r-lpsymphony: fix depends, use metadata checks

BioArchLinux/r-lpsymphony/PKGBUILD

@@ -1,49 +1,50 @@
-# 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=lpsymphony
 _pkgver=1.28.1
 pkgname=r-${_pkgname,,}
-pkgver=1.28.1
+pkgver=${_pkgver//[:-]/.}
 pkgrel=0
-pkgdesc='Symphony integer linear programming solver in R'
-arch=('x86_64')
+pkgdesc="Symphony integer linear programming solver in R"
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('EPL')
+license=(EPL)
 depends=(
+  coin-or-symphony
   r
-  coin-or-asl
-  coin-or-clp
-  coin-or-coinutils
-  coin-or-osi
-  coin-or-cgl
-  make
-  glpk
 )
-makedepends=(
-  gcc-fortran
+checkdepends=(
+  r-testthat
 )
 optdepends=(
   r-biocstyle
   r-knitr
-  r-slam
   r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('4d46f81f6bc676167c5dbd498c8415d97434274b885f11de5d29745ce6696421')
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "system-symphony.patch")
+md5sums=('a04276f8329ae09e82e3e16bc3a7b78e'
+         '5fe82566bce5f45a9d9d8682e51ebfaa')
+sha256sums=('4d46f81f6bc676167c5dbd498c8415d97434274b885f11de5d29745ce6696421'
+            'e4ffaac1444e128a63ba43d0adbd3dd8b6acac0ca5e8b2d8fe43ab3ffcb92e5a')
 
 prepare() {
-  sed -i 's#CXXFLAGS="-w -g -O2"#CXXFLAGS="-w -g -O2 -I/usr/include/coin"#' "${srcdir}/${_pkgname}/configure"
-  tar cfz "${_pkgname}.tar.gz" "${_pkgname}"
+  # build against system SYMPHONY
+  patch -Np1 -i system-symphony.patch
 }
 
 build() {
-  #R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
-  R CMD INSTALL ${_pkgname}.tar.gz -l "${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:

BioArchLinux/r-lpsymphony/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()

BioArchLinux/r-lpsymphony/lilac.yaml

@@ -1,9 +1,14 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
-  email: kuoi@bioarchlinux.org
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- coin-or-symphony
+repo_makedepends:
+- r-testthat
 update_on:
-- regex: lpsymphony_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/lpsymphony
+- source: rpkgs
+  pkgname: lpsymphony
+  repo: bioc
+  md5: true
 - alias: r

BioArchLinux/r-lpsymphony/system-symphony.patch

@@ -0,0 +1,15 @@
+diff --git a/lpsymphony/configure b/lpsymphony/configure
+index b3975c2..f1488ff 100755
+--- a/lpsymphony/configure
++++ b/lpsymphony/configure
+@@ -9,8 +9,8 @@ fi
+ 
+ R="${R_HOME}/bin/R"
+ 
+-SYMPHONY_CPPFLAGS=`pkg-config --cflags SYMPHONY >/dev/null 2>&1`
+-SYMPHONY_LIBS=`pkg-config --libs SYMPHONY >/dev/null 2>&1`
++SYMPHONY_CPPFLAGS=`pkg-config --cflags symphony 2>/dev/null`
++SYMPHONY_LIBS=`pkg-config --libs symphony 2>/dev/null`
+ 
+ test -z "${SYMPHONY_LIBS}" && SYMPHONY_LIBS="-lSym -lCgl -lOsiClp -lClp -lOsi -lCoinUtils"
+ 

lilac-extensions/lilac_r_utils.py

@@ -187,6 +187,7 @@ license_map = {
     "BSD_2_clause + file LICENSE": "BSD",
     "BSD_3_clause + file LICENSE": "BSD",
     "BSL-1.0": "Boost",
+    "EPL": "EPL",
     "GPL": "GPL",
     "GPL (>= 2)": "GPL",
     "GPL (>= 3)": "GPL3",