From 703cf04958764b13280b60a40baf2babeb82c524 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 13 Feb 2024 19:04:41 +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-cellscape/PKGBUILD    | 24 ++++++-------
 BioArchLinux/r-cellscape/lilac.py    | 11 +++---
 BioArchLinux/r-cellscape/lilac.yaml  |  5 ++-
 BioArchLinux/r-gscreend/PKGBUILD     | 24 ++++++-------
 BioArchLinux/r-gscreend/lilac.py     | 11 +++---
 BioArchLinux/r-gscreend/lilac.yaml   |  5 ++-
 BioArchLinux/r-iloreg/PKGBUILD       | 24 ++++++-------
 BioArchLinux/r-iloreg/lilac.py       | 11 +++---
 BioArchLinux/r-iloreg/lilac.yaml     |  5 ++-
 BioArchLinux/r-metagene/PKGBUILD     | 24 ++++++-------
 BioArchLinux/r-metagene/lilac.py     | 14 +++++---
 BioArchLinux/r-metagene/lilac.yaml   |  5 ++-
 BioArchLinux/r-multisight/PKGBUILD   | 30 +++++++++--------
 BioArchLinux/r-multisight/lilac.py   | 14 +++++---
 BioArchLinux/r-multisight/lilac.yaml |  5 ++-
 BioArchLinux/r-pfp/PKGBUILD          | 24 ++++++-------
 BioArchLinux/r-pfp/lilac.py          | 11 +++---
 BioArchLinux/r-pfp/lilac.yaml        |  5 ++-
 BioArchLinux/r-pwrewas/PKGBUILD      | 24 ++++++-------
 BioArchLinux/r-pwrewas/lilac.py      | 11 +++---
 BioArchLinux/r-pwrewas/lilac.yaml    |  5 ++-
 BioArchLinux/r-rcsl/PKGBUILD         | 25 +++++++-------
 BioArchLinux/r-rcsl/lilac.py         | 11 +++---
 BioArchLinux/r-rcsl/lilac.yaml       |  5 ++-
 BioArchLinux/r-sepira/PKGBUILD       | 24 ++++++-------
 BioArchLinux/r-sepira/lilac.py       | 11 +++---
 BioArchLinux/r-sepira/lilac.yaml     |  5 ++-
 BioArchLinux/r-sispa/PKGBUILD        | 24 ++++++-------
 BioArchLinux/r-sispa/lilac.py        | 11 +++---
 BioArchLinux/r-sispa/lilac.yaml      |  5 ++-
 BioArchLinux/r-sponge/PKGBUILD       | 50 ++++++++++++++--------------
 BioArchLinux/r-sponge/lilac.py       | 14 +++++---
 BioArchLinux/r-sponge/lilac.yaml     |  5 ++-
 33 files changed, 246 insertions(+), 236 deletions(-)

diff --git a/BioArchLinux/r-cellscape/PKGBUILD b/BioArchLinux/r-cellscape/PKGBUILD
index c3f004ce21..e1082c80d7 100644
--- a/BioArchLinux/r-cellscape/PKGBUILD
+++ b/BioArchLinux/r-cellscape/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=cellscape
 _pkgver=1.24.0
 pkgname=r-${_pkgname,,}
-pkgver=1.24.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Explores single cell copy number profiles in the context of a single cell tree'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Explores single cell copy number profiles in the context of a single cell tree"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-dplyr
   r-gtools
   r-htmlwidgets
@@ -23,15 +22,16 @@ optdepends=(
   r-knitr
   r-rmarkdown
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('4c3d82b3d8938f0e22797db3c0ea9c047afb4f2a646f6304eaadf6a39157fc3c')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('7df865c4752c43a3745b01f93654a00a')
+b2sums=('bf465c04a58beaef4f43856afce370abf722489eec6267b2f36e3b5a925a2e74eadb052662ceeb9f073174727f4ae69e256c4f60ae72fa147f09c88e248c203d')
 
