From dffad489c10cf5b7f8648e5c4f6ddf308269d0c3 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 10 Oct 2023 18:34:30 +0300
Subject: [PATCH] r-hibag: use metadata checks

---
 BioArchLinux/r-hibag/PKGBUILD   | 37 ++++++++++++++++++++-------------
 BioArchLinux/r-hibag/lilac.py   | 14 ++++++++-----
 BioArchLinux/r-hibag/lilac.yaml | 16 +++++++++-----
 3 files changed, 43 insertions(+), 24 deletions(-)

diff --git a/BioArchLinux/r-hibag/PKGBUILD b/BioArchLinux/r-hibag/PKGBUILD
index 678529c0e7..1f74c54bbe 100644
--- a/BioArchLinux/r-hibag/PKGBUILD
+++ b/BioArchLinux/r-hibag/PKGBUILD
@@ -1,41 +1,50 @@
-# system requirements: C++11, GNU make
-# 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=HIBAG
 _pkgver=1.36.4
 pkgname=r-${_pkgname,,}
-pkgver=1.36.4
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='HLA Genotype Imputation with Attribute Bagging'
-arch=('x86_64')
+pkgdesc="HLA Genotype Imputation with Attribute Bagging"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+license=(GPL3)
 depends=(
-  r
   r-rcppparallel
-  gcc
-  make
+)
+checkdepends=(
+  r-gdsfmt
+  r-ggplot2
+  r-reshape2
+  r-snprelate
 )
 optdepends=(
   r-gdsfmt
   r-ggplot2
   r-knitr
   r-markdown
-  r-parallel
   r-reshape2
   r-rmarkdown
+  r-rsamtools
   r-seqarray
   r-snprelate
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('db885989e0e66d6ddad9fa71425a34d2')
 sha256sums=('8a5c38950418db1cd6ab9c017d4c7c715b31b4b94d878d17bd6219934e3b93b1')
 
 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" Rscript --vanilla runTests.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-hibag/lilac.py b/BioArchLinux/r-hibag/lilac.py
index bd219c037c..2bb127545f 100644
--- a/BioArchLinux/r-hibag/lilac.py
+++ b/BioArchLinux/r-hibag/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 = "C++11, GNU make",
+    )
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-hibag/lilac.yaml b/BioArchLinux/r-hibag/lilac.yaml
index 91b60b8d72..2fc6ae6694 100644
--- a/BioArchLinux/r-hibag/lilac.yaml
+++ b/BioArchLinux/r-hibag/lilac.yaml
@@ -1,11 +1,17 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-rcppparallel
+repo_makedepends:
+- r-gdsfmt
+- r-ggplot2
+- r-reshape2
+- r-snprelate
 update_on:
-- regex: HIBAG_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/HIBAG
+- source: rpkgs
+  pkgname: HIBAG
+  repo: bioc
+  md5: true
 - alias: r