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 · 2024-02-14 18:18:59 +02:00 · 2024-02-14 18:18:59 +02:00 · 61cc099471
commit 61cc099471
parent 8e2ac0a4a6
18 changed files with 123 additions and 125 deletions
--- a/BioArchLinux/r-crisprseekplus/PKGBUILD
+++ b/BioArchLinux/r-crisprseekplus/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=crisprseekplus
 _pkgver=1.26.0
 pkgname=r-${_pkgname,,}
-pkgver=1.26.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='crisprseekplus'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="crisprseekplus"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
  r-annotationdbi
  r-biocmanager
  r-bsgenome
@ -29,15 +28,16 @@ optdepends=(
  r-rmarkdown
  r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('c83cbc49101db844801b6115a3fd3576805598ab4a05d8327596512e09499fb1')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('2a26cd0c67eb1679895c3cbc4573e502')
+b2sums=('d408573f89e95cb9ace597c4ad187f40767dfcaeeb9d51a9c3da72a420c3d92d36710be4bffda296470db6670609aefd348a38886bf0e70f94cd288b8486f4e9')

 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-crisprseekplus/lilac.py
+++ b/BioArchLinux/r-crisprseekplus/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()
--- a/BioArchLinux/r-crisprseekplus/lilac.yaml
+++ b/BioArchLinux/r-crisprseekplus/lilac.yaml
@ -15,7 +15,6 @@ repo_depends:
 - r-shiny
 - r-shinyjs
 update_on:
- regex: crisprseekplus_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/crisprseekplus
+- source: manual
+  manual: 1.26.0#2a26cd0c67eb1679895c3cbc4573e502
 - alias: r
--- a/BioArchLinux/r-eegc/PKGBUILD
+++ b/BioArchLinux/r-eegc/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=eegc
 _pkgver=1.26.0
 pkgname=r-${_pkgname,,}
-pkgver=1.26.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Engineering Evaluation by Gene Categorization (eegc)'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Engineering Evaluation by Gene Categorization (eegc)"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
-  r
  r-annotationdbi
  r-clusterprofiler
  r-deseq2
@ -31,15 +30,16 @@ depends=(
 optdepends=(
  r-knitr
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('6b61cdb9c22ea4b288adb0aca69b88ecb94591a40d829b4512f37781b5fcc754')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('898230d2d6431f622202416e172d64e2')
+b2sums=('fb0eb18232a94d8517531151d771fa36a03ed5a52e7ccee64f338a55397f8b3a26ad3a158ff7b0d4a25049e428f15d7fda5a8d839b265b8ccecd2bd081c17307')

 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-eegc/lilac.py
+++ b/BioArchLinux/r-eegc/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-eegc/lilac.yaml
+++ b/BioArchLinux/r-eegc/lilac.yaml
@ -20,7 +20,6 @@ repo_depends:
 - r-sna
 - r-wordcloud
 update_on:
- regex: eegc_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/eegc
+- source: manual
+  manual: 1.26.0#898230d2d6431f622202416e172d64e2
 - alias: r
--- a/BioArchLinux/r-farms/PKGBUILD
+++ b/BioArchLinux/r-farms/PKGBUILD
@ -3,31 +3,29 @@
 _pkgname=farms
 _pkgver=1.52.0
 pkgname=r-${_pkgname,,}
-pkgver=1.52.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='FARMS - Factor Analysis for Robust Microarray Summarization'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('LGPL')
+pkgdesc="Factor Analysis for Robust Microarray Summarization"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('LGPL-2.1-or-later')
 depends=(
-  r
  r-affy
  r-biobase
 )
 optdepends=(
  r-affydata
-  r-biobase
-  r-utils
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5224e912ed83ab7e094ab398d1f6121d1516282f1ab13dd0d7b232fa16e22bf0')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('47741e71448e6a0b2b47309b31572a2d')
+b2sums=('1ee08038bc8d2c9e100afede45528f752c9a61bfb9042e685c17473b612f417ce353378dde572c9c186853f4fac26e1a9fe438943393d6cbe952485be6ec6851')

