From 4c71a31fc595545f5b0fd327e554fb3030f21761 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Thu, 15 Feb 2024 19:36:32 +0200
Subject: [PATCH] r-*: use old Bioconductor sources for some packages

These packages don't have a source archive in the latest
Bioconductor release.
---
 BioArchLinux/r-cancerinsilico/PKGBUILD   | 32 ++++++++++++------------
 BioArchLinux/r-cancerinsilico/lilac.py   | 11 ++++----
 BioArchLinux/r-cancerinsilico/lilac.yaml |  8 +++---
 BioArchLinux/r-cancersubtypes/PKGBUILD   | 24 +++++++++---------
 BioArchLinux/r-cancersubtypes/lilac.py   | 11 ++++----
 BioArchLinux/r-cancersubtypes/lilac.yaml |  5 ++--
 BioArchLinux/r-flowmap/PKGBUILD          | 24 +++++++++---------
 BioArchLinux/r-flowmap/lilac.py          | 11 ++++----
 BioArchLinux/r-flowmap/lilac.yaml        |  5 ++--
 BioArchLinux/r-foldgo/PKGBUILD           | 24 +++++++++---------
 BioArchLinux/r-foldgo/lilac.py           | 11 ++++----
 BioArchLinux/r-foldgo/lilac.yaml         |  5 ++--
 BioArchLinux/r-lowmaca/PKGBUILD          | 26 +++++++++----------
 BioArchLinux/r-lowmaca/lilac.py          | 14 +++++++----
 BioArchLinux/r-lowmaca/lilac.yaml        |  5 ++--
 BioArchLinux/r-metab/PKGBUILD            | 24 +++++++++---------
 BioArchLinux/r-metab/lilac.py            | 11 ++++----
 BioArchLinux/r-metab/lilac.yaml          |  5 ++--
 BioArchLinux/r-multiomicsviz/PKGBUILD    | 24 +++++++++---------
 BioArchLinux/r-multiomicsviz/lilac.py    | 11 ++++----
 BioArchLinux/r-multiomicsviz/lilac.yaml  |  5 ++--
 BioArchLinux/r-onesense/PKGBUILD         | 24 +++++++++---------
 BioArchLinux/r-onesense/lilac.py         | 14 +++++++----
 BioArchLinux/r-onesense/lilac.yaml       |  5 ++--
 BioArchLinux/r-regenrich/PKGBUILD        | 24 +++++++++---------
 BioArchLinux/r-regenrich/lilac.py        | 11 ++++----
 BioArchLinux/r-regenrich/lilac.yaml      |  5 ++--
 BioArchLinux/r-sscore/PKGBUILD           | 24 +++++++++---------
 BioArchLinux/r-sscore/lilac.py           | 11 ++++----
 BioArchLinux/r-sscore/lilac.yaml         |  5 ++--
 30 files changed, 212 insertions(+), 207 deletions(-)

diff --git a/BioArchLinux/r-cancerinsilico/PKGBUILD b/BioArchLinux/r-cancerinsilico/PKGBUILD
index 4c59a18144..722b4e6f01 100644
--- a/BioArchLinux/r-cancerinsilico/PKGBUILD
+++ b/BioArchLinux/r-cancerinsilico/PKGBUILD
@@ -3,17 +3,18 @@
 _pkgname=CancerInSilico
 _pkgver=2.18.0
 pkgname=r-${_pkgname,,}
-pkgver=2.18.0
+pkgver=${_pkgver//-/.}
 pkgrel=2
-pkgdesc='An R interface for computational modeling of tumor progression'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="An R interface for computational modeling of tumor progression"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
-  r
-  r-bh
   r-rcpp
 )
+makedepends=(
+  r-bh
+)
 optdepends=(
   r-biocstyle
   r-gplots
@@ -24,22 +25,21 @@ optdepends=(
   r-testthat
   r-viridis
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('9ed927e877b8741e80c894e69dae7e49e409cd8611ae348f5b6d64cb11faeb6b')
+source=("https://bioconductor.org/packages/3.16/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('716dc250caa885da7b8b0783f0871e16')
+b2sums=('b31faa8a63654a7c91dd93a0b24a835981e411580e0f1e365c27534eba580ef5f1fcec4ca2ad656213fb75c1741c0828a36a1a26cddfdefa79fd6e6f1a5cba99')
 
