r-*: use metadata checks for several packages

BioArchLinux/r-flowplots/PKGBUILD

@@ -3,12 +3,12 @@
 _pkgname=flowPlots
 _pkgver=1.50.0
 pkgname=r-${_pkgname,,}
-pkgver=1.50.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='flowPlots: analysis plots and data class for gated flow cytometry data'
+pkgdesc="analysis plots and data class for gated flow cytometry data"
-arch=('any')
+arch=(any)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('Artistic2.0')
+license=('Artistic-2.0')
 depends=(
   r
 )
@@ -16,14 +16,15 @@ optdepends=(
   r-vcd
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('9ac84c0a3af3071a4dd2dbc70883105eced78c1996f1f282002dd0ccea7cb8d1')
+md5sums=('523b0d79646813f56d711d3e0f38a5e9')
+b2sums=('5b35b308070ff5bef1d1dd8ade1633843eb34202f32dcc311fe8519b28184e4d940446bec0f71d898d13acdc70a9899338f3d10753f62aeee544ede5ca309b92')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${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-flowplots/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'):
+    r_pre_build(_G)
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-flowplots/lilac.yaml

@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: flowPlots_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: flowPlots
-  url: https://bioconductor.org/packages/flowPlots
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-fmrs/PKGBUILD

@@ -3,12 +3,12 @@
 _pkgname=fmrs
 _pkgver=1.12.0
 pkgname=r-${_pkgname,,}
-pkgver=1.12.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Variable Selection in Finite Mixture of AFT Regression and FMR'
+pkgdesc="Variable Selection in Finite Mixture of AFT Regression and FMR Models"
-arch=('x86_64')
+arch=(x86_64)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('GPL')
+license=('GPL-3.0-only')
 depends=(
   r
 )
@@ -16,17 +16,17 @@ optdepends=(
   r-biocgenerics
   r-knitr
   r-testthat
-  r-utils
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('6a9566cda423e834136eed456b6f702de7ed37c7624b06656d60417b793e57e3')
+md5sums=('ccf41504ab27d93464e555b363ef406a')
+b2sums=('f8b92bfe2b48cf70c50532ab837b13924006632d4265f4382ccc4609bcd9ea2fc0495fe4a2bb42a124482ed867444684272b235533bf2c367c6703b93854f0ca')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${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-fmrs/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'):
+    r_pre_build(_G)
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-fmrs/lilac.yaml

@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: fmrs_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: fmrs
-  url: https://bioconductor.org/packages/fmrs
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-garfield/PKGBUILD

@@ -3,12 +3,12 @@
 _pkgname=garfield
 _pkgver=1.30.0
 pkgname=r-${_pkgname,,}
-pkgver=1.30.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction'
+pkgdesc="GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction"
-arch=('x86_64')
+arch=(x86_64)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('GPL')
+license=('GPL-3.0-only')
 depends=(
   r
 )
@@ -16,14 +16,15 @@ optdepends=(
   r-knitr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5841ed36941fad56a90d254a6396301432014af124144593d88e0efd72008a06')
+md5sums=('bf1974925a6c10b95ada01ff6d46bf15')
+b2sums=('df24e1ee2360e81ee2ac1b7f4a8a32e9dfa14610575d4dbc85831859960ceaa796c0c7b9cceed05ea933411aadd31ac8ef8af77f4809a9970ee9ed39bf40c467')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${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-garfield/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'):
+    r_pre_build(_G)
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-garfield/lilac.yaml

@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: garfield_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: garfield
-  url: https://bioconductor.org/packages/garfield
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-gbrd/PKGBUILD

@@ -4,24 +4,25 @@
 _pkgname=gbRd
 _pkgver=0.4-11
 pkgname=r-${_pkgname,,}
-pkgver=0.4.11
+pkgver=${_pkgver//-/.}
 pkgrel=3
-pkgdesc='Utilities for processing Rd objects and files'
+pkgdesc="Utilities for processing Rd objects and files"
-arch=('any')
+arch=(any)
-url="https://cran.r-project.org/package=${_pkgname}"
+url="https://cran.r-project.org/package=$_pkgname"
-license=('GPL')
+license=('GPL-2.0-or-later')
 depends=(
   r
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('0251f6dd6ca987a74acc4765838b858f1edb08b71dbad9e563669b58783ea91b')
+md5sums=('7d43d8e79f3cbdc917f44817a34d2d37')
+b2sums=('a7a68f4c58848057567252e2b437016a17bb95d98449b7268a5327d9c40d88863572342add28735599965308e7bba25d3c1e7be8b06c3283e6402ccec3082665')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${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-gbrd/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'):
+    r_pre_build(
-        if line.startswith('_pkgver='):
+        _G,
-            line = f'_pkgver={_G.newver}'
+        expect_needscompilation = "",
-        print(line)
+    )
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-gbrd/lilac.yaml

