From d8bf5f6d19ba93220fdab911f598b0d2352b2b26 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Mon, 11 Mar 2024 15:48:06 +0200
Subject: [PATCH] r-*: use metadata checks for several packages

---
 BioArchLinux/r-gfa/PKGBUILD           | 22 +++++++++++++---------
 BioArchLinux/r-gfa/lilac.py           | 11 ++++++-----
 BioArchLinux/r-gfa/lilac.yaml         |  7 ++++---
 BioArchLinux/r-pma/PKGBUILD           | 21 +++++++++++----------
 BioArchLinux/r-pma/lilac.py           | 11 ++++++-----
 BioArchLinux/r-pma/lilac.yaml         |  7 ++++---
 BioArchLinux/r-segmented/PKGBUILD     | 21 +++++++++++----------
 BioArchLinux/r-segmented/lilac.py     | 11 ++++++-----
 BioArchLinux/r-segmented/lilac.yaml   |  7 ++++---
 BioArchLinux/r-tmvnsim/PKGBUILD       | 21 +++++++++++----------
 BioArchLinux/r-tmvnsim/lilac.py       | 11 ++++++-----
 BioArchLinux/r-tmvnsim/lilac.yaml     |  7 ++++---
 BioArchLinux/r-wesanderson/PKGBUILD   | 23 +++++++++++++----------
 BioArchLinux/r-wesanderson/lilac.py   | 11 ++++++-----
 BioArchLinux/r-wesanderson/lilac.yaml |  7 ++++---
 15 files changed, 109 insertions(+), 89 deletions(-)

diff --git a/BioArchLinux/r-gfa/PKGBUILD b/BioArchLinux/r-gfa/PKGBUILD
index 9603d12723..1de41c2ff2 100644
--- a/BioArchLinux/r-gfa/PKGBUILD
+++ b/BioArchLinux/r-gfa/PKGBUILD
@@ -3,24 +3,28 @@
 _pkgname=GFA
 _pkgver=1.0.5
 pkgname=r-${_pkgname,,}
-pkgver=1.0.5
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Group Factor Analysis'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
+pkgdesc="Group Factor Analysis"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
 license=('MIT')
 depends=(
   r
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('4d75b1effb0e31821b07386a900cf68e304c9925c3f2226c45ad2cae4450b7d1')
+md5sums=('120596244929ae4a15d1266567bc2b75')
+b2sums=('e51a23c416022af743db7bbbb39a06638dfede53a1bd9058d3875eb1b4d0e04a52a8fadf334d9a197a9ea0a684d47e547b2b7e30d1701e50ad5dc3611aaed064')
 
 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"
+
+  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:
diff --git a/BioArchLinux/r-gfa/lilac.py b/BioArchLinux/r-gfa/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-gfa/lilac.py
+++ b/BioArchLinux/r-gfa/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-gfa/lilac.yaml b/BioArchLinux/r-gfa/lilac.yaml
index 2b843adc5f..2fe8696167 100644
--- a/BioArchLinux/r-gfa/lilac.yaml
+++ b/BioArchLinux/r-gfa/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: GFA_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=GFA
+- source: rpkgs
+  pkgname: GFA
+  repo: cran
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-pma/PKGBUILD b/BioArchLinux/r-pma/PKGBUILD
index 2e514b8ca3..d63738e43e 100644
--- a/BioArchLinux/r-pma/PKGBUILD
+++ b/BioArchLinux/r-pma/PKGBUILD
@@ -3,24 +3,25 @@
 _pkgname=PMA
 _pkgver=1.2-3
 pkgname=r-${_pkgname,,}
-pkgver=1.2.3
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Penalized Multivariate Analysis'
-arch=('x86_64')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Penalized Multivariate Analysis"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
   r
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('e7572f82c159f34058fdec4c8158d394d6cf68b7978953c8893315e298cc6d06')
+md5sums=('f4761339585ee1f7a86562b6863cd985')
+b2sums=('689f0a63a3d33599ce54f7f8db557f14e78fddfe6a613ca333a02cde48a401356800a7372873ef8bc0b64bf2f29ccd0f08f43e4a442e50189c5ef33479306a13')
 
