From ebdb6303c5fddb40d30e1d5d702d1b04ec9b3194 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Wed, 29 Nov 2023 17:22:25 +0200
Subject: [PATCH] r-xml: fix build, use metadata checks

---
 BioArchLinux/r-xml/PKGBUILD        | 45 ++++++++++++++++++++----------
 BioArchLinux/r-xml/fix-build.patch | 24 ++++++++++++++++
 BioArchLinux/r-xml/lilac.py        | 14 ++++++----
 BioArchLinux/r-xml/lilac.yaml      | 16 +++++++----
 4 files changed, 74 insertions(+), 25 deletions(-)
 create mode 100644 BioArchLinux/r-xml/fix-build.patch

diff --git a/BioArchLinux/r-xml/PKGBUILD b/BioArchLinux/r-xml/PKGBUILD
index d91802a6ca..ee2e78587a 100644
--- a/BioArchLinux/r-xml/PKGBUILD
+++ b/BioArchLinux/r-xml/PKGBUILD
@@ -1,32 +1,47 @@
-# system requirements: libxml2 (>= 2.6.3)
-# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
+# Contributor: Alex Branham <branham@utexas.edu>
+# Contributor: fordprefect <fordprefect@dukun.de>
+# Contributor: Nick B <Shirakawasuna at gmail _dot_com>
 
 _pkgname=XML
-_pkgver=3.99-0.15
+_pkgver=3.99-0.16
 pkgname=r-${_pkgname,,}
-pkgver=3.99.0.15
-pkgrel=1
-pkgdesc='Tools for Parsing and Generating XML Within R and S-Plus'
-arch=('x86_64')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Tools for Parsing and Generating XML Within R and S-Plus"
+arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
-license=('BSD')
+license=(BSD)
 depends=(
+  libxml2
   r
 )
 optdepends=(
   r-bitops
   r-rcurl
 )
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('98a14694670a8a1d9a03e184ec60203180fb8eca9fb3da086693b01ed7003b3e')
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "fix-build.patch")
+md5sums=('afa1fd1496595b5aa4f6cb758bad0122'
+         'fe644b51ff4b55a2b594a6c7dda5bc25')
+sha256sums=('350d37bab99ba3dac03313fa3901cc053ab2d962a94a9c3404fb3ad0a91cc95b'
+            '5fd93db9dbd4100d4db55714c62340b025d0a871eaf61bffe145fb743e5d26da')
+
+prepare() {
+  # fix build
+  patch -Np1 -i fix-build.patch
+}
 
 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}" "${pkgdir}/usr/lib/R/library"
-  install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}"
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
 }
-# vim:set ts=2 sw=2 et:
diff --git a/BioArchLinux/r-xml/fix-build.patch b/BioArchLinux/r-xml/fix-build.patch
new file mode 100644
index 0000000000..24e2b94038
--- /dev/null
+++ b/BioArchLinux/r-xml/fix-build.patch
@@ -0,0 +1,24 @@
+diff --git a/XML/src/HTMLParse.c b/XML/src/HTMLParse.c
+index 8d71f9f..7dea289 100644
+--- a/XML/src/HTMLParse.c
++++ b/XML/src/HTMLParse.c
+@@ -11,6 +11,7 @@
+ 
+ #include "libxml/HTMLparser.h"
+ #include "libxml/HTMLtree.h"
++#include "libxml/xmlsave.h"
+ 
+ #include <sys/stat.h>
+ #include <unistd.h>  
+diff --git a/XML/src/XMLTree.c b/XML/src/XMLTree.c
+index 6047de0..c28d5d0 100644
+--- a/XML/src/XMLTree.c
++++ b/XML/src/XMLTree.c
+@@ -35,6 +35,7 @@
+ #include <libxml/HTMLtree.h>
+ #endif
+ 
++#include <libxml/xmlsave.h>
+ 
+ #define R_USE_XML_ENCODING 1
+ #include "Utils.h"  /* R_createXMLNodeRef, Encoding macros. */
diff --git a/BioArchLinux/r-xml/lilac.py b/BioArchLinux/r-xml/lilac.py
index 620556bc87..01a0c6a3f8 100644
--- a/BioArchLinux/r-xml/lilac.py
+++ b/BioArchLinux/r-xml/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 = "libxml2 (>= 2.6.3)",
+    )
 
 def post_build():
     git_pkgbuild_commit()
diff --git a/BioArchLinux/r-xml/lilac.yaml b/BioArchLinux/r-xml/lilac.yaml
index be5fa5c839..623548a6df 100644
--- a/BioArchLinux/r-xml/lilac.yaml
+++ b/BioArchLinux/r-xml/lilac.yaml
@@ -1,9 +1,15 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
 update_on:
-- regex: XML_([\d._-]+).tar.gz
-  source: regex
-  url: https://cran.r-project.org/package=XML
+- source: rpkgs
+  pkgname: XML
+  repo: cran
+  md5: true
 - alias: r
+- source: alpm
+  alpm: libxml2
+  repo: core
+  provided: libxml2.so
+  strip_release: true