From 16efce03d43da7200636e62ea493f0fe517591a9 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Fri, 22 Sep 2023 22:13:53 +0300
Subject: [PATCH] r-biodbhmdb: fix depends, use metadata checks

---
 BioArchLinux/r-biodbhmdb/PKGBUILD   | 38 +++++++++++++++++++----------
 BioArchLinux/r-biodbhmdb/lilac.py   | 11 +++++----
 BioArchLinux/r-biodbhmdb/lilac.yaml | 14 +++++++----
 3 files changed, 40 insertions(+), 23 deletions(-)

diff --git a/BioArchLinux/r-biodbhmdb/PKGBUILD b/BioArchLinux/r-biodbhmdb/PKGBUILD
index 31c75eebf9..636dba5598 100644
--- a/BioArchLinux/r-biodbhmdb/PKGBUILD
+++ b/BioArchLinux/r-biodbhmdb/PKGBUILD
@@ -1,21 +1,27 @@
-# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=biodbHmdb
-_pkgver=1.6.0
+_pkgver=1.6.1
 pkgname=r-${_pkgname,,}
-pkgver=1.6.0
-pkgrel=1
-pkgdesc='biodbHmdb, a library for connecting to the HMDB Database'
-arch=('x86_64')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="biodbHmdb, a library for connecting to the HMDB Database"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('AGPL')
+license=(AGPL3)
 depends=(
-  r
   r-biodb
   r-r6
   r-rcpp
+  r-zip
+)
+makedepends=(
   r-testthat
 )
+checkdepends=(
+  r-xml2
+)
 optdepends=(
   r-biocstyle
   r-covr
@@ -27,14 +33,20 @@ optdepends=(
   r-testthat
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('883e86fa568deb09cd835174da77c186b6b08d0e655ccfbbecd05834e7960862')
+md5sums=('3e2269f5f98740e0a8caad6610ba960b')
+sha256sums=('b704087955926d42c01e624b39b8504f3ca63f587c8494ad37240cdcbabd7c9c')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
 }
 
 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-biodbhmdb/lilac.py b/BioArchLinux/r-biodbhmdb/lilac.py
index bd219c037c..b5cdb057c5 100644
--- a/BioArchLinux/r-biodbhmdb/lilac.py
+++ b/BioArchLinux/r-biodbhmdb/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-biodbhmdb/lilac.yaml b/BioArchLinux/r-biodbhmdb/lilac.yaml
index cbe3d38e2d..26b6fa3b14 100644
--- a/BioArchLinux/r-biodbhmdb/lilac.yaml
+++ b/BioArchLinux/r-biodbhmdb/lilac.yaml
@@ -1,14 +1,18 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-biodb
 - r-r6
 - r-rcpp
+- r-zip
+repo_makedepends:
 - r-testthat
+- r-xml2
 update_on:
-- regex: biodbHmdb_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/biodbHmdb
+- source: rpkgs
+  pkgname: biodbHmdb
+  repo: bioc
+  md5: true
 - alias: r