*: Merge branch 'master' of github.com:BioArchLinux/Packages

BioArchLinux/r-assertive.reflection/PKGBUILD

@@ -3,28 +3,28 @@
 _pkgname=assertive.reflection
 _pkgver=0.0-5
 pkgname=r-${_pkgname,,}
-pkgver=0.0.5
+pkgver=${_pkgver//-/.}
-pkgrel=6
+pkgrel=7
-pkgdesc='Assertions for Checking the State of R'
+pkgdesc="Assertions for Checking the State of R"
-arch=('any')
+arch=(any)
-url="https://cran.r-project.org/package=${_pkgname}"
+url="https://cran.r-project.org/package=$_pkgname"
-license=('GPL')
+license=('GPL-3.0-or-later')
 depends=(
-  r
   r-assertive.base
 )
 optdepends=(
   r-testthat
 )
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+source=("https://cran.r-project.org/src/contrib/Archive/$_pkgname/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('c2ca9b27cdddb9b9876351afd2ebfaf0fbe72c636cd12aa2af5d64e33fbf34bd')
+md5sums=('e5b52b04481fe2b713a668262fb1c642')
+b2sums=('3091e695854ccd6ac3d0febb22e8a45249f21a176b212e37b9f208bafc6aa526a60b2bfca648338b222cd6c7b6a2bb00a70349d3beda891f915e2703cccfaa10')
 
 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-assertive.reflection/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-assertive.reflection/lilac.yaml

@@ -5,7 +5,6 @@ maintainers:
 repo_depends:
 - r-assertive.base
 update_on:
-- regex: assertive.reflection_([\d._-]+).tar.gz
+- source: manual
-  source: regex
+  manual: 0.0-5#e5b52b04481fe2b713a668262fb1c642
-  url: https://cran.r-project.org/package=assertive.reflection
 - alias: r

BioArchLinux/r-autonomics/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=autonomics
 _pkgver=1.10.2
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=1
+pkgrel=2
 pkgdesc="Generifying and intuifying cross-platform omics analysis"
 arch=(any)
 url="https://bioconductor.org/packages/$_pkgname"

BioArchLinux/r-forecast/PKGBUILD

@@ -1,9 +1,9 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=forecast
-_pkgver=8.21.1
+_pkgver=8.22.0
 pkgname=r-${_pkgname,,}
-pkgver=8.21.1
+pkgver=8.22.0
 pkgrel=1
 pkgdesc='Forecasting Functions for Time Series and Linear Models'
 arch=('x86_64')
@@ -35,7 +35,7 @@ optdepends=(
   r-uroot
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('811eace27c7f6e99e1048b8f2522e67bb3620471c5431e0ef83c396612dc8127')
+sha256sums=('1c355c032baaa5e6c47613e054fee663ba424dabd2fae31ba2c519f67d734527')
 
 build() {
   R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"

BioArchLinux/r-hrbrthemes/PKGBUILD

@@ -4,7 +4,7 @@ _pkgname=hrbrthemes
 _pkgver=0.8.7
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=0
+pkgrel=1
 pkgdesc="Additional Themes, Theme Components and Utilities for 'ggplot2'"
 arch=(any)
 url="https://cran.r-project.org/package=$_pkgname"

BioArchLinux/r-multicrispr/PKGBUILD

@@ -3,15 +3,18 @@
 _pkgname=multicrispr
 _pkgver=1.12.3
 pkgname=r-${_pkgname,,}
-pkgver=1.12.3
+pkgver=${_pkgver//-/.}
-pkgrel=1
+pkgrel=2
-pkgdesc='Multi-locus multi-purpose Crispr/Cas design'
+pkgdesc="Multi-locus multi-purpose Crispr/Cas design"
-arch=('any')
+arch=(any)
-url="https://bioconductor.org/packages/${_pkgname}"
+url="https://bioconductor.org/packages/$_pkgname"
-license=('GPL')
+license=('GPL-2.0-only')
 depends=(
-  r
+  r-assertive.base
-  r-assertive
+  r-assertive.files
+  r-assertive.numbers
+  r-assertive.reflection
+  r-assertive.sets
   r-biocgenerics
   r-biostrings
   r-bsgenome
@@ -46,14 +49,15 @@ optdepends=(
   r-txdb.mmusculus.ucsc.mm10.knowngene
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('abf0ec2d4d8e9030e86a42449b5729a08e292040e4af711bcc72ca72bbdb508d')
+md5sums=('d0bbc847e39772348376d944c884290a')
+b2sums=('ed79977a043b0bf57b139d7f304568fd88d7bb7317c673e58f459908fb0330c545243798cdaec86fd56bdf3f0c2e67270e67e0f8f341d280b35b130d4d898be8')
 