 prepare() {
   # replace SIGSTKSZ with a constant number
-  sed -i "s,SIGSTKSZ,8192,g" "${_pkgname}/src/Tests/catch.h"
-  tar cfz "${_pkgname}.tar.gz" "${_pkgname}"
+  sed -i "s,SIGSTKSZ,8192,g" "$_pkgname/src/Tests/catch.h"
 }
 
 build() {
-  # R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
-  R CMD INSTALL ${_pkgname}.tar.gz -l "${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-cancerinsilico/lilac.py b/BioArchLinux/r-cancerinsilico/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-cancerinsilico/lilac.py
+++ b/BioArchLinux/r-cancerinsilico/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-cancerinsilico/lilac.yaml b/BioArchLinux/r-cancerinsilico/lilac.yaml
index 3bf494f236..59607f03b3 100644
--- a/BioArchLinux/r-cancerinsilico/lilac.yaml
+++ b/BioArchLinux/r-cancerinsilico/lilac.yaml
@@ -3,10 +3,10 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-bh
 - r-rcpp
+repo_makedepends:
+- r-bh
 update_on:
-- regex: CancerInSilico_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/CancerInSilico
+- source: manual
+  manual: 2.18.0#716dc250caa885da7b8b0783f0871e16
 - alias: r
diff --git a/BioArchLinux/r-cancersubtypes/PKGBUILD b/BioArchLinux/r-cancersubtypes/PKGBUILD
index 03f9be3dcb..db5bf0a133 100644
--- a/BioArchLinux/r-cancersubtypes/PKGBUILD
+++ b/BioArchLinux/r-cancersubtypes/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=CancerSubtypes
 _pkgver=1.26.0
 pkgname=r-${_pkgname,,}
-pkgver=1.26.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Cancer subtypes identification, validation and visualization based on multiple genomic data sets'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Cancer subtypes identification, validation and visualization based on multiple genomic data sets"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-consensusclusterplus
   r-impute
   r-limma
@@ -23,15 +22,16 @@ optdepends=(
   r-rmarkdown
   r-rtcga.mrna
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('b9ce6665cbf7a813de63009551fa34f5196c8e89e170701029057237c83a9c1a')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('60441ccfd99126a3727c0621d087d526')
+b2sums=('20e321bbad6b017f1a9916df6844d37b5cf500173fe38e2cccfa136728f913e966271933d2c646e666fbb0de3d3f4a7d9c7025a22bfdf8812594c99bfe3ea702')
 
 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-cancersubtypes/lilac.py b/BioArchLinux/r-cancersubtypes/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-cancersubtypes/lilac.py
+++ b/BioArchLinux/r-cancersubtypes/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-cancersubtypes/lilac.yaml b/BioArchLinux/r-cancersubtypes/lilac.yaml
index 3847b134f9..a723cb0faa 100644
--- a/BioArchLinux/r-cancersubtypes/lilac.yaml
+++ b/BioArchLinux/r-cancersubtypes/lilac.yaml
@@ -9,7 +9,6 @@ repo_depends:
 - r-nmf
 - r-sigclust
 update_on:
-- regex: CancerSubtypes_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/CancerSubtypes
+- source: manual
+  manual: 1.26.0#60441ccfd99126a3727c0621d087d526
 - alias: r
diff --git a/BioArchLinux/r-flowmap/PKGBUILD b/BioArchLinux/r-flowmap/PKGBUILD
index 254b021453..41b3d55a59 100644
--- a/BioArchLinux/r-flowmap/PKGBUILD
+++ b/BioArchLinux/r-flowmap/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=flowMap
 _pkgver=1.38.0
 pkgname=r-${_pkgname,,}
-pkgver=1.38.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-Rafsky Test"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-abind
   r-ade4
   r-doparallel
@@ -21,15 +20,16 @@ optdepends=(
   r-biocstyle
   r-knitr
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('b2ffa3e58ecb99a27c43322162165765c99b3f56051aabc5e8cfe0f258295bd6')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('1c8039dc003c35a4c0dbb45e03f7c8aa')
+b2sums=('87129d33702810e692c5838e6f704f6c87dded0bf6b251763765eb4f05e2ae74f38b292e5aa15735791991d3cba9f208664176b13b6bc9ef8323b5d6a6e5970e')
 
