From c567331d0b59c396967a24fb83b4c5be2ccfb16e Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Mon, 18 Mar 2024 19:28:49 +0200
Subject: [PATCH] r-*: use metadata checks for several packages

---
 BioArchLinux/r-bader/PKGBUILD        | 21 +++++++++++----------
 BioArchLinux/r-bader/lilac.py        | 11 ++++++-----
 BioArchLinux/r-bader/lilac.yaml      |  7 ++++---
 BioArchLinux/r-bhc/PKGBUILD          | 21 +++++++++++----------
 BioArchLinux/r-bhc/lilac.py          | 11 ++++++-----
 BioArchLinux/r-bhc/lilac.yaml        |  7 ++++---
 BioArchLinux/r-calm/PKGBUILD         | 21 +++++++++++----------
 BioArchLinux/r-calm/lilac.py         | 11 ++++++-----
 BioArchLinux/r-calm/lilac.yaml       |  7 ++++---
 BioArchLinux/r-cfassay/PKGBUILD      | 21 +++++++++++----------
 BioArchLinux/r-cfassay/lilac.py      | 11 ++++++-----
 BioArchLinux/r-cfassay/lilac.yaml    |  7 ++++---
 BioArchLinux/r-chopsticks/PKGBUILD   | 19 ++++++++++---------
 BioArchLinux/r-chopsticks/lilac.py   | 11 ++++++-----
 BioArchLinux/r-chopsticks/lilac.yaml |  7 ++++---
 BioArchLinux/r-cispath/PKGBUILD      | 21 +++++++++++----------
 BioArchLinux/r-cispath/lilac.py      | 11 ++++++-----
 BioArchLinux/r-cispath/lilac.yaml    |  7 ++++---
 BioArchLinux/r-cogps/PKGBUILD        | 21 +++++++++++----------
 BioArchLinux/r-cogps/lilac.py        | 11 ++++++-----
 BioArchLinux/r-cogps/lilac.yaml      |  7 ++++---
 BioArchLinux/r-comprehenr/PKGBUILD   | 21 +++++++++++----------
 BioArchLinux/r-comprehenr/lilac.py   | 11 ++++++-----
 BioArchLinux/r-comprehenr/lilac.yaml | 13 +++++++------
 24 files changed, 170 insertions(+), 146 deletions(-)

diff --git a/BioArchLinux/r-bader/PKGBUILD b/BioArchLinux/r-bader/PKGBUILD
index f3742dd4f0..b6455f8d41 100644
--- a/BioArchLinux/r-bader/PKGBUILD
+++ b/BioArchLinux/r-bader/PKGBUILD
@@ -3,12 +3,12 @@
 _pkgname=BADER
 _pkgver=1.40.0
 pkgname=r-${_pkgname,,}
-pkgver=1.40.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Bayesian Analysis of Differential Expression in RNA Sequencing Data'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Bayesian Analysis of Differential Expression in RNA Sequencing Data"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
   r
 )
@@ -16,14 +16,15 @@ optdepends=(
   r-pasilla
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d597dfa44e9c0dffc8bae73cced5b21bfeea76fb7523f2d84bd36a4e8f3aae7e')
+md5sums=('10d4e5e231ff178df7922078024f9d89')
+b2sums=('6a606f37c1030404208913db504f22877c1f13095c78fbe6e2928a9763134f990f3371a95f12972200baf143dbe3ecdc7660a372e4359c2b92f483dc4e4886e1')
 
