From ee659e9c40a4a70d38a884f7dd3413b496719034 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Wed, 25 Oct 2023 23:25:02 +0300
Subject: [PATCH] r-ebseq: fix depends, use metadata checks

---
 BioArchLinux/r-ebseq/PKGBUILD   | 32 +++++++++++++++++++-------------
 BioArchLinux/r-ebseq/lilac.py   | 14 +++++++++-----
 BioArchLinux/r-ebseq/lilac.yaml | 15 ++++++++++-----
 3 files changed, 38 insertions(+), 23 deletions(-)

diff --git a/BioArchLinux/r-ebseq/PKGBUILD b/BioArchLinux/r-ebseq/PKGBUILD
index 7bf726b444..84643339a5 100644
--- a/BioArchLinux/r-ebseq/PKGBUILD
+++ b/BioArchLinux/r-ebseq/PKGBUILD
@@ -1,29 +1,35 @@
-# 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=EBSeq
-_pkgver=1.40.0
+_pkgver=2.0.0
 pkgname=r-${_pkgname,,}
-pkgver=1.40.0
-pkgrel=1
-pkgdesc='An R package for gene and isoform differential expression analysis of RNA-seq data'
-arch=('any')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="An R package for gene and isoform differential expression analysis of RNA-seq data"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('Artistic2.0')
+license=(Artistic2.0)
 depends=(
-  r
   r-blockmodeling
   r-gplots
+  r-rcpp
+  r-rcppeigen
   r-testthat
 )
+makedepends=(
+  r-bh
+)
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('a5d3a88743d61062c6d68a426b19c53a4afd2fa216abc884d42c187780994378')
+md5sums=('e64aabb38197aba0ee5985a1558cce60')
+sha256sums=('9c5818ed988a1b3e416f3300ad56d4ae778485deb3b51eb6ee31bea91074a91f')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
 }
 
 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-ebseq/lilac.py b/BioArchLinux/r-ebseq/lilac.py
index bd219c037c..c6f3eb1305 100644
--- a/BioArchLinux/r-ebseq/lilac.py
+++ b/BioArchLinux/r-ebseq/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",
+    )
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-ebseq/lilac.yaml b/BioArchLinux/r-ebseq/lilac.yaml
index e99b45f91e..465e9e6b97 100644
--- a/BioArchLinux/r-ebseq/lilac.yaml
+++ b/BioArchLinux/r-ebseq/lilac.yaml
@@ -1,13 +1,18 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-blockmodeling
 - r-gplots
+- r-rcpp
+- r-rcppeigen
 - r-testthat
+repo_makedepends:
+- r-bh
 update_on:
-- regex: EBSeq_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/EBSeq
+- source: rpkgs
+  pkgname: EBSeq
+  repo: bioc
+  md5: true
 - alias: r