 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-cellscape/lilac.py b/BioArchLinux/r-cellscape/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-cellscape/lilac.py
+++ b/BioArchLinux/r-cellscape/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-cellscape/lilac.yaml b/BioArchLinux/r-cellscape/lilac.yaml
index bc37cf0fdb..fef4d78412 100644
--- a/BioArchLinux/r-cellscape/lilac.yaml
+++ b/BioArchLinux/r-cellscape/lilac.yaml
@@ -11,7 +11,6 @@ repo_depends:
 - r-reshape2
 - r-stringr
 update_on:
-- regex: cellscape_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/cellscape
+- source: manual
+  manual: 1.24.0#7df865c4752c43a3745b01f93654a00a
 - alias: r
diff --git a/BioArchLinux/r-gscreend/PKGBUILD b/BioArchLinux/r-gscreend/PKGBUILD
index 8c1a7c12ed..1621ff6eb1 100644
--- a/BioArchLinux/r-gscreend/PKGBUILD
+++ b/BioArchLinux/r-gscreend/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=gscreend
 _pkgver=1.14.0
 pkgname=r-${_pkgname,,}
-pkgver=1.14.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Analysis of pooled genetic screens'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Analysis of pooled genetic screens"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-biocparallel
   r-fgarch
   r-nloptr
@@ -21,15 +20,16 @@ optdepends=(
   r-rmarkdown
   r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('84ca69a87b7cca79ee2c59292836436840c9e921ac1fb2ec5ebb47bdb100dd9d')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('6d79483ce0c766b1779a2dab5614e249')
+b2sums=('0df96be2c84afbeb760dbe395c0b03bb7998afd87c84f4ce4b8d91a88d9f6a9476ed7643e844703f90e292394a8e9178a1322847577cef0f8938da7304ddaa73')
 
 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-gscreend/lilac.py b/BioArchLinux/r-gscreend/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-gscreend/lilac.py
+++ b/BioArchLinux/r-gscreend/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-gscreend/lilac.yaml b/BioArchLinux/r-gscreend/lilac.yaml
index 262c44031e..8c5df769b3 100644
--- a/BioArchLinux/r-gscreend/lilac.yaml
+++ b/BioArchLinux/r-gscreend/lilac.yaml
@@ -8,7 +8,6 @@ repo_depends:
 - r-nloptr
 - r-summarizedexperiment
 update_on:
-- regex: gscreend_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/gscreend
+- source: manual
+  manual: 1.14.0#6d79483ce0c766b1779a2dab5614e249
 - alias: r
diff --git a/BioArchLinux/r-iloreg/PKGBUILD b/BioArchLinux/r-iloreg/PKGBUILD
index 522c8a4b41..8e677d2c35 100644
--- a/BioArchLinux/r-iloreg/PKGBUILD
+++ b/BioArchLinux/r-iloreg/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=ILoReg
 _pkgver=1.10.0
 pkgname=r-${_pkgname,,}
-pkgver=1.10.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="a tool for high-resolution cell population identification from scRNA-Seq data"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-aricode
   r-cowplot
   r-dendextend
@@ -39,15 +38,16 @@ optdepends=(
   r-knitr
   r-rmarkdown
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('51a19f5568dc5d849d344000f82059b0087946e7d544bd1b7edb56242e224182')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('5b4425d7d9a6bc0201dcd9c1d0b1c98c')
+b2sums=('bcffc5e3e0e453858d6d98ab5edac1063df56f3419ece1926ab5c1ebea83c5c09e124a802dc109c4c9efe4c23bb0851dbbda7a6e1cd6d8cfe8b4a501f8e0a791')
 
 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-iloreg/lilac.py b/BioArchLinux/r-iloreg/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-iloreg/lilac.py
+++ b/BioArchLinux/r-iloreg/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-iloreg/lilac.yaml b/BioArchLinux/r-iloreg/lilac.yaml
index 70cce878ba..6ec7cbc42d 100644
--- a/BioArchLinux/r-iloreg/lilac.yaml
+++ b/BioArchLinux/r-iloreg/lilac.yaml
@@ -27,7 +27,6 @@ repo_depends:
 - r-summarizedexperiment
 - r-umap
 update_on:
-- regex: ILoReg_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/ILoReg
+- source: manual
+  manual: 1.10.0#5b4425d7d9a6bc0201dcd9c1d0b1c98c
 - alias: r
diff --git a/BioArchLinux/r-metagene/PKGBUILD b/BioArchLinux/r-metagene/PKGBUILD
index c63ce2e8f2..1263cdc935 100644
--- a/BioArchLinux/r-metagene/PKGBUILD
+++ b/BioArchLinux/r-metagene/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=metagene
 _pkgver=2.31.0
 pkgname=r-${_pkgname,,}
-pkgver=2.31.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='A package to produce metagene plots'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgdesc="A package to produce metagene plots"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-biocparallel
   r-data.table
   r-ensdb.hsapiens.v86
@@ -38,15 +37,16 @@ optdepends=(
   r-runit
   r-similarpeak
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('e8b2391a7db54ab6b9da01843faaaf8ec1d0fd0d0e8df3cae473f5f0c4c2cd4f')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('4709f553e306643ec3d37860f4092ddc')
+b2sums=('eea5068082af2b3e785b155c257df1638c3599ddfea17fbb09b59aa995dfbddfa7c801a9f14fad5732d8d927a50ce4747217249c7b939c081c6ada4959f5e2d2')
 
 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-metagene/lilac.py b/BioArchLinux/r-metagene/lilac.py
index bd219c037c..185a57179c 100644
--- a/BioArchLinux/r-metagene/lilac.py
+++ b/BioArchLinux/r-metagene/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 = "Artistic-2.0 | file LICENSE",
+    )
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-metagene/lilac.yaml b/BioArchLinux/r-metagene/lilac.yaml
index 592e22b9d0..db8cb4cbcd 100644
--- a/BioArchLinux/r-metagene/lilac.yaml
+++ b/BioArchLinux/r-metagene/lilac.yaml
@@ -22,7 +22,6 @@ repo_depends:
 - r-rtracklayer
 - r-stringr
 update_on:
-- regex: metagene_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/metagene
+- source: manual
+  manual: 2.31.0#4709f553e306643ec3d37860f4092ddc
 - alias: r
diff --git a/BioArchLinux/r-multisight/PKGBUILD b/BioArchLinux/r-multisight/PKGBUILD
index f4756e3d08..5bb7335ac0 100644
--- a/BioArchLinux/r-multisight/PKGBUILD
+++ b/BioArchLinux/r-multisight/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=multiSight
 _pkgver=1.7.0
 pkgname=r-${_pkgname,,}
-pkgver=1.7.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Multi-omics Classification, Functional Enrichment and Network Inference analysis'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('CeCILL')
+pkgdesc="Multi-omics Classification, Functional Enrichment and Network Inference analysis"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('CECILL-2.1')
 depends=(
-  r
   r-anylib
   r-biosigner
   r-caret
@@ -21,6 +20,7 @@ depends=(
   r-dt
   r-easypubmed
   r-enrichplot
+  r-ggnewscale
   r-golem
   r-htmltools
   r-igraph
@@ -36,7 +36,6 @@ depends=(
   r-shiny
   r-shinydashboard
   r-stringr
-  r-ggnewscale
 )
 optdepends=(
   r-attempt
@@ -48,16 +47,19 @@ optdepends=(
   r-rlang
   r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('2cad84a8893d54a48bc5039c6b9056a2f5d5c722bc03556a8b14140171a055ec')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('441d8e6ab1b689928f6f623551fe1459')
+b2sums=('53069027a9cbc203591ba8a0a5309a90f900385691c0d49692bfa8e1bdf7651f2e573032f6c37b9627e58bbec40a3a022c1d637e4be040bdd59045622cf00dfb')
 
 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-multisight/lilac.py b/BioArchLinux/r-multisight/lilac.py
index bd219c037c..613059d94b 100644
--- a/BioArchLinux/r-multisight/lilac.py
+++ b/BioArchLinux/r-multisight/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 = "CeCILL + file LICENSE",
+    )
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-multisight/lilac.yaml b/BioArchLinux/r-multisight/lilac.yaml
index 655f78a991..c6808093e4 100644
--- a/BioArchLinux/r-multisight/lilac.yaml
+++ b/BioArchLinux/r-multisight/lilac.yaml
@@ -30,7 +30,6 @@ repo_depends:
 - r-shinydashboard
 - r-stringr
 update_on:
-- regex: multiSight_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/multiSight
+- source: manual
+  manual: 1.7.0#441d8e6ab1b689928f6f623551fe1459
 - alias: r
diff --git a/BioArchLinux/r-pfp/PKGBUILD b/BioArchLinux/r-pfp/PKGBUILD
index 150344b9ca..86b7b5f589 100644
--- a/BioArchLinux/r-pfp/PKGBUILD
+++ b/BioArchLinux/r-pfp/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=PFP
 _pkgver=1.7.0
 pkgname=r-${_pkgname,,}
-pkgver=1.7.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Pathway Fingerprint Framework in R'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Pathway Fingerprint Framework in R"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
-  r
   r-clusterprofiler
   r-ggplot2
   r-graph
@@ -26,15 +25,16 @@ optdepends=(
   r-rmarkdown
   r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('b1813682708fc81e90aba288192c9c036dba993c66d725730bf4bcf7c651488c')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('c360bbdb9e54a148f40c161c5691eceb')
+b2sums=('0c5c132c587dca3566e75640dd581a1ef68969bc66e3eb107d2ed1e146e767edea8bc553727e1eab321ee44f30c18b103b2da4863aa9fba327b60cb64d1cfe5d')
 
 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-pfp/lilac.py b/BioArchLinux/r-pfp/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-pfp/lilac.py
+++ b/BioArchLinux/r-pfp/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-pfp/lilac.yaml b/BioArchLinux/r-pfp/lilac.yaml
index 7c284b4451..9e0617c6db 100644
--- a/BioArchLinux/r-pfp/lilac.yaml
+++ b/BioArchLinux/r-pfp/lilac.yaml
@@ -12,7 +12,6 @@ repo_depends:
 - r-plyr
 - r-tidyr
 update_on:
-- regex: PFP_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/PFP
+- source: manual
+  manual: 1.7.0#c360bbdb9e54a148f40c161c5691eceb
 - alias: r
diff --git a/BioArchLinux/r-pwrewas/PKGBUILD b/BioArchLinux/r-pwrewas/PKGBUILD
index e7c40b25da..82789eeea1 100644
--- a/BioArchLinux/r-pwrewas/PKGBUILD
+++ b/BioArchLinux/r-pwrewas/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=pwrEWAS
 _pkgver=1.14.0
 pkgname=r-${_pkgname,,}
-pkgver=1.14.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+pkgdesc="A user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS)"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('Artistic-2.0')
 depends=(
-  r
   r-abind
   r-biocmanager
   r-cpgassoc
@@ -32,15 +31,16 @@ optdepends=(
   r-rmarkdown
   r-runit
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('0a9599d174af835e6c2640d284285b74b25c41e5b96ed9af763535e5b58023a4')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('72989b16264534ad1fa6fdadda1ff618')
+b2sums=('b6f186cf7b2c178a58006565bad4e4bc84717c2bc476980492e39bd1ac195d4e5b6f6b26813f4f2f8395936d7df1a76996c8a99c07483266d273ae7377e12960')
 
 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-pwrewas/lilac.py b/BioArchLinux/r-pwrewas/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-pwrewas/lilac.py
+++ b/BioArchLinux/r-pwrewas/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-pwrewas/lilac.yaml b/BioArchLinux/r-pwrewas/lilac.yaml
index a2e1858b48..1f2ff7396a 100644
--- a/BioArchLinux/r-pwrewas/lilac.yaml
+++ b/BioArchLinux/r-pwrewas/lilac.yaml
@@ -18,7 +18,6 @@ repo_depends:
 - r-shinywidgets
 - r-truncnorm
 update_on:
-- regex: pwrEWAS_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/pwrEWAS
+- source: manual
+  manual: 1.14.0#72989b16264534ad1fa6fdadda1ff618
 - alias: r
diff --git a/BioArchLinux/r-rcsl/PKGBUILD b/BioArchLinux/r-rcsl/PKGBUILD
index 011c6b9328..9de987bc40 100644
--- a/BioArchLinux/r-rcsl/PKGBUILD
+++ b/BioArchLinux/r-rcsl/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=RCSL
 _pkgver=1.8.0
 pkgname=r-${_pkgname,,}
-pkgver=1.8.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Rank Constrained Similarity Learning for single cell RNA sequencing data'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Rank Constrained Similarity Learning for single cell RNA sequencing data"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-ggplot2
   r-igraph
   r-nbclust
@@ -22,18 +21,18 @@ depends=(
 optdepends=(
   r-knitr
   r-mclust
-  r-rcppannoy
   r-rmarkdown
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('162605ec54ceafb4fcc2617cb010672034c4514dd42ecb047a3841d356822b91')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('014987c88b4b2941c8badfc38c37db2c')
+b2sums=('0b445b6f5d9eb345fb443dda312c3b70c825098e2af32bbc34fde98f11fbf9444dead674acebdd98d538401a1fa47f50c013a767f8c637d35ef84f7abc4287ac')
 
 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-rcsl/lilac.py b/BioArchLinux/r-rcsl/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-rcsl/lilac.py
+++ b/BioArchLinux/r-rcsl/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-rcsl/lilac.yaml b/BioArchLinux/r-rcsl/lilac.yaml
index 2d55a42e3d..e9fa1f95b6 100644
--- a/BioArchLinux/r-rcsl/lilac.yaml
+++ b/BioArchLinux/r-rcsl/lilac.yaml
@@ -11,7 +11,6 @@ repo_depends:
 - r-rtsne
 - r-umap
 update_on:
-- regex: RCSL_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/RCSL
+- source: manual
+  manual: 1.8.0#014987c88b4b2941c8badfc38c37db2c
 - alias: r
diff --git a/BioArchLinux/r-sepira/PKGBUILD b/BioArchLinux/r-sepira/PKGBUILD
index f1f2be1265..959d858ceb 100644
--- a/BioArchLinux/r-sepira/PKGBUILD
+++ b/BioArchLinux/r-sepira/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=SEPIRA
 _pkgver=1.20.0
 pkgname=r-${_pkgname,,}
-pkgver=1.20.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Systems EPigenomics Inference of Regulatory Activity'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Systems EPigenomics Inference of Regulatory Activity"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
   r-corpcor
   r-limma
 )
@@ -20,15 +19,16 @@ optdepends=(
   r-rmarkdown
   r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('87804976d95662add92ba81f24140d37dbdb18ca475e6861830e6d99a8a914fa')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('c7ed46a5810d2e91210561758428a7fb')
+b2sums=('c29ec1fec144374cea25210d248323d1bd3492eae239a20e5f47abc62632b7ecdc4ca9a3dc1bbb8f6394920bf744a7105364af88bcd3ad313b8e02009883518a')
 
 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-sepira/lilac.py b/BioArchLinux/r-sepira/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-sepira/lilac.py
+++ b/BioArchLinux/r-sepira/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-sepira/lilac.yaml b/BioArchLinux/r-sepira/lilac.yaml
index ec31bbdcc7..b6b88ed4f4 100644
--- a/BioArchLinux/r-sepira/lilac.yaml
+++ b/BioArchLinux/r-sepira/lilac.yaml
@@ -6,7 +6,6 @@ repo_depends:
 - r-corpcor
 - r-limma
 update_on:
-- regex: SEPIRA_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/SEPIRA
+- source: manual
+  manual: 1.20.0#c7ed46a5810d2e91210561758428a7fb
 - alias: r
diff --git a/BioArchLinux/r-sispa/PKGBUILD b/BioArchLinux/r-sispa/PKGBUILD
index 04a6a9d87d..16c07c1005 100644
--- a/BioArchLinux/r-sispa/PKGBUILD
+++ b/BioArchLinux/r-sispa/PKGBUILD
@@ -3,14 +3,13 @@
 _pkgname=SISPA
 _pkgver=1.30.0
 pkgname=r-${_pkgname,,}
-pkgver=1.30.0
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='SISPA: Method for Sample Integrated Set Profile Analysis'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Method for Sample Integrated Set Profile Analysis"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
-  r
   r-changepoint
   r-data.table
   r-genefilter
@@ -21,15 +20,16 @@ depends=(
 optdepends=(
   r-knitr
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('837efd2a7277865869764f0bf8a3c0d00af405a091b17c934a3c2f03ae98983e')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('390f6b86b0a21440799868d3a554c834')
+b2sums=('b4fe530cba88ee907b3052d6390b49e0c1619878f9da832c79bde0ac30ea5cfa07b20ba9ae6c4291f6c19f030c075b572cfb534314e3efbcd88ac00113997df5')
 
 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-sispa/lilac.py b/BioArchLinux/r-sispa/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-sispa/lilac.py
+++ b/BioArchLinux/r-sispa/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-sispa/lilac.yaml b/BioArchLinux/r-sispa/lilac.yaml
index f79f311d6b..141ac0ce79 100644
--- a/BioArchLinux/r-sispa/lilac.yaml
+++ b/BioArchLinux/r-sispa/lilac.yaml
@@ -10,7 +10,6 @@ repo_depends:
 - r-gsva
 - r-plyr
 update_on:
-- regex: SISPA_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/SISPA
+- source: manual
+  manual: 1.30.0#390f6b86b0a21440799868d3a554c834
 - alias: r
diff --git a/BioArchLinux/r-sponge/PKGBUILD b/BioArchLinux/r-sponge/PKGBUILD
index 3a93598b47..e312a2073b 100644
--- a/BioArchLinux/r-sponge/PKGBUILD
+++ b/BioArchLinux/r-sponge/PKGBUILD
@@ -3,41 +3,40 @@
 _pkgname=SPONGE
 _pkgver=1.22.0
 pkgname=r-${_pkgname,,}
-pkgver=1.22.0
+pkgver=${_pkgver//-/.}
 pkgrel=3
-pkgdesc='Sparse Partial Correlations On Gene Expression'
-arch=('any')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgdesc="Sparse Partial Correlations On Gene Expression"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-or-later')
 depends=(
-  r
   r-biobase
+  r-biomart
+  r-caret
+  r-complexheatmap
+  r-cvms
   r-data.table
   r-dorng
+  r-dplyr
   r-expm
   r-foreach
+  r-ggplot2
+  r-ggpubr
+  r-ggridges
   r-glmnet
   r-grbase
   r-igraph
   r-iterators
   r-logging
-  r-ppcor
-  r-tidyverse
-  r-caret
-  r-dplyr
-  r-biomart
-  r-randomforest
-  r-ggridges
-  r-cvms
-  r-mirbaseconverter
-  r-complexheatmap
-  r-ggplot2
   r-metbrewer
+  r-mirbaseconverter
+  r-ppcor
+  r-randomforest
   r-rlang
-  r-tnet
-  r-ggpubr
   r-stringr
   r-tidyr
+  r-tidyverse
+  r-tnet
 )
 optdepends=(
   r-bigmemory
@@ -51,15 +50,16 @@ optdepends=(
   r-testthat
   r-visnetwork
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d7d6e0778f2f79a8dfbba0208964e205fd51c757d0df170638fac822f18bdbab')
+source=("https://bioconductor.org/packages/3.17/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('4ec8bdffb258be839e469d1baa50c4e9')
+b2sums=('706ad7cd66b21bf22ba2d75d7e6c7cddbdfbdb7847ac46b45ececf10a8d1900ced409e3a487ae4f672095c30629f76529e69b2e5c83fdf38bee59dba1d7ae81a')
 
 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-sponge/lilac.py b/BioArchLinux/r-sponge/lilac.py
index bd219c037c..e8e1284a30 100644
--- a/BioArchLinux/r-sponge/lilac.py
+++ b/BioArchLinux/r-sponge/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-sponge/lilac.yaml b/BioArchLinux/r-sponge/lilac.yaml
index 34c7bf68d5..79bde54d08 100644
--- a/BioArchLinux/r-sponge/lilac.yaml
+++ b/BioArchLinux/r-sponge/lilac.yaml
@@ -31,7 +31,6 @@ repo_depends:
 - r-tidyverse
 - r-tnet
 update_on:
-- regex: SPONGE_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/SPONGE
+- source: manual
+  manual: 1.22.0#4ec8bdffb258be839e469d1baa50c4e9
 - alias: r