r-*: use archived CRAN sources for some packages

These packages have been removed from CRAN, but are required
by other packages and thus cannot be removed from the repo.

- r-dnet: dependency of r-pi and r-randomwalkrestartmh
- r-qlcmatrix: dependency of r-cliquems and r-monocle
- r-rbokeh: dependency of r-seqsqc

BioArchLinux/r-dnet/PKGBUILD

@@ -3,14 +3,13 @@
 _pkgname=dnet
 _pkgver=1.1.7
 pkgname=r-${_pkgname,,}
-pkgver=1.1.7
+pkgver=${_pkgver//-/.}
 pkgrel=6
-pkgdesc='Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-only')
 depends=(
-  r
   r-graph
   r-igraph
   r-rgraphviz
@@ -21,17 +20,17 @@ optdepends=(
   r-doparallel
   r-foreach
   r-limma
-  r-survival
 )
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('ac2be6d2b64dd6f63002c80b4646506fadf3ec9dc690249193db40d1d17db816')
+source=("https://cran.r-project.org/src/contrib/Archive/$_pkgname/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('0a42f86fab2e9288eb4ebfcaa0e94d13')
+b2sums=('804eb4f2f409a438bc772b1f3ee7fb9ceaedbc642cbcb92bd1c41404adb47cce7ea6dc84b369ed1c7dbf4ba63263d8f58be4a585b0c2f04d56fbf561bd52dfc1')
 
 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-dnet/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-dnet/lilac.yaml

@@ -8,7 +8,6 @@ repo_depends:
 - r-rgraphviz
 - r-suprahex
 update_on:
-- regex: dnet_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=dnet
+- source: manual
+  manual: 1.1.7#0a42f86fab2e9288eb4ebfcaa0e94d13
 - alias: r

BioArchLinux/r-qlcmatrix/PKGBUILD

@@ -3,31 +3,30 @@
 _pkgname=qlcMatrix
 _pkgver=0.9.7
 pkgname=r-${_pkgname,,}
-pkgver=0.9.7
+pkgver=${_pkgver//-/.}
 pkgrel=6
-pkgdesc='Utility Sparse Matrix Functions for Quantitative Language Comparison'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Utility Sparse Matrix Functions for Quantitative Language Comparison"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-docopt
   r-slam
   r-sparsesvd
 )
 optdepends=(
   r-knitr
-  r-mass
 )
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('1ef5e0350cfbdb07fca761fc7251584d39d3da2958ea813498b467e4f7661347')
+source=("https://cran.r-project.org/src/contrib/Archive/$_pkgname/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('3b0734cb96c9cae62f760de1d4a4a8a7')
+b2sums=('4985f5c329070efa2565f0d531938b0d5be653757ba9d62082d3b98294b389f3c5d0394a6fda8a8cf21aad94d0bb53bbbadeaf7ff3c66627787fc2052de47080')
 
 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-qlcmatrix/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-qlcmatrix/lilac.yaml

@@ -7,7 +7,6 @@ repo_depends:
 - r-slam
 - r-sparsesvd
 update_on:
-- regex: qlcMatrix_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=qlcMatrix
+- source: manual
+  manual: 0.9.7#3b0734cb96c9cae62f760de1d4a4a8a7
 - alias: r

BioArchLinux/r-rbokeh/PKGBUILD

@@ -3,14 +3,13 @@
 _pkgname=rbokeh
 _pkgver=0.5.2
 pkgname=r-${_pkgname,,}
-pkgver=0.5.2
+pkgver=${_pkgver//-/.}
 pkgrel=6
-pkgdesc='R Interface for Bokeh'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
+pkgdesc="R Interface for Bokeh"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
 license=('MIT')
 depends=(
-  r
   r-digest
   r-gistr
   r-hexbin
@@ -25,25 +24,26 @@ depends=(
 optdepends=(
   r-data.table
   r-knitr
-  r-lattice
   r-latticeextra
   r-lintr
   r-markdown
   r-rmarkdown
   r-roxygen2
-  r-shiny
   r-testthat
 )
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d8c47dbd978efce04e5676a3a91d511517a9bb8fe1859c404bfc9ee0f0bf4ec0')
+source=("https://cran.r-project.org/src/contrib/Archive/$_pkgname/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('08b834ae99835c679c717c7c8537e196')
+b2sums=('69bb6adb62b4e05bbffb5247423b6cbcffaeae09eefc150bcf888e8e1a5b027733ce80972e03a9aed95ab605cdcf3768bb9f366f36ef9c77269b5e75e1d58167')
 
 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-rbokeh/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-rbokeh/lilac.yaml

@@ -14,7 +14,6 @@ repo_depends:
 - r-pryr
 - r-scales
 update_on:
-- regex: rbokeh_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=rbokeh
+- source: manual
+  manual: 0.5.2#08b834ae99835c679c717c7c8537e196
 - alias: r