 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-farms/lilac.py
+++ b/BioArchLinux/r-farms/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-farms/lilac.yaml
+++ b/BioArchLinux/r-farms/lilac.yaml
@ -6,7 +6,6 @@ repo_depends:
 - r-affy
 - r-biobase
 update_on:
- regex: farms_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/farms
+- source: manual
+  manual: 1.52.0#47741e71448e6a0b2b47309b31572a2d
 - alias: r
--- a/BioArchLinux/r-mirsm/PKGBUILD
+++ b/BioArchLinux/r-mirsm/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=miRSM
 _pkgver=1.18.0
 pkgname=r-${_pkgname,,}
-pkgver=1.18.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Inferring miRNA sponge modules in heterogeneous data'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Inferring miRNA sponge modules in heterogeneous data"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
  r-bibitr
  r-bicare
  r-biclust
@ -48,15 +47,16 @@ optdepends=(
  r-rmarkdown
  r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('33345d8b1a25d09d0b8c441ba15581eefad3edb9b068b72ceb3f0c6d4f498bea')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('2c9037736a60c1bbcd546542c1d70f41')
+b2sums=('4421f08a1ffa59d75acfc7924b3dd1db0039d558371dd97e295a1cbe48b4d0bf5b6ea7801bf7dd727cf9cae908a8b840fd52bf6cb69c09e2b16e153815be018a')

 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-mirsm/lilac.py
+++ b/BioArchLinux/r-mirsm/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-mirsm/lilac.yaml
+++ b/BioArchLinux/r-mirsm/lilac.yaml
@ -34,7 +34,6 @@ repo_depends:
 - r-summarizedexperiment
 - r-wgcna
 update_on:
- regex: miRSM_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/miRSM
+- source: manual
+  manual: 1.18.0#2c9037736a60c1bbcd546542c1d70f41
 - alias: r
--- a/BioArchLinux/r-mirsponger/PKGBUILD
+++ b/BioArchLinux/r-mirsponger/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=miRspongeR
 _pkgver=2.4.0
 pkgname=r-${_pkgname,,}
-pkgver=2.4.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Identification and analysis of miRNA sponge interaction networks and modules'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Identification and analysis of miRNA sponge regulation"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
  r-clusterprofiler
  r-corpcor
  r-doparallel
@ -30,15 +29,16 @@ optdepends=(
  r-rmarkdown
  r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('60f6a38bf6a1064b8ad3bb84174827875a8fd2f346b9c707ef6c69512503f0d7')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('52c6fe3ed5a289fd16c2e8c549402eb8')
+b2sums=('6e52fe85bd718a33be2fe3b6448b9639a951e44a75b4097cbe35de09fbf53f989b5e12d1f6d06dd2ad1d3657b0cccc812b33e145a14f181beb5845881cf144c5')

 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-mirsponger/lilac.py
+++ b/BioArchLinux/r-mirsponger/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-mirsponger/lilac.yaml
+++ b/BioArchLinux/r-mirsponger/lilac.yaml
@ -16,7 +16,6 @@ repo_depends:
 - r-reactomepa
 - r-sponge
 update_on:
- regex: miRspongeR_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/miRspongeR
+- source: manual
+  manual: 2.4.0#52c6fe3ed5a289fd16c2e8c549402eb8
 - alias: r
--- a/BioArchLinux/r-rcistarget/PKGBUILD
+++ b/BioArchLinux/r-rcistarget/PKGBUILD
@ -3,14 +3,13 @@
 _pkgname=RcisTarget
 _pkgver=1.20.0
 pkgname=r-${_pkgname,,}
-pkgver=1.20.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
  r-arrow
  r-aucell
  r-biocgenerics
@ -28,9 +27,7 @@ optdepends=(
  r-biobase
  r-biocparallel
  r-biocstyle
-  r-domc
  r-doparallel
-  r-dorng
  r-dt
  r-foreach
  r-gplots
@ -41,17 +38,17 @@ optdepends=(
  r-rtracklayer
  r-testthat
  r-visnetwork
-  r-zoo
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('b4db98a76dd45d264cefd74bbfc0436d863f69b71d25f3762e2959570bf2e236')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('0f7605c0a9396d116b777b4954011027')
+b2sums=('c566bd26dd1a7fbec7628d048d4d5d533c34a893c08eddfdd441ff9cfd57af727d99f31e7993e0e6f6a7cb59bc779e22a7da84cdb7a73cbfe4bc7a00c9b5ba90')

 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-rcistarget/lilac.py
+++ b/BioArchLinux/r-rcistarget/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-rcistarget/lilac.yaml
+++ b/BioArchLinux/r-rcistarget/lilac.yaml
@ -16,7 +16,6 @@ repo_depends:
 - r-summarizedexperiment
 - r-tibble
 update_on:
- regex: RcisTarget_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/RcisTarget
+- source: manual
+  manual: 1.20.0#0f7605c0a9396d116b777b4954011027
 - alias: r