r-*: use metadata checks for several packages

BioArchLinux/r-adehabitatma/PKGBUILD

@@ -3,29 +3,28 @@
 _pkgname=adehabitatMA
 _pkgver=0.3.16
 pkgname=r-${_pkgname,,}
-pkgver=0.3.16
+pkgver=${_pkgver//-/.}
 pkgrel=4
-pkgdesc='Tools to Deal with Raster Maps'
-arch=('x86_64')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Tools to Deal with Raster Maps"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-sp
 )
 optdepends=(
-  r-mass
   r-tkrplot
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('089e415a26b6c45023d04ef64c9cf6d336a233f0b0078fc72adbe601b389b5ca')
+md5sums=('8c4f737241fa734be5603a940ae86270')
+b2sums=('4bd7a3583331aed034ebab62c2e39ae73cdc5e44e135001f47b23fc50908ce6c4cc5191fd9aa006b4bfa61f65a3f8663c175399b94fe9907af40317eb2594d54')
 
 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-adehabitatma/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-adehabitatma/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-sp
 update_on:
-- regex: adehabitatMA_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=adehabitatMA
+- source: rpkgs
+  pkgname: adehabitatMA
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-affyio/PKGBUILD

@@ -3,25 +3,26 @@
 _pkgname=affyio
 _pkgver=1.72.0
 pkgname=r-${_pkgname,,}
-pkgver=1.72.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Tools for parsing Affymetrix data files'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('LGPL')
+pkgdesc="Tools for parsing Affymetrix data files"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('LGPL-2.0-or-later')
 depends=(
-  r
   r-zlibbioc
+  zlib
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('e98fc0f5acba44885b9b7962d2b3d85e8972e8675ab7d9adf7653133d2d95007')
+md5sums=('9bd1e4acedbf756386f96d4c1ebb21f3')
+b2sums=('f6f89fc05c0da4f2f45fde959387fd133030d179f316adb6d6d8a1cb1483f6e34d111e2015098906a49a40f7efd7bbaf5aa461e8547d96a4fb6eaf96c3a53169')
 
 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-affyio/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-affyio/lilac.yaml

@@ -5,7 +5,13 @@ maintainers:
 repo_depends:
 - r-zlibbioc
 update_on:
-- regex: affyio_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/affyio
+- source: rpkgs
+  pkgname: affyio
+  repo: bioc
+  md5: true
 - alias: r
+- source: alpm
+  alpm: zlib
+  repo: core
+  provided: libz.so
+  strip_release: true

BioArchLinux/r-akima/PKGBUILD

@@ -3,32 +3,31 @@
 _pkgname=akima
 _pkgver=0.6-3.4
 pkgname=r-${_pkgname,,}
-pkgver=0.6.3.4
+pkgver=${_pkgver//-/.}
 pkgrel=5
-pkgdesc='Interpolation of Irregularly and Regularly Spaced Data'
-arch=('x86_64')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('ACM')
+pkgdesc="Interpolation of Irregularly and Regularly Spaced Data"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('LicenseRef-scancode-acm-sla')
 depends=(
-  r
   r-sp
 )
-optdepends=(
-  r-tripack
-)
 makedepends=(
   gcc-fortran
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('95657592a81d2e3628cb054b60127827ae64e65c58b77d059aa510bc6781ad3e')
+md5sums=('55d36a85ecb1c2f82d22bdcec6f9ee3e')
+b2sums=('688c8d0319290f16379c526fae9a2b7ee7cd69704dae0a4b8f1387f14d92780f2d3c657d0d1fac3fc3239ae58ba183b1a8a5d522c23c85c88c15452acb9af8c0')
 
 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-akima/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 = "ACM | file LICENSE",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-akima/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-sp
 update_on:
-- regex: akima_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=akima
+- source: rpkgs
+  pkgname: akima
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-attempt/PKGBUILD