 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-flowmap/lilac.py b/BioArchLinux/r-flowmap/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-flowmap/lilac.py
+++ b/BioArchLinux/r-flowmap/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-flowmap/lilac.yaml b/BioArchLinux/r-flowmap/lilac.yaml
index 26c4f20185..95c971f4ac 100644
--- a/BioArchLinux/r-flowmap/lilac.yaml
+++ b/BioArchLinux/r-flowmap/lilac.yaml
@@ -9,7 +9,6 @@ repo_depends:
 - r-reshape2
 - r-scales
 update_on:
-- regex: flowMap_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/flowMap
+- source: manual
+  manual: 1.38.0#1c8039dc003c35a4c0dbb45e03f7c8aa
 - alias: r
diff --git a/BioArchLinux/r-foldgo/PKGBUILD b/BioArchLinux/r-foldgo/PKGBUILD
index e2e76c2f42..025b0875b6 100644
--- a/BioArchLinux/r-foldgo/PKGBUILD
+++ b/BioArchLinux/r-foldgo/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=FoldGO
 _pkgver=1.18.0
 pkgname=r-${_pkgname,,}
-pkgver=1.18.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Package for Fold-specific GO Terms Recognition'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Package for Fold-specific GO Terms Recognition"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-ggplot2
   r-tidyr
   r-topgo
@@ -21,15 +20,16 @@ optdepends=(
   r-knitr
   r-rmarkdown
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d3f3aff453062e6a89500b334e1a3b2c4a3536675698c2ac52944e3fc3f60840')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('230ddc55d983a828d401eac9e44590d4')
+b2sums=('4ccd80ab4f92ef3772377935aef4d90bd408bb1ff9c0a08f3781d186b75162f1ad1afb8afd806e117e818afeb00add0e3b43c99d3578d4fe93e41cc2f42ea28c')
 
 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-foldgo/lilac.py b/BioArchLinux/r-foldgo/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-foldgo/lilac.py
+++ b/BioArchLinux/r-foldgo/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-foldgo/lilac.yaml b/BioArchLinux/r-foldgo/lilac.yaml
index c51edd44eb..2898de1b93 100644
--- a/BioArchLinux/r-foldgo/lilac.yaml
+++ b/BioArchLinux/r-foldgo/lilac.yaml
@@ -7,7 +7,6 @@ repo_depends:
 - r-tidyr
 - r-topgo
 update_on:
-- regex: FoldGO_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/FoldGO
+- source: manual
+  manual: 1.18.0#230ddc55d983a828d401eac9e44590d4
 - alias: r
diff --git a/BioArchLinux/r-lowmaca/PKGBUILD b/BioArchLinux/r-lowmaca/PKGBUILD
index 63e8be1d26..4aad7ad534 100644
--- a/BioArchLinux/r-lowmaca/PKGBUILD
+++ b/BioArchLinux/r-lowmaca/PKGBUILD
@@ -1,22 +1,19 @@
-# system requirements: clustalo, gs, perl
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=LowMACA
 _pkgver=1.28.0
 pkgname=r-${_pkgname,,}
-pkgver=1.28.0
+pkgver=${_pkgver//-/.}
 pkgrel=2
-pkgdesc='LowMACA - Low frequency Mutation Analysis via Consensus Alignment'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Low frequency Mutation Analysis via Consensus Alignment"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
   clustal-omega
   ghostscript
-  perl
   perl-lwp-protocol-https
   perl-xml-simple
-  r
   r-biocparallel
   r-biostrings
   r-cbioportaldata
@@ -35,15 +32,16 @@ optdepends=(
   r-knitr
   r-rmarkdown
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('1b37fd41e3a41169d52cd5164972d3455c4d914bedfa5ccc54fcebf8fb18a248')
+source=("https://bioconductor.org/packages/3.16/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('00d852771a79338dfdd5f41318672af1')
+b2sums=('0e4e8ea737873f018fbc49dbf5502b45bde931b9f6fa19fc64cbd03015e627b75e92ed9aab184b43fa4102c65222a26db19145d9555f335f03f0181326640b62')
 