 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-pma/lilac.py b/BioArchLinux/r-pma/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-pma/lilac.py
+++ b/BioArchLinux/r-pma/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-pma/lilac.yaml b/BioArchLinux/r-pma/lilac.yaml
index c63c138045..e5116eca44 100644
--- a/BioArchLinux/r-pma/lilac.yaml
+++ b/BioArchLinux/r-pma/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: PMA_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=PMA
+- source: rpkgs
+  pkgname: PMA
+  repo: cran
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-segmented/PKGBUILD b/BioArchLinux/r-segmented/PKGBUILD
index 5485c4a6de..2dd9a53262 100644
--- a/BioArchLinux/r-segmented/PKGBUILD
+++ b/BioArchLinux/r-segmented/PKGBUILD
@@ -3,24 +3,25 @@
 _pkgname=segmented
 _pkgver=2.0-3
 pkgname=r-${_pkgname,,}
-pkgver=2.0.3
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Regression Models with Break-Points / Change-Points Estimation'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Regression Models with Break-Points / Change-Points Estimation (with Possibly Random Effects)"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
   r
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('e7a88ae270ecb853067fbe26e21477dd369b47cefc443c3af486f2bebed909b9')
+md5sums=('1ea139e06c62456571430a62cc3cbc8b')
+b2sums=('96d706f1df10c0b9ffba604bc1e8d684ebaaf153224f754fad90379b8f240b3d4e78580ea5c761faf989a244e6f7c632619ac6862d64590964e925570dbd78c2')
 
 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-segmented/lilac.py b/BioArchLinux/r-segmented/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-segmented/lilac.py
+++ b/BioArchLinux/r-segmented/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-segmented/lilac.yaml b/BioArchLinux/r-segmented/lilac.yaml
index 6d65d8ee3e..e6ac704e05 100644
--- a/BioArchLinux/r-segmented/lilac.yaml
+++ b/BioArchLinux/r-segmented/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: segmented_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=segmented
+- source: rpkgs
+  pkgname: segmented
+  repo: cran
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-tmvnsim/PKGBUILD b/BioArchLinux/r-tmvnsim/PKGBUILD
index 0f409164f2..bd9a245c88 100644
--- a/BioArchLinux/r-tmvnsim/PKGBUILD
+++ b/BioArchLinux/r-tmvnsim/PKGBUILD
@@ -4,12 +4,12 @@
 _pkgname=tmvnsim
 _pkgver=1.0-2
 pkgname=r-${_pkgname,,}
-pkgver=1.0.2
+pkgver=${_pkgver//-/.}
 pkgrel=10
-pkgdesc='Truncated Multivariate Normal Simulation'
-arch=('x86_64')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="Truncated Multivariate Normal Simulation"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-only')
 depends=(
   r
 )
@@ -17,14 +17,15 @@ makedepends=(
   gcc-fortran
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('97f63d0bab3b240cc7bdbe6e6e74e90ad25a4382a345ee51a26fe3959edeba0f')
+md5sums=('50a38f2142ee328060aca7d2672b5dcf')
+b2sums=('09105660070368676a161201c1e0a8b12ab265353ef51f4fcb4e223b0fa7a3261d531dc8a629620f0c9d17ade5e5689d7e50bdb8a8266ccb8166f54e98408286')
 
 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-tmvnsim/lilac.py b/BioArchLinux/r-tmvnsim/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-tmvnsim/lilac.py
+++ b/BioArchLinux/r-tmvnsim/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-tmvnsim/lilac.yaml b/BioArchLinux/r-tmvnsim/lilac.yaml
index 784d17c67d..b635838bab 100644
--- a/BioArchLinux/r-tmvnsim/lilac.yaml
+++ b/BioArchLinux/r-tmvnsim/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: tmvnsim_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=tmvnsim
+- source: rpkgs
+  pkgname: tmvnsim
+  repo: cran
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-wesanderson/PKGBUILD b/BioArchLinux/r-wesanderson/PKGBUILD
index 72e6b74fbf..e7d8ca8483 100644
--- a/BioArchLinux/r-wesanderson/PKGBUILD
+++ b/BioArchLinux/r-wesanderson/PKGBUILD
@@ -3,11 +3,11 @@
 _pkgname=wesanderson
 _pkgver=0.3.7
 pkgname=r-${_pkgname,,}
-pkgver=0.3.7
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='A Wes Anderson Palette Generator'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
+pkgdesc="A Wes Anderson Palette Generator"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
 license=('MIT')
 depends=(
   r
@@ -16,15 +16,18 @@ optdepends=(
   r-ggplot2
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('c92e5604e1e149e00f49fd236c6ab8cd09d96106eb14479f7839e6996bf95e4e')
+md5sums=('8becbb8ab06d2c694c06d0a1b10da95b')
+b2sums=('7fb2db1777ccf60ded0fa4e11079705c5c98a566a51ec88c911e5c64573c3a679102e8aa38e967decefe554b0504ea37628e89a391095ee8707e6d9296d49b54')
 
 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:
diff --git a/BioArchLinux/r-wesanderson/lilac.py b/BioArchLinux/r-wesanderson/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-wesanderson/lilac.py
+++ b/BioArchLinux/r-wesanderson/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-wesanderson/lilac.yaml b/BioArchLinux/r-wesanderson/lilac.yaml
index 051a694ba9..217c08d0ad 100644
--- a/BioArchLinux/r-wesanderson/lilac.yaml
+++ b/BioArchLinux/r-wesanderson/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: wesanderson_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=wesanderson
+- source: rpkgs
+  pkgname: wesanderson
+  repo: cran
+  md5: true
 - alias: r