@@ -3,14 +3,13 @@
 _pkgname=attempt
 _pkgver=0.3.1
 pkgname=r-${_pkgname,,}
-pkgver=0.3.1
+pkgver=${_pkgver//-/.}
 pkgrel=6
-pkgdesc='Tools for Defensive Programming'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
+pkgdesc="Tools for Defensive Programming"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
 license=('MIT')
 depends=(
-  r
   r-rlang
 )
 optdepends=(
@@ -20,15 +19,18 @@ optdepends=(
   r-testthat
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('15159d3d20198c6300874451e925ca154c23e0b6cdd7e05eaf98a3cbe4798ffa')
+md5sums=('b4cbba3e4a87008b3aa8c60251576ccc')
+b2sums=('ce366713bd58732895e5fa820221587ab88ab815658a8803516a5f836a7698b7fa3c67ee1ebff3b3876684debadff4033def7b9373c312849968c7a19f60a7c9')
 
 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-attempt/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-attempt/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-rlang
 update_on:
-- regex: attempt_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=attempt
+- source: rpkgs
+  pkgname: attempt
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-coro/PKGBUILD

@@ -3,14 +3,13 @@
 _pkgname=coro
 _pkgver=1.0.4
 pkgname=r-${_pkgname,,}
-pkgver=1.0.4
+pkgver=${_pkgver//-/.}
 pkgrel=1
 pkgdesc="'Coroutines' for R"
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
 license=('MIT')
 depends=(
-  r
   r-rlang
 )
 optdepends=(
@@ -23,15 +22,18 @@ optdepends=(
   r-testthat
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('8f21bf44ec46fa1da88e9232db5536f494cbd87aade3ef16957d27919f58cc64')
+md5sums=('20d535e6d36920c23c8e74442977806a')
+b2sums=('b164beab9bf7818939e835071b0b85a162505bd0eff42f87b751385f99d990ee4907ac6ac8097c75147cec5b12882ab26ab9cac4ccbd46cd7e34119d1a32104a')
 
 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-coro/lilac.py

@@ -1,9 +1,14 @@
 #!/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()
+    update_aur_repo()

BioArchLinux/r-coro/lilac.yaml

@@ -1,13 +1,12 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: sukanka
+- github: sukanka
   email: su975853527@gmail.com
-post_build_script: |
-  git_pkgbuild_commit()
-  update_aur_repo()
 repo_depends:
-  - r-rlang
+- r-rlang
 update_on:
-  - regex: coro_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=coro
+- source: rpkgs
+  pkgname: coro
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-diffobj/PKGBUILD

@@ -3,14 +3,13 @@
 _pkgname=diffobj
 _pkgver=0.3.5
 pkgname=r-${_pkgname,,}
-pkgver=0.3.5
+pkgver=${_pkgver//-/.}
 pkgrel=6
-pkgdesc='Diffs for R Objects'
-arch=('x86_64')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Diffs for R Objects"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-only OR GPL-3.0-only')
 depends=(
-  r
   r-crayon
 )
 optdepends=(
@@ -18,14 +17,15 @@ optdepends=(
   r-rmarkdown
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60')
+md5sums=('dffa0a111b1f8766d0b64a2cd7138d09')
+b2sums=('c593f790c121d53c540fc52fcf25aded44d0f56c696a7c2d222afed4f337c2b61331c5dd6058f0ee48959a1feb5d9cd11f6b81cf296244eb89ce116183b41e10')
 
 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-diffobj/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-diffobj/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-crayon
 update_on:
-- regex: diffobj_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=diffobj
+- source: rpkgs
+  pkgname: diffobj
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-genarise/PKGBUILD