@@ -3,7 +3,8 @@ maintainers:
 - github: sukanka
   email: su975853527@gmail.com
 update_on:
-  - regex: gbRd_([\d._-]+).tar.gz
+- source: rpkgs
-    source: regex
+  pkgname: gbRd
-    url: https://cran.r-project.org/package=gbRd
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-genocn/PKGBUILD

@@ -3,24 +3,25 @@
 _pkgname=genoCN
 _pkgver=1.54.0
 pkgname=r-${_pkgname,,}
-pkgver=1.54.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='genotyping and copy number study tools'
+pkgdesc="genotyping and copy number study tools"
-arch=('x86_64')
+arch=(x86_64)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('GPL')
+license=('GPL-2.0-or-later')
 depends=(
   r
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('f3ddee592b99af2e2fb9b564e58930f117e5dbbe5a794dc6eee6ecdaf8519f88')
+md5sums=('ebc7fc5cb3b5c2bcd98718a7bcd95d6a')
+b2sums=('f1ba4cf2c955c7ae94a4bca074110f396a08e2dc1e42fe534266d76848a5c2528ab434b0147c3f0406d5fb708dca1df0603c67709153b9854643bd26806df7c2')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${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-genocn/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'):
+    r_pre_build(_G)
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-genocn/lilac.yaml

@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: genoCN_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: genoCN
-  url: https://bioconductor.org/packages/genoCN
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-globalseq/PKGBUILD

@@ -3,12 +3,12 @@
 _pkgname=globalSeq
 _pkgver=1.30.0
 pkgname=r-${_pkgname,,}
-pkgver=1.30.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Global Test for Counts'
+pkgdesc="Global Test for Counts"
-arch=('any')
+arch=(any)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('GPL')
+license=('GPL-3.0-only')
 depends=(
   r
 )
@@ -19,14 +19,15 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('e71a151ac910673542fbb47fd6c453cc00c6f21630fde9cf645ba39a399318ac')
+md5sums=('1b427214cf1345b8d75ba69dc02adb77')
+b2sums=('aa04d988e6f966e02ab983eb008bf26df43741297f2d01159aabf9dd2b28fde158d6c41c71f7904fb85573e65a02db7b87930f40ef104fa533cf623991f5feb9')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${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-globalseq/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'):
+    r_pre_build(_G)
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-globalseq/lilac.yaml

@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: globalSeq_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: globalSeq
-  url: https://bioconductor.org/packages/globalSeq
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-gpls/PKGBUILD

@@ -3,27 +3,25 @@
 _pkgname=gpls
 _pkgver=1.74.0
 pkgname=r-${_pkgname,,}
-pkgver=1.74.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Classification using generalized partial least squares'
+pkgdesc="Classification using generalized partial least squares"
-arch=('any')
+arch=(any)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('Artistic2.0')
+license=('Artistic-2.0')
 depends=(
   r
 )
-optdepends=(
-  r-mass
-)
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('406afeee1ab2ebcc3a5ec952acf0143e558d130668a48e36147e612e196ed5fc')
+md5sums=('db6bc720156a5f7571a34e64b1189d3b')
+b2sums=('f647d89a455f050a3189a23cca82b14697f1ea5aebd6851900353cee91747f52f66f4d97550fa0d8c14a57fd97993ed8fadd11110aaf108cfd91e8d7a2ba61ca')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${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-gpls/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'):
+    r_pre_build(_G)
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-gpls/lilac.yaml

@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: gpls_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: gpls
-  url: https://bioconductor.org/packages/gpls
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-graphalignment/PKGBUILD

@@ -3,25 +3,28 @@
 _pkgname=GraphAlignment
 _pkgver=1.66.0
 pkgname=r-${_pkgname,,}
-pkgver=1.66.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='GraphAlignment'
+pkgdesc="GraphAlignment"
-arch=('x86_64')
+arch=(x86_64)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('custom')
+license=('LicenseRef-GraphAlignment')
 depends=(
   r
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('1a446d803266504325225dab0657932018e94c954fd2121769abd4baed90513e')
+md5sums=('0bc71a4722d0771d97671e81103bc8bb')
+b2sums=('e0a493bc0ef7423360c0dd3c9566666adbfcdb61410db2abb4fc34bc6582f0c651a7eefd58acf15d252fc15316534bba05d725b29587704eacdf37dea7ef8880')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 package() {
-  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
-  install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}"
+
+  install -d "$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-graphalignment/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'):
+    r_pre_build(
-        if line.startswith('_pkgver='):
+        _G,
-            line = f'_pkgver={_G.newver}'
+        expect_license = "file LICENSE",
-        print(line)
+    )
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-graphalignment/lilac.yaml

@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: GraphAlignment_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: GraphAlignment
-  url: https://bioconductor.org/packages/GraphAlignment
+  repo: bioc
+  md5: true
 - alias: r