 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-multicrispr/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-multicrispr/lilac.yaml

@@ -3,7 +3,11 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-assertive
+- r-assertive.base
+- r-assertive.files
+- r-assertive.numbers
+- r-assertive.reflection
+- r-assertive.sets
 - r-biocgenerics
 - r-biostrings
 - r-bsgenome
@@ -23,7 +27,8 @@ repo_depends:
 - r-tidyr
 - r-tidyselect
 update_on:
-- regex: multicrispr_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: multicrispr
-  url: https://bioconductor.org/packages/multicrispr
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-multipanelfigure/PKGBUILD

@@ -1,21 +1,18 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=multipanelfigure
-_pkgver=2.1.2
+_pkgver=2.1.5
 pkgname=r-${_pkgname,,}
-pkgver=2.1.2
+pkgver=${_pkgver//-/.}
-pkgrel=8
+pkgrel=1
-pkgdesc='Infrastructure to Assemble Multi-Panel Figures (from Grobs)'
+pkgdesc="Infrastructure to Assemble Multi-Panel Figures (from Grobs)"
-arch=('any')
+arch=(any)
-url="https://cran.r-project.org/package=${_pkgname}"
+url="https://cran.r-project.org/package=$_pkgname"
-license=('GPL')
+license=('GPL-3.0-or-later')
 depends=(
-  r
   r-assertive.base
   r-assertive.files
   r-assertive.numbers
-  r-assertive.properties
-  r-assertive.types
   r-ggplot2
   r-gridgraphics
   r-gtable
@@ -25,23 +22,22 @@ depends=(
 )
 optdepends=(
   r-complexheatmap
-  r-grdevices
   r-knitr
-  r-lattice
   r-markdown
   r-rmarkdown
   r-roxygen2
   r-venndiagram
 )
-source=("https://cran.r-project.org/src/contrib/Archive/${_pkgname}/${_pkgname}_${_pkgver}.tar.gz")
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('eca98888d2f7c8887764443633bd557e9100f73694b2e5df68a63b304f5ba532')
+md5sums=('e80c2af7114635a3cf1d01adf7d0207e')
+b2sums=('730435fc8dd88ba096bafa7f2d8474cb2b99f361ef2353a0ad144602942709629e83c95c3b887fb5fc3b368eb7de2cbe62606e85e5376f29f472e3b32f92e5d6')
 
 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-multipanelfigure/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-multipanelfigure/lilac.yaml

@@ -6,8 +6,6 @@ repo_depends:
 - r-assertive.base
 - r-assertive.files
 - r-assertive.numbers
-- r-assertive.properties
-- r-assertive.types
 - r-ggplot2
 - r-gridgraphics
 - r-gtable
@@ -15,7 +13,8 @@ repo_depends:
 - r-magrittr
 - r-stringi
 update_on:
-- regex: multipanelfigure_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: multipanelfigure
-  url: https://cran.r-project.org/src/contrib/Archive/multipanelfigure
+  repo: cran
+  md5: true
 - alias: r

BioArchLinux/r-pak/PKGBUILD

@@ -6,7 +6,7 @@ _pkgname=pak
 _pkgver=0.7.1
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=2
+pkgrel=3
 pkgdesc="Another Approach to Package Installation"
 arch=(any)
 url="https://cran.r-project.org/package=$_pkgname"
@@ -44,9 +44,9 @@ optdepends=(
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
         "system-libs.patch")
-md5sums=('9eddae8f9345c4e5ad3a9692be09e6f8'
+md5sums=('bc95a3a8966b8042d0201729e7ab186f'
          '29b1470e2d25f82ebeafc02fe3b2594a')
-b2sums=('2b5daa9c7c8e97907030933ede18e37a0f879dccfeebab7825b8475639663f757571a37d918e8ba4e724c0e34b8399b51e7ba8ca708acae87eef2291f279ed38'
+b2sums=('6792e3a9be1be2480a737dd0744ff2defb9444e3ee9cdadd1b8319a52dba9db4e37a8fa2f488a58d0e060bcd1485292d8448ad71bd33924b659bbdaef7cf97d9'
         'b422c6a23d6850831433fdcf3e81684189bdaea1735fcc85edeff3202fe084f4167876949ff9ddfd5654cb2ce202ed005800a217dfe9bb12fb8240456880b4f1')
 
 prepare() {