@@ -3,28 +3,30 @@
 _pkgname=genArise
 _pkgver=1.78.0
 pkgname=r-${_pkgname,,}
-pkgver=1.78.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Microarray Analysis tool'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('custom')
+pkgdesc="Microarray Analysis tool"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('LicenseRef-genArise')
 depends=(
-  r
   r-locfit
   r-tkrplot
   r-xtable
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('e095e1c32a8eac4d36e7a5387e86b03a23d65e24234967e3f72387ec9a7e6199')
+md5sums=('d81489147ccfe688c07c228b7fcfcf7d')
+b2sums=('95a674942bf301f6b4e8c227ac25d7810eec88e497448aa0b852d3701136b1ac4c05f590b6bb7082fef11186bca9536bcd7665ca826b66c703ba46ce2fd654d4')
 
 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-genarise/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 = "file LICENSE",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-genarise/lilac.yaml

@@ -7,7 +7,8 @@ repo_depends:
 - r-tkrplot
 - r-xtable
 update_on:
-- regex: genArise_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/genArise
+- source: rpkgs
+  pkgname: genArise
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-grimport/PKGBUILD

@@ -1,35 +1,31 @@
-# system requirements: ghostscript
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=grImport
 _pkgver=0.9-7
 pkgname=r-${_pkgname,,}
-pkgver=0.9.7
+pkgver=${_pkgver//-/.}
 pkgrel=2
-pkgdesc='Importing Vector Graphics'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Importing Vector Graphics"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
-  r-xml
   ghostscript
+  r-xml
 )
 optdepends=(
-  r-cluster
   r-colorspace
-  r-lattice
-  r-survival
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('05f8b65a55c5fabce2afb74c2b843f5df772d1f931d1ba3ce5f3bfe0493cd0a4')
+md5sums=('15b22fb059f5cc409231f1af50b7316d')
+b2sums=('e35f32334da85d0bfdce10443aed632637e21c18d96c148d0968711e154c7f5508c9c694f7905e0456a1137c451aaaaa96189cd10784646acc34a93bdcc55359')
 
 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-grimport/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 = "ghostscript",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-grimport/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-xml
 update_on:
-- regex: grImport_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=grImport
+- source: rpkgs
+  pkgname: grImport
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-htmlutils/PKGBUILD

@@ -3,25 +3,25 @@
 _pkgname=HTMLUtils
 _pkgver=0.1.9
 pkgname=r-${_pkgname,,}
-pkgver=0.1.9
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Facilitates Automated HTML Report Creation'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Facilitates Automated HTML Report Creation"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-r2html
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('14e92d45743a9adf21aab726be7d1aacdc901eae443da896b149a657183a8ec4')
+md5sums=('dfdfd0071ccdaf1d589c20a8513d9752')
+b2sums=('5b395b687bd257a77f271b4ae03893f94d26e9f3a8cb3bef0b06772240b736bcd7696b81c4dc96c1c6e1baad89c4af72fccb39e9e4a2355ec1fe3c79955f0849')
 
 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-htmlutils/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-htmlutils/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-r2html
 update_on:
-- regex: HTMLUtils_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=HTMLUtils
+- source: rpkgs
+  pkgname: HTMLUtils
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-irr/PKGBUILD

@@ -3,25 +3,25 @@
 _pkgname=irr
 _pkgver=0.84.1
 pkgname=r-${_pkgname,,}
-pkgver=0.84.1
+pkgver=${_pkgver//-/.}
 pkgrel=6
-pkgdesc='Various Coefficients of Interrater Reliability and Agreement'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Various Coefficients of Interrater Reliability and Agreement"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-lpsolve
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('e7bae8476b723a2246564c013194e8b7fcc9b34affc0ab5fcd55875231f544c3')
+md5sums=('802ae19d1fc45cede1afafb5012cfdf0')
+b2sums=('41f6e4046a498394cb53a1c4599a7ac6ec66b9301272f7bb523740887bd8c8ed3b23a74c48e5eb177042c36a9f968fb7e47b55426ea1318a71183c01e4c537fa')
 
 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-irr/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-irr/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-lpsolve
 update_on:
-- regex: irr_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=irr
+- source: rpkgs
+  pkgname: irr
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-pepxmltab/PKGBUILD

