git_pkgbuild_commit()
--- a/BioArchLinux/r-neighbornet/lilac.yaml
+++ b/BioArchLinux/r-neighbornet/lilac.yaml
@ -5,7 +5,6 @@ maintainers:
 repo_depends:
 - r-graph
 update_on:
- regex: NeighborNet_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/NeighborNet
+- source: manual
+  manual: 1.18.0#d39375ac39ea34b0bd06ffd019eac6ee
 - alias: r
--- a/BioArchLinux/r-pwrewas.data/PKGBUILD
+++ b/BioArchLinux/r-pwrewas.data/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=pwrEWAS.data
 _pkgver=1.14.0
 pkgname=r-${_pkgname,,}
-pkgver=1.14.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='pwrEWAS.data: Reference data accompanying pwrEWAS'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgdesc="Reference data accompanying pwrEWAS"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
  r-experimenthub
 )
 optdepends=(
@ -18,15 +17,16 @@ optdepends=(
  r-knitr
  r-runit
 )
-source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('9a4091eaf4533a21a8a64fe27a02bb5ed413fd8e7ae9f4b4fa9c97ade5f68dae')
+source=("https://bioconductor.org/packages/3.17/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('4bc800d4a20edec551cbbcbbffd3d107')
+b2sums=('e40e058ce5f2038dff62ee3f4ca36ee67dc5545711643277ecb28156874674196396d716182a7949445485611c4d42fd83ede61206dd283b2e26be76fc782f81')

 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:
--- a/BioArchLinux/r-pwrewas.data/lilac.py
+++ b/BioArchLinux/r-pwrewas.data/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()
--- a/BioArchLinux/r-pwrewas.data/lilac.yaml
+++ b/BioArchLinux/r-pwrewas.data/lilac.yaml
@ -5,7 +5,6 @@ maintainers:
 repo_depends:
 - r-experimenthub
 update_on:
- regex: pwrEWAS.data_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/pwrEWAS.data
+- source: manual
+  manual: 1.14.0#4bc800d4a20edec551cbbcbbffd3d107
 - alias: r
--- a/BioArchLinux/r-rlhub/PKGBUILD
+++ b/BioArchLinux/r-rlhub/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=RLHub
 _pkgver=1.6.0
 pkgname=r-${_pkgname,,}
-pkgver=1.6.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='An ExperimentHub package for accessing processed RLSuite data sets'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
+pkgdesc="An ExperimentHub package for accessing processed RLSuite data sets"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
 license=('MIT')
 depends=(
-  r
  r-annotationhub
  r-experimenthub
 )
@ -21,16 +20,19 @@ optdepends=(
  r-rmarkdown
  r-testthat
 )
-source=("https://bioconductor.org/packages/release/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('028e40b175865d358aabcc25e8faa10db4e60f8edd1f3fc91efdb7566ae2a4d3')
+source=("https://bioconductor.org/packages/3.17/data/experiment/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('9072a588ef09512493ea389c50984153')
+b2sums=('caceabbd6afbc8dc710d8a5de89d3359ee68497c57b4a7dc58997fe308d3fd0ae79cdfc4198f9d044733469c1dc0c78404529d7d97663517abc62e85eb443665')

 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:
--- a/BioArchLinux/r-rlhub/lilac.py
+++ b/BioArchLinux/r-rlhub/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()
--- a/BioArchLinux/r-rlhub/lilac.yaml
+++ b/BioArchLinux/r-rlhub/lilac.yaml
@ -6,7 +6,6 @@ repo_depends:
 - r-annotationhub
 - r-experimenthub
 update_on:
- regex: RLHub_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/RLHub
+- source: manual
+  manual: 1.6.0#9072a588ef09512493ea389c50984153
 - alias: r
--- a/BioArchLinux/r-stroma4/PKGBUILD
+++ b/BioArchLinux/r-stroma4/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=STROMA4
 _pkgver=1.24.0
 pkgname=r-${_pkgname,,}
-pkgver=1.24.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Assign Properties to TNBC Patients'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Assign Properties to TNBC Patients"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
  r-biobase
  r-biocparallel
  r-matrixstats
@ -18,15 +17,16 @@ depends=(
 optdepends=(
  r-breastcancermainz
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('2e19d4875c44509eac6aa6273789b12431522e2b84e29a10740e4dc6667f7ff4')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('c171d3ed28b97a1bfa044b8d360bf1f7')
+b2sums=('bc979e8d2abf6d778b06572fdc8e6ada54dc6dfd183ae2886d3a4d741530ef48686c0d5d16e3c3850266e2874c5d1c9d576f21f271adaca138e7125c268720b4')

 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:
--- a/BioArchLinux/r-stroma4/lilac.py
+++ b/BioArchLinux/r-stroma4/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()
--- a/BioArchLinux/r-stroma4/lilac.yaml
+++ b/BioArchLinux/r-stroma4/lilac.yaml
@ -7,7 +7,6 @@ repo_depends:
 - r-biocparallel
 - r-matrixstats
 update_on:
- regex: STROMA4_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/STROMA4
+- source: manual
+  manual: 1.24.0#c171d3ed28b97a1bfa044b8d360bf1f7
 - alias: r