r-*: use metadata checks for several packages

BioArchLinux/r-constand/PKGBUILD

@@ -3,12 +3,12 @@
 _pkgname=CONSTANd
 _pkgver=1.10.0
 pkgname=r-${_pkgname,,}
-pkgver=1.10.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Data normalization by matrix raking'
+pkgdesc="Data normalization by matrix raking"
-arch=('any')
+arch=(any)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('custom')
+license=('NPOSL-3.0')
 depends=(
   r
 )
@@ -24,15 +24,18 @@ optdepends=(
   r-tidyr
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d95083be200baac9f56d8d8f7cba928393cb088a556aee24b4b2a9f6e2d41e60')
+md5sums=('6337f6a248f820600a99fa9ef9fc1571')
+b2sums=('66f3c5461bd804d4c90ee6b3802c6b74237ce6df1a089e153856d41b15d5c6f5394f659ff6684bb0d2f28f2b7e8c875a746b9a55e4b297920872202692bda912')
 
 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-constand/lilac.py

@@ -1,12 +1,17 @@
 #!/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)
+        expect_systemrequirements = "",
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-constand/lilac.yaml

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

BioArchLinux/r-cosnet/PKGBUILD

@@ -3,12 +3,12 @@
 _pkgname=COSNet
 _pkgver=1.36.0
 pkgname=r-${_pkgname,,}
-pkgver=1.36.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings'
+pkgdesc="Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings"
-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
 )
@@ -19,14 +19,15 @@ optdepends=(
   r-runit
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('561cd82192772984c05e53970130aa6ea43e025f9788e4142807e68d9717d2f0')
+md5sums=('6648998ac68e41642f1a7bad77e0bb7f')
+b2sums=('c6a46e8c457658d86ea381ab390b689ee74a3efabb4be81f54f143751cc176c70156f12c0fbc995bc065944e2e0c470345cd992a84b569ceb2d9ca8539339b87')
 
 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-cosnet/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-cosnet/lilac.yaml

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

BioArchLinux/r-curry/PKGBUILD

@@ -3,24 +3,25 @@
 _pkgname=curry
 _pkgver=0.1.1
 pkgname=r-${_pkgname,,}
-pkgver=0.1.1
+pkgver=${_pkgver//-/.}
 pkgrel=8
-pkgdesc='Partial Function Application with %<%, %-<%, and %><%'
+pkgdesc="Partial Function Application with %<%, %-<%, and %><%"
-arch=('any')
+arch=(any)
-url="https://cran.r-project.org/package=${_pkgname}"
+url="https://cran.r-project.org/package=$_pkgname"
-license=('LGPL')
+license=('GPL-2.0-or-later')
 depends=(
   r
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('4930c6d5cdb6fa319b888d2220b9ded2c7bf786d8a700ad102558065d78649df')
+md5sums=('a2d43da3367e9506e4e4e8a4523faaf5')
+b2sums=('096e547915dae45e9f05a2d0c2ebec6aaebc12c21b192a5ee0e73f64ea909335571eb0c40313f4bfc9f29edc4d560db927b1434f4301680dac3f2e570d32a390')
 
 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-curry/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-curry/lilac.yaml

@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex:  curry_(\d+.\d+.\d+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: curry
-  url: https://cran.r-project.org/package=curry
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-dama/PKGBUILD

@@ -3,24 +3,25 @@
 _pkgname=daMA
 _pkgver=1.74.0
 pkgname=r-${_pkgname,,}
-pkgver=1.74.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Efficient design and analysis of factorial two-colour microarray data'
+pkgdesc="Efficient design and analysis of factorial two-colour microarray data"
-arch=('any')
+arch=(any)
-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=('668c9830927a9bb44df8f84565e9731ae6bc77aa9e04b80cee8afaa60c4473b2')
+md5sums=('ec7e80e81b9d6eb5a76ce06c761bb7da')
+b2sums=('53865c072c351452cb9439d2b3d995445a703d28c7d340453fe1e5199cff078cc7a322db5d9c1512fa0b58b07c27cd113d4e33fc01d4b676adf562e3186b8770')
 
 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-dama/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-dama/lilac.yaml

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

BioArchLinux/r-demand/PKGBUILD

@@ -3,25 +3,28 @@
 _pkgname=DeMAND
 _pkgver=1.32.0
 pkgname=r-${_pkgname,,}
-pkgver=1.32.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='DeMAND'
+pkgdesc="DeMAND"
-arch=('any')
+arch=(any)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('custom')
+license=('LicenseRef-DeMAND')
 depends=(
   r
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('0c0a0e866c909678c956551c7c6b35c5f52378a82f1ed88756eb4ef5ddfeec16')
+md5sums=('ccb354bddebbebda6c42453810f10e70')
+b2sums=('ff3cbfef53e18bd1e024f9ab55b3d239517dd7f95f21f14d08850ee2683fabcad6afd8f4b99701ae231f20b6c2e0680f2f99b9f4c91b6d1180e522e4207be932')
 
 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-demand/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-demand/lilac.yaml

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

BioArchLinux/r-drivernet/PKGBUILD

@@ -3,24 +3,25 @@
 _pkgname=DriverNet
 _pkgver=1.42.0
 pkgname=r-${_pkgname,,}
-pkgver=1.42.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Drivernet: uncovering somatic driver mutations modulating transcriptional networks in cancer'
+pkgdesc="uncovering somatic driver mutations modulating transcriptional networks in cancer"
-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
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('eeba1d7b1589b672069b4b01858c6a959bdaa318fe16277e86742c1aaf14caf2')
+md5sums=('78b923b016f6bd8097c1edc43ca0cca4')
+b2sums=('a900c82293b00cc8d1dcc16dd6a973efea1bdcadc7fb06c2bc71c5e32b62c13134a5ae7b7c9e174a5abda2f805a1a7fd1fee269035aabaea3131e51e7d56a2b6')
 
 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-drivernet/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-drivernet/lilac.yaml

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

BioArchLinux/r-fdrame/PKGBUILD

@@ -3,25 +3,25 @@
 _pkgname=fdrame
 _pkgver=1.74.0
 pkgname=r-${_pkgname,,}
-pkgver=1.74.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='FDR adjustments of Microarray Experiments (FDR-AME)'
+pkgdesc="FDR adjustments of Microarray Experiments (FDR-AME)"
-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
-  tk
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5c3fe0beaa45f50023560f4d2705c59d7a99e3f79a3835f3c11c9c6ac43cda0d')
+md5sums=('d7fafba89f784f421a43b4b4d9a10000')
+b2sums=('2174e67a4795c5b3def564c6c312a98a93e937d484ffd8e6fb3aca6c32023143c88924179bb78fb39f2a766c02b4cbeb8d131359e8e4a3e10eb931d16c3df8c9')
 
 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-fdrame/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-fdrame/lilac.yaml

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