@@ -3,14 +3,13 @@
 _pkgname=pepXMLTab
 _pkgver=1.36.0
 pkgname=r-${_pkgname,,}
-pkgver=1.36.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Parsing pepXML files and filter based on peptide FDR.'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgdesc="Parsing pepXML files and filter based on peptide FDR"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-xml
 )
 optdepends=(
@@ -18,14 +17,15 @@ optdepends=(
   r-runit
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('441a1a4c73d083e10cc95f4f80209f02f523af9085079d9857bd61effa1116b4')
+md5sums=('71d6bcb41c5a79bc2cfdd375c6468250')
+b2sums=('37e0d23e667c4f3720a7bf0305152c7f4540058cdba396edb13e7c1848b26a806bdbd840f6d133c9124ad7202c940e5c7963b8fa004420b6f94592e4404074e8')
 
 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-pepxmltab/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-pepxmltab/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-xml
 update_on:
-- regex: pepXMLTab_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/pepXMLTab
+- source: rpkgs
+  pkgname: pepXMLTab
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-polycor/PKGBUILD

@@ -3,26 +3,26 @@
 _pkgname=polycor
 _pkgver=0.8-1
 pkgname=r-${_pkgname,,}
-pkgver=0.8.1
+pkgver=${_pkgver//-/.}
 pkgrel=5
-pkgdesc='Polychoric and Polyserial Correlations'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Polychoric and Polyserial Correlations"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-admisc
   r-mvtnorm
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('f05f53e0b5c992de0e5b4c6b2e998148cf83310358821e1bba180d81face0509')
+md5sums=('bcf23e352787794c7e36875d6cd8d6f6')
+b2sums=('040a667cc6a0dceeac6fe85e011e54605c081259f998deb8aae3be4f6c57820aa34f63f1b27c2e7a40e9099b35c8e57ba6b1d76488e6389a7f8eb0c2f80ed57a')
 
 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-polycor/lilac.py

@@ -1,9 +1,14 @@
 #!/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()
+    update_aur_repo()

BioArchLinux/r-polycor/lilac.yaml

@@ -1,15 +1,13 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: sukanka
+- github: sukanka
   email: su975853527@gmail.com
-post_build_script: |
-  git_pkgbuild_commit()
-  update_aur_repo()
 repo_depends:
-  - r-admisc
-  - r-mvtnorm
+- r-admisc
+- r-mvtnorm
 update_on:
-  - regex: polycor_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=polycor
-  - alias: r
+- source: rpkgs
+  pkgname: polycor
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-prabclus/PKGBUILD

@@ -3,32 +3,31 @@
 _pkgname=prabclus
 _pkgver=2.3-3
 pkgname=r-${_pkgname,,}
-pkgver=2.3.3
+pkgver=${_pkgver//-/.}
 pkgrel=3
-pkgdesc='Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Functions for Clustering and Testing of Presence-Absence, Abundance and Multilocus Genetic Data"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-mclust
 )
 optdepends=(
   r-bootstrap
-  r-foreign
   r-mvtnorm
   r-spatialreg
   r-spdep
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('005d000a9ac357e670de26e5b8fc4ddb1617351275fa43bf6d2e88b8774358c1')
+md5sums=('a978397e43f43298a994a0c8fcc450c7')
+b2sums=('fe4edb65112dfec49f2ce877931d539a93fe478b106e4c45e429de9e850c9f4e4ef064164905b23999c548be5345944b58e8da7db4780904d245423a2b0d74eb')
 
 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-prabclus/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-prabclus/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-mclust
 update_on:
-- regex: prabclus_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=prabclus
+- source: rpkgs
+  pkgname: prabclus
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-rbiopaxparser/PKGBUILD

