From 3678dce269c36f0907ac8bb0702001b61bbfcf90 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Thu, 5 Oct 2023 18:27:54 +0300
Subject: [PATCH] r-rmixmod: use metadata checks

---
 BioArchLinux/r-rmixmod/PKGBUILD           | 43 +++++++++++++++--------
 BioArchLinux/r-rmixmod/fix-libxmlxx.patch | 11 ++++++
 BioArchLinux/r-rmixmod/lilac.py           | 14 +++++---
 BioArchLinux/r-rmixmod/lilac.yaml         | 22 +++++++++---
 4 files changed, 65 insertions(+), 25 deletions(-)
 create mode 100644 BioArchLinux/r-rmixmod/fix-libxmlxx.patch

diff --git a/BioArchLinux/r-rmixmod/PKGBUILD b/BioArchLinux/r-rmixmod/PKGBUILD
index a99c047273..1ba906a927 100644
--- a/BioArchLinux/r-rmixmod/PKGBUILD
+++ b/BioArchLinux/r-rmixmod/PKGBUILD
@@ -1,30 +1,43 @@
-# system requirements: 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=Rmixmod
 _pkgver=2.1.9
 pkgname=r-${_pkgname,,}
-pkgver=2.1.9
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='Classification with Mixture Modelling'
-arch=('x86_64')
+pkgdesc="Classification with Mixture Modelling"
+arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+license=(GPL3)
 depends=(
-  r
+  glibmm
+  libxml++2.6
   r-rcpp
-  r-rcppeigen
-  make
 )
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('d87eeb1de611ce0e421141a3b3d11cae819d327fbc510314a820ddf982a09453')
+makedepends=(
+  r-rcppeigen
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "fix-libxmlxx.patch")
+md5sums=('6e02da6f0e72ace0f2c6c9d761c6d67c'
+         '98c555181a4b06b18ad6565b22a43dbe')
+sha256sums=('d87eeb1de611ce0e421141a3b3d11cae819d327fbc510314a820ddf982a09453'
+            '2849f3da407a8d3fc6d081274d66af67f63879e9976fa1997bebf07112147cf5')
+
+prepare() {
+  # fix compilation with libxml++
+  patch -Np1 -i fix-libxmlxx.patch
+}
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build \
+      --configure-vars=RMIXMOD_WITH_XML=1 \
+      --configure-vars=RMIXMOD_WITH_OMP=1
 }
 
 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-rmixmod/fix-libxmlxx.patch b/BioArchLinux/r-rmixmod/fix-libxmlxx.patch
new file mode 100644
index 0000000000..2e128a654b
--- /dev/null
+++ b/BioArchLinux/r-rmixmod/fix-libxmlxx.patch
@@ -0,0 +1,11 @@
+diff --git a/Rmixmod/src/Makevars.in b/Rmixmod/src/Makevars.in
+index 7eb53d5..fa9730b 100644
+--- a/Rmixmod/src/Makevars.in
++++ b/Rmixmod/src/Makevars.in
+@@ -35,5 +35,5 @@ $(SHLIB): mixmod
+ 
+ mixmod:
+ 	(cd $(MIXMODDIR) && $(MAKE) -f mixmod_r.mk)
+-	(if test ! -z $(RMIXMOD_XML) ; then cd $(IOSTREAMDIR) && $(MAKE) -f mixmod_iostream_r.mk ; fi)
++	(if test ! -z $(RMIXMOD_XML) ; then cd $(IOSTREAMDIR) && $(MAKE) LIBXMLXX_CFLAGS="$(LIBXMLXX_CFLAGS)" -f mixmod_iostream_r.mk ; fi)
+ 	$(RANLIB) $(MIXMODLIB)
diff --git a/BioArchLinux/r-rmixmod/lilac.py b/BioArchLinux/r-rmixmod/lilac.py
index bd219c037c..6cfc1b802b 100644
--- a/BioArchLinux/r-rmixmod/lilac.py
+++ b/BioArchLinux/r-rmixmod/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 = "GNU make",
+    )
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-rmixmod/lilac.yaml b/BioArchLinux/r-rmixmod/lilac.yaml
index 24caeb75f9..db76dee788 100644
--- a/BioArchLinux/r-rmixmod/lilac.yaml
+++ b/BioArchLinux/r-rmixmod/lilac.yaml
@@ -1,12 +1,24 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 repo_depends:
 - r-rcpp
+repo_makedepends:
 - r-rcppeigen
 update_on:
-- regex: Rmixmod_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=Rmixmod
+- source: rpkgs
+  pkgname: Rmixmod
+  repo: cran
+  md5: true
 - alias: r
+- source: alpm
+  alpm: glibmm
+  repo: extra
+  provided: libglibmm-2.4.so
+  strip_release: true
+- source: alpm
+  alpm: libxml++2.6
+  repo: extra
+  provided: libxml++-2.6.so
+  strip_release: true