 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-lowmaca/lilac.py b/BioArchLinux/r-lowmaca/lilac.py
index bd219c037c..37c604335b 100644
--- a/BioArchLinux/r-lowmaca/lilac.py
+++ b/BioArchLinux/r-lowmaca/lilac.py
@@ -1,12 +1,16 @@
 #!/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,
+        expect_systemrequirements = "clustalo, gs, perl",
+    )
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-lowmaca/lilac.yaml b/BioArchLinux/r-lowmaca/lilac.yaml
index a3963acf44..65cb8c945e 100644
--- a/BioArchLinux/r-lowmaca/lilac.yaml
+++ b/BioArchLinux/r-lowmaca/lilac.yaml
@@ -17,7 +17,6 @@ repo_depends:
 - r-reshape2
 - r-stringr
 update_on:
-- regex: LowMACA_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/LowMACA
+- source: manual
+  manual: 1.28.0#00d852771a79338dfdd5f41318672af1
 - alias: r
diff --git a/BioArchLinux/r-metab/PKGBUILD b/BioArchLinux/r-metab/PKGBUILD
index 7dff54917d..4ed8e59ec0 100644
--- a/BioArchLinux/r-metab/PKGBUILD
+++ b/BioArchLinux/r-metab/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=Metab
 _pkgver=1.33.0
 pkgname=r-${_pkgname,,}
-pkgver=1.33.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Metab: An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS.'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="An R Package for a High-Throughput Analysis of Metabolomics Data Generated by GC-MS"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-pander
   r-svdialogs
   r-xcms
@@ -19,15 +18,16 @@ optdepends=(
   r-biocgenerics
   r-runit
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('7ef2bcab0a862f11524fa493ad939f5a620bc607d77568aa16df94e9c7222d3a')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('8b19a02165b42e95410fbcf5c44ee352')
+b2sums=('47a5849bb065e033cf96e4c2c05e9fafef02ceb715da508c889b6124efce179ea4b53f05b7a0490f5b7310bf3509eff3452f31429dae285d2e29644a3c1d7286')
 