@@ -3,14 +3,13 @@
 _pkgname=rBiopaxParser
 _pkgver=2.42.0
 pkgname=r-${_pkgname,,}
-pkgver=2.42.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Parses BioPax files and represents them in R'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Parses BioPax files and represents them in R"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-data.table
   r-xml
 )
@@ -24,14 +23,15 @@ optdepends=(
   r-runit
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('275cb296a6e9d262a2c853d85c0954fcf72a87197b482adfbb4c8e045346caff')
+md5sums=('53e24a8896bf17bd56fe48d62427eb33')
+b2sums=('46186aa0fd6c43330d8d928e39f3e4fda57afb0fab3e46f67c160ead21ff5260e35541ef1246f97b88d3df012c0fbafb4fbf13aa13ea8e7c737d2704eb9f359b')
 
 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-rbiopaxparser/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-rbiopaxparser/lilac.yaml

@@ -6,7 +6,8 @@ repo_depends:
 - r-data.table
 - r-xml
 update_on:
-- regex: rBiopaxParser_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/rBiopaxParser
+- source: rpkgs
+  pkgname: rBiopaxParser
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-rhtslib/PKGBUILD

@@ -1,22 +1,20 @@
-# system requirements: libbz2 & liblzma & libcurl (with header files), GNUmake
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=Rhtslib
 _pkgver=2.4.1
 pkgname=r-${_pkgname,,}
-pkgver=2.4.1
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='HTSlib high-throughput sequencing library as an R package'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('LGPL')
-options=(!lto staticlibs)
+pkgdesc="HTSlib high-throughput sequencing library as an R package"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('LGPL-2.0-or-later')
 depends=(
-  r
-  r-zlibbioc
   bzip2
-  xz
   curl
+  r-zlibbioc
+  xz
+  zlib
 )
 optdepends=(
   r-biocstyle
@@ -24,14 +22,15 @@ optdepends=(
   r-rmarkdown
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('0c34b951a0f15c26222a3dfd96700a0905c16c4cbe59db36374cf1ceab2a2b21')
+md5sums=('b7d295a694e865f4f4060c94c4bca446')
+b2sums=('003d61f9455981794724ab4e65eaf7f557d2bd394b58ba4e61eb895fbceb8117cb8a8fc6b99f7be71f2ec1b1641ea71867c6a083deba29991c630716de48e82c')
 
 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-rhtslib/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 = "libbz2 & liblzma & libcurl (with header files), GNU make",
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-rhtslib/lilac.yaml

@@ -5,7 +5,28 @@ maintainers:
 repo_depends:
 - r-zlibbioc
 update_on:
-- regex: Rhtslib_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/Rhtslib
+- source: rpkgs
+  pkgname: Rhtslib
+  repo: bioc
+  md5: true
 - alias: r
+- source: alpm
+  alpm: bzip2
+  repo: core
+  provided: libbz2.so
+  strip_release: true
+- source: alpm
+  alpm: curl
+  repo: core
+  provided: libcurl.so
+  strip_release: true
+- source: alpm
+  alpm: xz
+  repo: core
+  provided: liblzma.so
+  strip_release: true
+- source: alpm
+  alpm: zlib
+  repo: core
+  provided: libz.so
+  strip_release: true

BioArchLinux/r-sampling/PKGBUILD

@@ -3,26 +3,25 @@
 _pkgname=sampling
 _pkgver=2.10
 pkgname=r-${_pkgname,,}
-pkgver=2.10
+pkgver=${_pkgver//-/.}
 pkgrel=1
 pkgdesc="Survey Sampling"
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-lpsolve
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('fdec976ec0abfb5c690049d76f89ebcb8ab3650e2eb28a5b54c3984d17372775')
+md5sums=('42f9a999adb8edaa1aa1199d1774b8aa')
+b2sums=('022baa77d2b46732f55c5bfc451cc6cf900d8d9c5709dd35ca8f73b62e9ef49337c57d28eba01b73180d7f4bb4f83a6eb85d7a860683d6c20a37cd2b1c168bdb')
 
 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"
 }
-# vim:set ts=2 sw=2 et:

BioArchLinux/r-sampling/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-sampling/lilac.yaml

