From fd2772ed943ba6a6117f1a10dde91acaa05f427b Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 20 Feb 2024 17:31:54 +0200
Subject: [PATCH] r-*: use metadata checks for several packages

---
 BioArchLinux/r-biasedurn/PKGBUILD     | 21 +++++++++++----------
 BioArchLinux/r-biasedurn/lilac.py     | 11 ++++++-----
 BioArchLinux/r-biasedurn/lilac.yaml   |  7 ++++---
 BioArchLinux/r-jaspar2018/PKGBUILD    | 21 +++++++++++----------
 BioArchLinux/r-jaspar2018/lilac.py    | 11 ++++++-----
 BioArchLinux/r-jaspar2018/lilac.yaml  |  7 ++++---
 BioArchLinux/r-survivalroc/PKGBUILD   | 21 +++++++++++----------
 BioArchLinux/r-survivalroc/lilac.py   | 11 ++++++-----
 BioArchLinux/r-survivalroc/lilac.yaml |  7 ++++---
 9 files changed, 63 insertions(+), 54 deletions(-)

diff --git a/BioArchLinux/r-biasedurn/PKGBUILD b/BioArchLinux/r-biasedurn/PKGBUILD
index 7c384c4efd..07ca987d7e 100644
--- a/BioArchLinux/r-biasedurn/PKGBUILD
+++ b/BioArchLinux/r-biasedurn/PKGBUILD
@@ -3,24 +3,25 @@
 _pkgname=BiasedUrn
 _pkgver=2.0.11
 pkgname=r-${_pkgname,,}
-pkgver=2.0.11
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Biased Urn Model Distributions'
-arch=('x86_64')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Biased Urn Model Distributions"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-3.0-only')
 depends=(
   r
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('6295f1a12cd9d425cc03ec05a993fba04f539007c1754f23d7043a585b9e7537')
+md5sums=('435d436db9c8359cf99234f9468bfc78')
+b2sums=('9351d7487088136a2edf64b54486cfe03d79a27807013c3be391bcaf6e293cc1c6c8e1ac2932a3dc54c8874387423d25c8d522e40f1911a63248c17e8d79b136')
 
 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:
diff --git a/BioArchLinux/r-biasedurn/lilac.py b/BioArchLinux/r-biasedurn/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-biasedurn/lilac.py
+++ b/BioArchLinux/r-biasedurn/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()
diff --git a/BioArchLinux/r-biasedurn/lilac.yaml b/BioArchLinux/r-biasedurn/lilac.yaml
index 0d13cfa6ab..43212a984b 100644
--- a/BioArchLinux/r-biasedurn/lilac.yaml
+++ b/BioArchLinux/r-biasedurn/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: BiasedUrn_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=BiasedUrn
+- source: rpkgs
+  pkgname: BiasedUrn
+  repo: cran
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-jaspar2018/PKGBUILD b/BioArchLinux/r-jaspar2018/PKGBUILD
index c0345d3f3a..6bab8bd1f2 100644
--- a/BioArchLinux/r-jaspar2018/PKGBUILD
+++ b/BioArchLinux/r-jaspar2018/PKGBUILD
@@ -3,12 +3,12 @@
 _pkgname=JASPAR2018
 _pkgver=1.1.1
 pkgname=r-${_pkgname,,}
-pkgver=1.1.1
+pkgver=${_pkgver//-/.}
 pkgrel=6
-pkgdesc='Data package for JASPAR 2018'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Data package for JASPAR 2018"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
   r
 )
@@ -16,14 +16,15 @@ optdepends=(
   r-tfbstools
 )
 source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('87a22b2549eb6cd2f6db8692542fbb2a4aa1dc8bde9bd01b63022a9f435905c7')
+md5sums=('d91fce6ea0dc9fa6a3be6ebc05c1af5d')
+b2sums=('679990b0931d4e9e76f4dd4bc14fadb183caf8e9da225a86cebfeaf7d85954e3deb9d7d55ff1e8c0a6c21bd0941ebb86aa5f7c12b2a73508f907247e3f4c9eaf')
 
 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:
diff --git a/BioArchLinux/r-jaspar2018/lilac.py b/BioArchLinux/r-jaspar2018/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-jaspar2018/lilac.py
+++ b/BioArchLinux/r-jaspar2018/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()
diff --git a/BioArchLinux/r-jaspar2018/lilac.yaml b/BioArchLinux/r-jaspar2018/lilac.yaml
index 6f0a5f4225..ec171d3bbd 100644
--- a/BioArchLinux/r-jaspar2018/lilac.yaml
+++ b/BioArchLinux/r-jaspar2018/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: JASPAR2018_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/JASPAR2018
+- source: rpkgs
+  pkgname: JASPAR2018
+  repo: bioc-data-annotation
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-survivalroc/PKGBUILD b/BioArchLinux/r-survivalroc/PKGBUILD
index 9d4ef1e8bf..5a3d78d76b 100644
--- a/BioArchLinux/r-survivalroc/PKGBUILD
+++ b/BioArchLinux/r-survivalroc/PKGBUILD
@@ -3,24 +3,25 @@
 _pkgname=survivalROC
 _pkgver=1.0.3.1
 pkgname=r-${_pkgname,,}
-pkgver=1.0.3.1
+pkgver=${_pkgver//-/.}
 pkgrel=2
-pkgdesc='Time-dependent ROC curve estimation from censored survival data'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Time-Dependent ROC Curve Estimation from Censored Survival Data"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
   r
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('8174afebaf239dfda979c8c7e1e219624576d577c983ae787fbd2785b4ccd15c')
+md5sums=('f902d8d1d91cbed98b43ca3cfb9cddaa')
+b2sums=('b81a3a9b002fe63c793757bfd2f582c1a24257b0731290334c88751e9d03691f56031c87008c28675bb21ecb93c4775f2dd76c6b83411736e729307e2d13e44a')
 
 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:
diff --git a/BioArchLinux/r-survivalroc/lilac.py b/BioArchLinux/r-survivalroc/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-survivalroc/lilac.py
+++ b/BioArchLinux/r-survivalroc/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()
diff --git a/BioArchLinux/r-survivalroc/lilac.yaml b/BioArchLinux/r-survivalroc/lilac.yaml
index 1a4fc28550..6df4789dc2 100644
--- a/BioArchLinux/r-survivalroc/lilac.yaml
+++ b/BioArchLinux/r-survivalroc/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: survivalROC_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=survivalROC
+- source: rpkgs
+  pkgname: survivalROC
+  repo: cran
+  md5: true
 - alias: r