From 80cb7846179708ea2a75536ef5af3ed0707682e7 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Wed, 20 Mar 2024 19:58:47 +0200
Subject: [PATCH] r-enmcb: use latest sources, use metadata checks

---
 BioArchLinux/r-enmcb/PKGBUILD   | 28 ++++++++++++++--------------
 BioArchLinux/r-enmcb/lilac.py   | 11 ++++++-----
 BioArchLinux/r-enmcb/lilac.yaml |  7 ++++---
 3 files changed, 24 insertions(+), 22 deletions(-)

diff --git a/BioArchLinux/r-enmcb/PKGBUILD b/BioArchLinux/r-enmcb/PKGBUILD
index 98bb268da8..7eb4fbc7b4 100644
--- a/BioArchLinux/r-enmcb/PKGBUILD
+++ b/BioArchLinux/r-enmcb/PKGBUILD
@@ -1,16 +1,15 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=EnMCB
-_pkgver=1.8.2
+_pkgver=1.14.0
 pkgname=r-${_pkgname,,}
-pkgver=1.8.2
-pkgrel=9
-pkgdesc='Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models'
-arch=('any')
-url="https://bioconductor.org/packages/3.15/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models"
+arch=(any)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
-  r
   r-biocfilecache
   r-e1071
   r-ggplot2
@@ -32,15 +31,16 @@ optdepends=(
   r-survminer
   r-testthat
 )
-source=("https://bioconductor.org/packages/3.15/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('847b4ad1e11d292f898f5221fc4f54bba9f8d5cf1530be8f54b4969f893ecace')
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('f9fee363d9285ffdf2895062fc0cf26b')
+b2sums=('a5de7b457fd8eaddf133739616afe80daf7935a3715e38d4d096108c1a272f96ac2ba23fa40ff309e917230cba6326f8f2680db6d365fcb30b2243ac8c74805a')
 
 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-enmcb/lilac.py b/BioArchLinux/r-enmcb/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-enmcb/lilac.py
+++ b/BioArchLinux/r-enmcb/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-enmcb/lilac.yaml b/BioArchLinux/r-enmcb/lilac.yaml
index e598587cb7..cd30fd9c02 100644
--- a/BioArchLinux/r-enmcb/lilac.yaml
+++ b/BioArchLinux/r-enmcb/lilac.yaml
@@ -13,7 +13,8 @@ repo_depends:
 - r-survivalroc
 - r-survivalsvm
 update_on:
-- regex: EnMCB_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/3.15/EnMCB
+- source: rpkgs
+  pkgname: EnMCB
+  repo: bioc
+  md5: true
 - alias: r