@@ -2,10 +2,11 @@ build_prefix: extra-x86_64
 maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
-update_on:
-- regex: sampling_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=sampling
-- alias: r
 repo_depends:
 - r-lpsolve
+update_on:
+- source: rpkgs
+  pkgname: sampling
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-semisup/PKGBUILD

@@ -3,14 +3,13 @@
 _pkgname=semisup
 _pkgver=1.26.0
 pkgname=r-${_pkgname,,}
-pkgver=1.26.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Semi-Supervised Mixture Model'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Semi-Supervised Mixture Model"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-vgam
 )
 optdepends=(
@@ -19,14 +18,15 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('a9b0a2eb85fe87ff5f7397d5a966637f07cbbe66b88a1ebb72391cfef8676376')
+md5sums=('fb3d32c07acbfadbbee01f9a6c8333fe')
+b2sums=('0f2feb4757068304cac0398c4bbf5d79ac07cefa2e191703cedea9e5fc446cababbac8ec9c5ef9f82ab36a9e904a563eb2b1b995f7c7379692b6b0ffcede6c32')
 
 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-semisup/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-semisup/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-vgam
 update_on:
-- regex: semisup_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/semisup
+- source: rpkgs
+  pkgname: semisup
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-seqtools/PKGBUILD

@@ -3,29 +3,30 @@
 _pkgname=seqTools
 _pkgver=1.36.0
 pkgname=r-${_pkgname,,}
-pkgver=1.36.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Analysis of nucleotide, sequence and quality content on fastq files'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgdesc="Analysis of nucleotide, sequence and quality content on fastq files"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-zlibbioc
+  zlib
 )
 optdepends=(
   r-biocgenerics
   r-runit
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('559031059a9315d8b0912d5334c91cb5176427e09586df400b3eeff58b9a1584')
+md5sums=('be9be6eb0ee1ff4ab001720970d68da8')
+b2sums=('d813ac5feb6ac445a2462b4ac4aeb2c36837cb7101a210c64922561051b222c2c3126f11c1121f3a36e56a64fe903229a42495a72547ab7376ff1499ba2be96f')
 
 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-seqtools/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-seqtools/lilac.yaml

@@ -5,7 +5,13 @@ maintainers:
 repo_depends:
 - r-zlibbioc
 update_on:
-- regex: seqTools_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/seqTools
+- source: rpkgs
+  pkgname: seqTools
+  repo: bioc
+  md5: true
 - alias: r
+- source: alpm
+  alpm: zlib
+  repo: core
+  provided: libz.so
+  strip_release: true

BioArchLinux/r-snowfall/PKGBUILD

@@ -3,28 +3,28 @@
 _pkgname=snowfall
 _pkgver=1.84-6.3
 pkgname=r-${_pkgname,,}
-pkgver=1.84.6.3
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Easier cluster computing (based on snow).'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Easier Cluster Computing (Based on 'snow')"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-snow
 )
 optdepends=(
   r-rmpi
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('2641932b01041e34b7afb1261f649755b4c8d6560080e0e2ee549ffdf3b8b143')
+md5sums=('4ca758a26dd4e862cc9ffd43ae16b2d3')
+b2sums=('f641aeef1a201c75424f61db662bf523fc277ac4d4abfb113588f52757c5b93c77af17bf97282dbd85604ff7099e9b62f6f80b7a672064447a9dc5512850e61e')
 
 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-snowfall/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-snowfall/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-snow
 update_on:
-- regex: snowfall_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=snowfall
+- source: rpkgs
+  pkgname: snowfall
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-snpstats/PKGBUILD

@@ -3,29 +3,30 @@
 _pkgname=snpStats
 _pkgver=1.52.0
 pkgname=r-${_pkgname,,}
-pkgver=1.52.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='SnpMatrix and XSnpMatrix classes and methods'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="SnpMatrix and XSnpMatrix classes and methods"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-biocgenerics
   r-zlibbioc
+  zlib
 )
 optdepends=(
   r-hexbin
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d9af4679d0dcb74895b62825902925826b8303a2c674f884b1674b3ad2f69328')
+md5sums=('0625c920470937a31fd278cf8bd8982a')
+b2sums=('2ada9c7f21a9f59558519c9e34328101acd7815e153674a17cb65815471b6ec3570da2daf9f9cf5d4c78fa0c496b350973de312bfdbd223a5180f5ca4e21e2c0')
 