 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-bader/lilac.py b/BioArchLinux/r-bader/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-bader/lilac.py
+++ b/BioArchLinux/r-bader/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-bader/lilac.yaml b/BioArchLinux/r-bader/lilac.yaml
index 28653080f4..ec84c652cf 100644
--- a/BioArchLinux/r-bader/lilac.yaml
+++ b/BioArchLinux/r-bader/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: BADER_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/BADER
+- source: rpkgs
+  pkgname: BADER
+  repo: bioc
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-bhc/PKGBUILD b/BioArchLinux/r-bhc/PKGBUILD
index 30fe6eab66..f3b160f1d2 100644
--- a/BioArchLinux/r-bhc/PKGBUILD
+++ b/BioArchLinux/r-bhc/PKGBUILD
@@ -3,24 +3,25 @@
 _pkgname=BHC
 _pkgver=1.54.0
 pkgname=r-${_pkgname,,}
-pkgver=1.54.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Bayesian Hierarchical Clustering'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Bayesian Hierarchical Clustering"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
   r
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('c1bba8450c9bf689949f944694afc6f65e7ff8afedd7f24a68271ebd124e48d4')
+md5sums=('855087c8854bd3014111477e1c3cdcb9')
+b2sums=('8618c469025c895d42d5e6cd12099b8e25ec6b77b0e56371987d88bdece28d36248435d2ff7e748e08862fa74c4d30b8d41dd6a66fc335f6faf91b434ef76ae4')
 
 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-bhc/lilac.py b/BioArchLinux/r-bhc/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-bhc/lilac.py
+++ b/BioArchLinux/r-bhc/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-bhc/lilac.yaml b/BioArchLinux/r-bhc/lilac.yaml
index 308c788a34..1496bc86d1 100644
--- a/BioArchLinux/r-bhc/lilac.yaml
+++ b/BioArchLinux/r-bhc/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: BHC_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/BHC
+- source: rpkgs
+  pkgname: BHC
+  repo: bioc
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-calm/PKGBUILD b/BioArchLinux/r-calm/PKGBUILD
index 42644eaf0f..23d6f119e6 100644
--- a/BioArchLinux/r-calm/PKGBUILD
+++ b/BioArchLinux/r-calm/PKGBUILD
@@ -3,12 +3,12 @@
 _pkgname=calm
 _pkgver=1.16.0
 pkgname=r-${_pkgname,,}
-pkgver=1.16.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Covariate Assisted Large-scale Multiple testing'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Covariate Assisted Large-scale Multiple testing"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
   r
 )
@@ -17,14 +17,15 @@ optdepends=(
   r-rmarkdown
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('db9d2c3f5b53c0bca13351fae104aac9177c35ccf0c7fc6fcd4f38082342028c')
+md5sums=('9a2b4c48021193636c88c997331ede2d')
+b2sums=('220688663275c68e39e6fbe7fef558da6e6761d067aef930d91a6e802c4fbcbdebea81366aa838355ee08956e330789b8337afe1359879f032d0fdf5c2c610f1')
 
 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-calm/lilac.py b/BioArchLinux/r-calm/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-calm/lilac.py
+++ b/BioArchLinux/r-calm/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-calm/lilac.yaml b/BioArchLinux/r-calm/lilac.yaml
index 1b449dd09f..9ee42c2d4e 100644
--- a/BioArchLinux/r-calm/lilac.yaml
+++ b/BioArchLinux/r-calm/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: calm_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/calm
+- source: rpkgs
+  pkgname: calm
+  repo: bioc
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-cfassay/PKGBUILD b/BioArchLinux/r-cfassay/PKGBUILD
index d30eef47b3..4516623b03 100644
--- a/BioArchLinux/r-cfassay/PKGBUILD
+++ b/BioArchLinux/r-cfassay/PKGBUILD
@@ -3,24 +3,25 @@
 _pkgname=CFAssay
 _pkgver=1.36.0
 pkgname=r-${_pkgname,,}
-pkgver=1.36.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Statistical analysis for the Colony Formation Assay'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('LGPL')
+pkgdesc="Statistical analysis for the Colony Formation Assay"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('LGPL-2.0-or-later')
 depends=(
   r
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('44a819139501cf2bee863a9d0a0e624f19c9a3e0a2cc6755f2020a7e886e133a')
+md5sums=('122c969248ffd92330d93a266db6cb3c')
+b2sums=('53dae0fb1b19bb5e90cc870ed8226c2a97449d73e186e2f79bd45272d615d45d50f77dc26dcc15c9cd7e58f75d2d5c2d410c7af91a5dc75dc2ca6ffbd39aa02c')
 
