From 37aca33b46a93c0d69fa7765f0f9b23241667374 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Mon, 27 Nov 2023 21:14:46 +0200
Subject: [PATCH] r-seqminer: use metadata checks

---
 BioArchLinux/r-seqminer/PKGBUILD   | 44 ++++++++++++++++++++++--------
 BioArchLinux/r-seqminer/lilac.py   | 15 ++++++----
 BioArchLinux/r-seqminer/lilac.yaml | 33 ++++++++++++++++++----
 3 files changed, 70 insertions(+), 22 deletions(-)

diff --git a/BioArchLinux/r-seqminer/PKGBUILD b/BioArchLinux/r-seqminer/PKGBUILD
index 2a277239b5..a4ba9989e9 100644
--- a/BioArchLinux/r-seqminer/PKGBUILD
+++ b/BioArchLinux/r-seqminer/PKGBUILD
@@ -1,31 +1,51 @@
-# system requirements: C++11, zlib headers and libraries, GNU make,optionally also bzip2 and POSIX-compliant regex functions.
-# 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=seqminer
 _pkgver=9.1
 pkgname=r-${_pkgname,,}
-pkgver=9.1
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R'
-arch=('x86_64')
+pkgdesc="Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R"
+arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+license=(GPL)
 depends=(
+  bzip2
   r
+  sqlite
+  zlib
+  zstd
+)
+checkdepends=(
+  r-testthat
 )
 optdepends=(
   r-skat
   r-testthat
 )
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('79e2e74cdc20cf00d7c78354c5de5511140c6265af0f32cb4dac11dfb5cab76d')
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "$_pkgname-fix-buffer-overflows.patch::https://github.com/zhanxw/seqminer/pull/29.patch")
+md5sums=('c1a395cd5a427013fc7b784d35ec37ac'
+         'e156bd312594f28f4f9b90d050e06d05')
+sha256sums=('79e2e74cdc20cf00d7c78354c5de5511140c6265af0f32cb4dac11dfb5cab76d'
+            '6f4d3fd8acf0d370ca3100ff85f1ae8eb409cfc15a88585e4b5d8c92e1e69527')
+
+prepare() {
+  patch -Np1 -d "$_pkgname" < "$_pkgname-fix-buffer-overflows.patch"
+}
 
 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-seqminer/lilac.py b/BioArchLinux/r-seqminer/lilac.py
index bd219c037c..c9efad6a6d 100644
--- a/BioArchLinux/r-seqminer/lilac.py
+++ b/BioArchLinux/r-seqminer/lilac.py
@@ -1,12 +1,17 @@
 #!/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 | file LICENSE",
+        expect_systemrequirements = "C++17, zlib headers and libraries, GNU make, optionally also bzip2 and POSIX-compliant regex functions.",
+    )
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-seqminer/lilac.yaml b/BioArchLinux/r-seqminer/lilac.yaml
index 48e6b2d49b..28ef33167c 100644
--- a/BioArchLinux/r-seqminer/lilac.yaml
+++ b/BioArchLinux/r-seqminer/lilac.yaml
@@ -1,9 +1,32 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_makedepends:
+- r-testthat
 update_on:
-- regex: seqminer_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=seqminer
+- source: rpkgs
+  pkgname: seqminer
+  repo: cran
+  md5: true
 - alias: r
+- source: alpm
+  alpm: bzip2
+  repo: core
+  provided: libbz2.so
+  strip_release: true
+- source: alpm
+  alpm: sqlite
+  repo: core
+  provided: libsqlite3.so
+  strip_release: true
+- source: alpm
+  alpm: zlib
+  repo: core
+  provided: libz.so
+  strip_release: true
+- source: alpm
+  alpm: zstd
+  repo: core
+  provided: libzstd.so
+  strip_release: true