 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-metab/lilac.py b/BioArchLinux/r-metab/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-metab/lilac.py
+++ b/BioArchLinux/r-metab/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-metab/lilac.yaml b/BioArchLinux/r-metab/lilac.yaml
index fde3ee4fc4..f18ef24370 100644
--- a/BioArchLinux/r-metab/lilac.yaml
+++ b/BioArchLinux/r-metab/lilac.yaml
@@ -7,7 +7,6 @@ repo_depends:
 - r-svdialogs
 - r-xcms
 update_on:
-- regex: Metab_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/Metab
+- source: manual
+  manual: 1.33.0#8b19a02165b42e95410fbcf5c44ee352
 - alias: r
diff --git a/BioArchLinux/r-multiomicsviz/PKGBUILD b/BioArchLinux/r-multiomicsviz/PKGBUILD
index 6fc211f892..c354565a5a 100644
--- a/BioArchLinux/r-multiomicsviz/PKGBUILD
+++ b/BioArchLinux/r-multiomicsviz/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=multiOmicsViz
 _pkgver=1.24.0
 pkgname=r-${_pkgname,,}
-pkgver=1.24.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Plot the effect of one omics data on other omics data along the chromosome'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('LGPL')
+pkgdesc="Plot the effect of one omics data on other omics data along the chromosome"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('LGPL-2.0-or-later')
 depends=(
-  r
   r-doparallel
   r-foreach
   r-summarizedexperiment
@@ -18,15 +17,16 @@ depends=(
 optdepends=(
   r-biocgenerics
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('3a53cb2abad8e3314e430a10dc2509179dbed5fa37ce318be003105a49023389')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('a051b5e32c72385f4463cbe1751c1484')
+b2sums=('640ba46dbe596ee7d58ea4be34fa5a08408c0f369d0830429b70416909873dcffe39d25b08c38745e4816562aca4b7eee6f991db536c724a6acfbf98d1f76161')
 
 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-multiomicsviz/lilac.py b/BioArchLinux/r-multiomicsviz/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-multiomicsviz/lilac.py
+++ b/BioArchLinux/r-multiomicsviz/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-multiomicsviz/lilac.yaml b/BioArchLinux/r-multiomicsviz/lilac.yaml
index 8d937571ee..7276ecb864 100644
--- a/BioArchLinux/r-multiomicsviz/lilac.yaml
+++ b/BioArchLinux/r-multiomicsviz/lilac.yaml
@@ -7,7 +7,6 @@ repo_depends:
 - r-foreach
 - r-summarizedexperiment
 update_on:
-- regex: multiOmicsViz_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/multiOmicsViz
+- source: manual
+  manual: 1.24.0#a051b5e32c72385f4463cbe1751c1484
 - alias: r
diff --git a/BioArchLinux/r-onesense/PKGBUILD b/BioArchLinux/r-onesense/PKGBUILD
index fe0d0834ad..5dbd199571 100644
--- a/BioArchLinux/r-onesense/PKGBUILD
+++ b/BioArchLinux/r-onesense/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=oneSENSE
 _pkgver=1.20.0
 pkgname=r-${_pkgname,,}
-pkgver=1.20.0
+pkgver=${_pkgver//-/.}
 pkgrel=2
-pkgdesc='One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
   r-flowcore
   r-gplots
   r-plotly
@@ -24,15 +23,16 @@ optdepends=(
   r-knitr
   r-rmarkdown
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('6313f630175714483008dd215ffc84d6e7afb9b49c3e24b0507becec4644ebd3')
+source=("https://bioconductor.org/packages/3.16/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('c89540d29c09f4cb0e00a650ca5a7f20')
+b2sums=('7e94e918dc4b35a74e435bf2530840b3398e3cfd5fb3a705c608f04d71b425f3735b3536e2a654b4296250a84671ba3702ea3967ca68462be3ddcd973e88c4d5')
 