 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-snpstats/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-snpstats/lilac.yaml

@@ -6,7 +6,13 @@ repo_depends:
 - r-biocgenerics
 - r-zlibbioc
 update_on:
-- regex: snpStats_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/snpStats
+- source: rpkgs
+  pkgname: snpStats
+  repo: bioc
+  md5: true
 - alias: r
+- source: alpm
+  alpm: zlib
+  repo: core
+  provided: libz.so
+  strip_release: true

BioArchLinux/r-sparsepca/PKGBUILD

@@ -3,25 +3,25 @@
 _pkgname=sparsepca
 _pkgver=0.1.2
 pkgname=r-${_pkgname,,}
-pkgver=0.1.2
+pkgver=${_pkgver//-/.}
 pkgrel=6
-pkgdesc='Sparse Principal Component Analysis (SPCA)'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Sparse Principal Component Analysis (SPCA)"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
   r-rsvd
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('646f2244a57ae8d2e490e0913d4dc9dcf3dafeffb1104d225aaf847b46b56272')
+md5sums=('fbbc7e20a66da7f318e3d8f87791a201')
+b2sums=('5a484f636279744d341f83c50280821b3fe72daee1de596a22e07f743879674f654e5935bfd29779980f2b9c1ff5251a94c45403f9396b378e1c59db959b3ad8')
 
 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-sparsepca/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-sparsepca/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-rsvd
 update_on:
-- regex: sparsepca_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=sparsepca
+- source: rpkgs
+  pkgname: sparsepca
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-splancs/PKGBUILD

@@ -3,28 +3,28 @@
 _pkgname=splancs
 _pkgver=2.01-44
 pkgname=r-${_pkgname,,}
-pkgver=2.01.44
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Spatial and Space-Time Point Pattern Analysis'
-arch=('x86_64')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Spatial and Space-Time Point Pattern Analysis"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-sp
 )
 makedepends=(
   gcc-fortran
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('08d46df9b56488925cc1b66261cf1134292ce4b5174b45e066eeb1e951dec171')
+md5sums=('44e5896425648e699fb0fe15fef191fc')
+b2sums=('5a5b355941c1fc3da3ac67b34c0b132aa6b2cb20b21dcc1f01cc3fa9a09146b9bbfea3ed0fb67d89a4828edfc93550ed8377deac6fad535ec61a7414faf6df05')
 
 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-splancs/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-splancs/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-sp
 update_on:
-- regex: splancs_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=splancs
+- source: rpkgs
+  pkgname: splancs
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-venn/PKGBUILD

@@ -3,14 +3,13 @@
 _pkgname=venn
 _pkgver=1.12
 pkgname=r-${_pkgname,,}
-pkgver=1.12
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Draw Venn Diagrams'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Draw Venn Diagrams"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
   r-admisc
 )
 optdepends=(
@@ -19,14 +18,15 @@ optdepends=(
   r-qca
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('ed86b69bd99ceea93352a30699a0baba3fd8cdcde907a9476e92be202ad8721d')
+md5sums=('29b0e3dd951c8626b126705d88f8303a')
+b2sums=('09b3727890b2b2447a076c94e8449e20e39c4cf2eaaf9c8ff9573dd1ede01ae6ea8f10f3a0342910e717bf49b6079329fcf66184c30ea215198d24c514ec9102')
 
 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-venn/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-venn/lilac.yaml

@@ -5,7 +5,8 @@ maintainers:
 repo_depends:
 - r-admisc
 update_on:
-- regex: venn_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=venn
+- source: rpkgs
+  pkgname: venn
+  repo: cran
+  md5: true
 - alias: r