 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-cfassay/lilac.py b/BioArchLinux/r-cfassay/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-cfassay/lilac.py
+++ b/BioArchLinux/r-cfassay/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-cfassay/lilac.yaml b/BioArchLinux/r-cfassay/lilac.yaml
index 5ed83fd9be..82abf2c09e 100644
--- a/BioArchLinux/r-cfassay/lilac.yaml
+++ b/BioArchLinux/r-cfassay/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: CFAssay_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/CFAssay
+- source: rpkgs
+  pkgname: CFAssay
+  repo: bioc
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-chopsticks/PKGBUILD b/BioArchLinux/r-chopsticks/PKGBUILD
index aeb62b0fa7..0734f29dd5 100644
--- a/BioArchLinux/r-chopsticks/PKGBUILD
+++ b/BioArchLinux/r-chopsticks/PKGBUILD
@@ -3,12 +3,12 @@
 _pkgname=chopsticks
 _pkgver=1.68.0
 pkgname=r-${_pkgname,,}
-pkgver=1.68.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
 pkgdesc="The 'snp.matrix' and 'X.snp.matrix' Classes"
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
   r
 )
@@ -16,14 +16,15 @@ optdepends=(
   r-hexbin
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5fe024c809302807edf170ad1108e25519b240415c25a7a2efb8584e91e0880b')
+md5sums=('b63b111068a6d42f7812010d1dc31047')
+b2sums=('cb710bc38ba57bc9ecb7e9e81ff0dbcf8e1fe1fca33f22546a3a04c3771bdde027984a8dc443cc146ef8ac7e2ebe362e76cf4db896b18ab6a44f0c656adf611a')
 
 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-chopsticks/lilac.py b/BioArchLinux/r-chopsticks/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-chopsticks/lilac.py
+++ b/BioArchLinux/r-chopsticks/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-chopsticks/lilac.yaml b/BioArchLinux/r-chopsticks/lilac.yaml
index 6f24413870..83b6afc9f5 100644
--- a/BioArchLinux/r-chopsticks/lilac.yaml
+++ b/BioArchLinux/r-chopsticks/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: chopsticks_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/chopsticks
+- source: rpkgs
+  pkgname: chopsticks
+  repo: bioc
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-cispath/PKGBUILD b/BioArchLinux/r-cispath/PKGBUILD
index d292b8dfee..8faef5d9ff 100644
--- a/BioArchLinux/r-cispath/PKGBUILD
+++ b/BioArchLinux/r-cispath/PKGBUILD
@@ -3,24 +3,25 @@
 _pkgname=cisPath
 _pkgver=1.42.0
 pkgname=r-${_pkgname,,}
-pkgver=1.42.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Visualization and management of the protein-protein interaction networks.'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Visualization and management of the protein-protein interaction networks"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
   r
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('16419352d21278d62543ff2de4be4fbc30575ef2feaa4812a488f9bf5556b603')
+md5sums=('958a35281b9aa98b2d5c3a5c4e9c8824')
+b2sums=('6c481e29e057a916b9302de8e6027926d12bf449eedf8f10a192e34397eff5091c1e8efbcde5e831fe08d25327e30592f5d43502f076b7d54db1f513756d56d5')
 