 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-onesense/lilac.py b/BioArchLinux/r-onesense/lilac.py
index bd219c037c..e8e1284a30 100644
--- a/BioArchLinux/r-onesense/lilac.py
+++ b/BioArchLinux/r-onesense/lilac.py
@@ -1,12 +1,16 @@
 #!/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,
+        expect_license = "GPL (>=3)",
+    )
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-onesense/lilac.yaml b/BioArchLinux/r-onesense/lilac.yaml
index b225ee7d01..7380b6405c 100644
--- a/BioArchLinux/r-onesense/lilac.yaml
+++ b/BioArchLinux/r-onesense/lilac.yaml
@@ -12,7 +12,6 @@ repo_depends:
 - r-shinyfiles
 - r-webshot
 update_on:
-- regex: oneSENSE_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/oneSENSE
+- source: manual
+  manual: 1.20.0#c89540d29c09f4cb0e00a650ca5a7f20
 - alias: r
diff --git a/BioArchLinux/r-regenrich/PKGBUILD b/BioArchLinux/r-regenrich/PKGBUILD
index b949f2871f..105ec3c8af 100644
--- a/BioArchLinux/r-regenrich/PKGBUILD
+++ b/BioArchLinux/r-regenrich/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=RegEnrich
 _pkgver=1.10.0
 pkgname=r-${_pkgname,,}
-pkgver=1.10.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Gene regulator enrichment analysis'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Gene regulator enrichment analysis"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-biocparallel
   r-biocset
   r-deseq2
@@ -34,15 +33,16 @@ optdepends=(
   r-rmarkdown
   r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('0dde07642599f4aaa7238e1ccb2c149dda9935ce94067c2ba8a5033e94adf325')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('afbd8028754ca907215ba26c3eae83f8')
+b2sums=('51ee19ecda2bc70a0f3a3e458224d4bfd9d963b5a89eb121be06221b1e2ab331b9ca926e8e0bad9dab5212dbdb940b759c881fb22c9a4c635c44bc3d4847c5c6')
 
 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-regenrich/lilac.py b/BioArchLinux/r-regenrich/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-regenrich/lilac.py
+++ b/BioArchLinux/r-regenrich/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-regenrich/lilac.yaml b/BioArchLinux/r-regenrich/lilac.yaml
index 80dd6a8157..f15d886191 100644
--- a/BioArchLinux/r-regenrich/lilac.yaml
+++ b/BioArchLinux/r-regenrich/lilac.yaml
@@ -19,7 +19,6 @@ repo_depends:
 - r-tibble
 - r-wgcna
 update_on:
-- regex: RegEnrich_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/RegEnrich
+- source: manual
+  manual: 1.10.0#afbd8028754ca907215ba26c3eae83f8
 - alias: r
diff --git a/BioArchLinux/r-sscore/PKGBUILD b/BioArchLinux/r-sscore/PKGBUILD
index 70d8a152f4..a4ac3ceb01 100644
--- a/BioArchLinux/r-sscore/PKGBUILD
+++ b/BioArchLinux/r-sscore/PKGBUILD
@@ -3,29 +3,29 @@
 _pkgname=sscore
 _pkgver=1.72.0
 pkgname=r-${_pkgname,,}
-pkgver=1.72.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='S-Score Algorithm for Affymetrix Oligonucleotide Microarrays'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="S-Score Algorithm for Affymetrix Oligonucleotide Microarrays"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-affy
   r-affyio
 )
 optdepends=(
   r-affydata
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('345698825276ca1055228942d28694a2f80af8ce2da6991238bafaac2241c60b')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('3f61e0bf6176b6ee7f4b29b0af6e2091')
+b2sums=('1a9672fd09cfb1a4ea6cb695a352111db352502a1d1cc5b93102143441ebc30400ca7d6c9061966c7311e001ad1a1105dcf6ead4e1a54bf8eda79004f772dca8')
 
 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-sscore/lilac.py b/BioArchLinux/r-sscore/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-sscore/lilac.py
+++ b/BioArchLinux/r-sscore/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-sscore/lilac.yaml b/BioArchLinux/r-sscore/lilac.yaml
index 1a13acd070..eb5357b6c9 100644
--- a/BioArchLinux/r-sscore/lilac.yaml
+++ b/BioArchLinux/r-sscore/lilac.yaml
@@ -6,7 +6,6 @@ repo_depends:
 - r-affy
 - r-affyio
 update_on:
-- regex: sscore_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/sscore
+- source: manual
+  manual: 1.72.0#3f61e0bf6176b6ee7f4b29b0af6e2091
 - alias: r