r-igraph: fix depends, use metadata checks

BioArchLinux/r-igraph/PKGBUILD

@@ -1,27 +1,42 @@
-# system requirements: gmp (>= 4.38, optional), libxml2 (optional), glpk(optional)
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
-# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
+# Contributor: Alex Branham <branham@utexas.edu>
 
 _pkgname=igraph
-_pkgver=1.4.3
+_pkgver=1.5.0
 pkgname=r-${_pkgname,,}
-pkgver=1.4.3
+pkgver=${_pkgver//[:-]/.}
-pkgrel=1
+pkgrel=0
-pkgdesc='Network Analysis and Visualization'
+pkgdesc="Network Analysis and Visualization"
-arch=('x86_64')
+arch=(x86_64)
 url="https://cran.r-project.org/package=${_pkgname}"
-license=('GPL')
+license=(GPL)
 depends=(
-  r
+  arpack
-  r-cpp11
+  blas
+  glpk
+  gmp
+  lapack
+  libxml2
+  plfit
+  r-cli
   r-magrittr
   r-pkgconfig
   r-rlang
+  suitesparse
+  util-linux-libs
+)
+makedepends=(
+  r-cpp11
+)
+checkdepends=(
+  r-graph
+  r-testthat
+  r-vdiffr
 )
 optdepends=(
-  glpk
-  gmp
-  libxml2
   r-ape
+  r-callr
   r-decor
   r-digest
   r-graph
@@ -30,24 +45,35 @@ optdepends=(
   r-rgl
   r-rmarkdown
   r-scales
-  r-stats4
-  r-tcltk
   r-testthat
   r-vdiffr
   r-withr
 )
-makedepends=(
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
-  gcc-fortran
+        "igraph-system-libs.patch")
-)
+md5sums=('5e77d6cd9b04e72ceb0d51d2e5a232c8'
-source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+         '34283a0a206240ab1f33f83d2526ffca')
-sha256sums=('06bdb3fa6cced6a5990268f9f26c5ef129df1dc2d4ff2806fe36f3b45cc16021')
+sha256sums=('d80778ff0fd0ee00a348c5d63b3b398b7467a1af49d85dc57fbee0a900fd7306'
+            '38731c656da7f1fe34a4d21c3e3dcae65592898ba81620b96cd27c7894539530')
+
+prepare() {
+  cd "$_pkgname"
+  # Build using system libraries
+  patch -Np1 -i ../igraph-system-libs.patch
+  autoconf
+}
 
 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 "${pkgdir}/usr/lib/R/library"
+  install -d "$pkgdir/usr/lib/R/library"
-  cp -a --no-preserve=ownership "${_pkgname}" "${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-igraph/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'):
+    r_pre_build(
-        if line.startswith('_pkgver='):
+        _G,
-            line = f'_pkgver={_G.newver}'
+        expect_systemrequirements = "gmp (optional), libxml2 (optional), glpk (>= 4.57, optional)",
-        print(line)
+        ignore_fortran_files = True,
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-igraph/lilac.yaml

@@ -1,14 +1,30 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
+- github: pekkarr
-  email: kuoi@bioarchlinux.org
+  email: pekkarr@protonmail.com
 repo_depends:
-- r-cpp11
+- r-cli
 - r-magrittr
 - r-pkgconfig
 - r-rlang
+repo_makedepends:
+- r-cpp11
+- r-graph
+- r-testthat
+- r-vdiffr
 update_on:
-- regex: igraph_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: igraph
-  url: https://cran.r-project.org/package=igraph
+  repo: cran
+  md5: true
 - alias: r
+- source: alpm
+  alpm: libxml2
+  repo: core
+  provided: libxml2.so
+  strip_release: true
+- source: alpm
+  alpm: util-linux-libs
+  repo: core
+  provided: libuuid.so
+  strip_release: true

lilac-extensions/lilac_r_utils.py

@@ -211,9 +211,14 @@ class CheckFailed(Exception):
         self.msg = msg
 
 class CheckConfig:
-    def __init__(self, expect_license: str = None, expect_systemrequirements: str = None):
+    def __init__(self,
+        expect_license: str = None,
+        expect_systemrequirements: str = None,
+        ignore_fortran_files: bool = False,
+    ):
         self.expect_license = expect_license
         self.expect_systemrequirements = expect_systemrequirements
+        self.ignore_fortran_files = ignore_fortran_files
 
 def check_default_pkgs(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
     errors = set()
@@ -285,9 +290,12 @@ def check_fortran(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
     fortran_dep = "gcc-fortran" in pkg.makedepends
 
     if fortran_files and not fortran_dep:
-        raise CheckFailed("Missing make dependency: gcc-fortran")
+        if not cfg.ignore_fortran_files:
+            raise CheckFailed("Missing make dependency: gcc-fortran")
     elif not fortran_files and fortran_dep:
         raise CheckFailed("Unnecessary make dependency: gcc-fortran")
+    elif cfg.ignore_fortran_files and not fortran_files:
+        raise CheckFailed("Unnecessary config 'ignore_fortran_files'");
 
 def check_systemrequirements(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
     if cfg.expect_systemrequirements != desc.systemrequirements: