From adea37bee5a0adc0a25b5bb8f3673d33c222f2dd Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 30 Apr 2024 01:46:41 +0300
Subject: [PATCH] r-doby: fix depends, use metadata checks

---
 BioArchLinux/r-doby/PKGBUILD   | 33 ++++++++++++++++++---------------
 BioArchLinux/r-doby/lilac.py   | 11 ++++++-----
 BioArchLinux/r-doby/lilac.yaml | 12 ++++++++----
 3 files changed, 32 insertions(+), 24 deletions(-)

diff --git a/BioArchLinux/r-doby/PKGBUILD b/BioArchLinux/r-doby/PKGBUILD
index c7caae01db..d289f7f1c5 100644
--- a/BioArchLinux/r-doby/PKGBUILD
+++ b/BioArchLinux/r-doby/PKGBUILD
@@ -1,42 +1,45 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=doBy
-_pkgver=4.6.20
+_pkgver=4.6.21
 pkgname=r-${_pkgname,,}
-pkgver=4.6.20
-pkgrel=2
-pkgdesc='Groupwise Statistics, LSmeans, Linear Contrasts, Utilities'
-arch=('any')
-url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Groupwise Statistics, LSmeans, Linear Estimates, Utilities"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
 depends=(
-  r
   r-broom
+  r-cowplot
   r-deriv
   r-dplyr
   r-ggplot2
-  r-magrittr
   r-microbenchmark
+  r-modelr
   r-pbkrtest
+  r-rlang
   r-tibble
+  r-tidyr
 )
 optdepends=(
   r-geepack
   r-knitr
   r-lme4
+  r-markdown
   r-multcomp
-  r-survival
   r-testthat
 )
 source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('7a0a7fab5bcdd7e62e42a3d2f2d307519e635d48b626c5673f5344ff7ba2da22')
+md5sums=('0430aff54f4be6fa47c7eca903d2f81b')
+b2sums=('b2d58dbdf2e24b9ff21b8e27300414a001a35d9029adcc3d6aca12f88aca1dca690031b7867e178c6aee765d5d2d536a4be78b6a94dec2ef9ebad4b484883d5a')
 
 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-doby/lilac.py b/BioArchLinux/r-doby/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-doby/lilac.py
+++ b/BioArchLinux/r-doby/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-doby/lilac.yaml b/BioArchLinux/r-doby/lilac.yaml
index cfc1279d87..59a0565073 100644
--- a/BioArchLinux/r-doby/lilac.yaml
+++ b/BioArchLinux/r-doby/lilac.yaml
@@ -4,15 +4,19 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-broom
+- r-cowplot
 - r-deriv
 - r-dplyr
 - r-ggplot2
-- r-magrittr
 - r-microbenchmark
+- r-modelr
 - r-pbkrtest
+- r-rlang
 - r-tibble
+- r-tidyr
 update_on:
-- regex: doBy_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=doBy
+- source: rpkgs
+  pkgname: doBy
+  repo: cran
+  md5: true
 - alias: r