 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-cispath/lilac.py b/BioArchLinux/r-cispath/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-cispath/lilac.py
+++ b/BioArchLinux/r-cispath/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-cispath/lilac.yaml b/BioArchLinux/r-cispath/lilac.yaml
index 9543ccddfd..c10ee53a91 100644
--- a/BioArchLinux/r-cispath/lilac.yaml
+++ b/BioArchLinux/r-cispath/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: cisPath_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/cisPath
+- source: rpkgs
+  pkgname: cisPath
+  repo: bioc
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-cogps/PKGBUILD b/BioArchLinux/r-cogps/PKGBUILD
index 7d9855d03f..d99280ae86 100644
--- a/BioArchLinux/r-cogps/PKGBUILD
+++ b/BioArchLinux/r-cogps/PKGBUILD
@@ -3,12 +3,12 @@
 _pkgname=coGPS
 _pkgver=1.46.0
 pkgname=r-${_pkgname,,}
-pkgver=1.46.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='cancer outlier Gene Profile Sets'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="cancer outlier Gene Profile Sets"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
   r
 )
@@ -16,14 +16,15 @@ optdepends=(
   r-limma
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('a7d77ed813ee2901ad1504856720f0735aabf19e76b95edf99a3da6c911a1752')
+md5sums=('a824d8a41fee47628eb7f369adef4a2c')
+b2sums=('93638d4629abbc5660873ef47fe7c49025cfa8dc8d3bde46631c7c96b014a382560a6e5f7be643d6a0ef622d90cf32de3eed9cdcd82808b06898004b218ef4f6')
 
 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-cogps/lilac.py b/BioArchLinux/r-cogps/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-cogps/lilac.py
+++ b/BioArchLinux/r-cogps/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-cogps/lilac.yaml b/BioArchLinux/r-cogps/lilac.yaml
index a5293435e2..3f69b14a78 100644
--- a/BioArchLinux/r-cogps/lilac.yaml
+++ b/BioArchLinux/r-cogps/lilac.yaml
@@ -3,7 +3,8 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 update_on:
-- regex: coGPS_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/coGPS
+- source: rpkgs
+  pkgname: coGPS
+  repo: bioc
+  md5: true
 - alias: r
diff --git a/BioArchLinux/r-comprehenr/PKGBUILD b/BioArchLinux/r-comprehenr/PKGBUILD
index 87d0b6ebf6..fd758e1cfe 100644
--- a/BioArchLinux/r-comprehenr/PKGBUILD
+++ b/BioArchLinux/r-comprehenr/PKGBUILD
@@ -3,12 +3,12 @@
 _pkgname=comprehenr
 _pkgver=0.6.10
 pkgname=r-${_pkgname,,}
-pkgver=0.6.10
+pkgver=${_pkgver//-/.}
 pkgrel=3
-pkgdesc='List Comprehensions'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgdesc="List Comprehensions"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-only')
 depends=(
   r
 )
@@ -18,14 +18,15 @@ optdepends=(
   r-tinytest
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5c08efe824278b086a9f45823b2239206b3190e463c607d3ebb690cab5018cf2')
+md5sums=('02f3c79d161b77c46295adda537a9ade')
+b2sums=('808cc93182286ed4f0de2002c4537d5887dbceb2dc8f55ad6d61e2b739f618f529791915b603c49da478bf5eaec4062c7a8f6d18a96918c8e9fec59ac5c13539')
 
 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-comprehenr/lilac.py b/BioArchLinux/r-comprehenr/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-comprehenr/lilac.py
+++ b/BioArchLinux/r-comprehenr/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-comprehenr/lilac.yaml b/BioArchLinux/r-comprehenr/lilac.yaml
index d1d715196b..20c33029ce 100644
--- a/BioArchLinux/r-comprehenr/lilac.yaml
+++ b/BioArchLinux/r-comprehenr/lilac.yaml
@@ -1,9 +1,10 @@
 build_prefix: extra-x86_64
 maintainers:
-  - github: sukanka
-    email: su975853527@gmail.com
+- github: sukanka
+  email: su975853527@gmail.com
 update_on:
-  - regex: comprehenr_([\d._-]+).tar.gz
-    source: regex
-    url: https://cran.r-project.org/package=comprehenr
-  - alias: r
+- source: rpkgs
+  pkgname: comprehenr
+  repo: cran
+  md5: true
+- alias: r