r-rnadecay: fix makedepends, use metadata checks

BioArchLinux/r-rnadecay/PKGBUILD

@@ -1,37 +1,41 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=RNAdecay
-_pkgver=1.22.2
+_pkgver=1.24.0
 pkgname=r-${_pkgname,,}
-pkgver=1.22.2
-pkgrel=1
-pkgdesc='Maximum Likelihood Decay Modeling of RNA Degradation Data'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="Maximum Likelihood Decay Modeling of RNA Degradation Data"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-2.0-only')
 depends=(
-  r
   r-ggplot2
   r-gplots
   r-nloptr
   r-scales
   r-tmb
 )
+makedepends=(
+  r-rcppeigen
+)
 optdepends=(
   r-knitr
-  r-parallel
   r-reshape2
   r-rmarkdown
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('c7ee3059b07ee28c2814ee9104e02259f5c53681cf04de9a311bc81a82c0ebdb')
+md5sums=('4b013eb50cd972559df41fb6361bf1bc')
+b2sums=('5481d2048fdab3c21ebf0aceacdfe0cd9ffdcfb89c2ae5b82c72028a6cd477725ba78c73a32bea94a49e2d0f47111886072c0ccdfeed517434e212ad409281f8')
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  # compilation needs a lot of memory
+  MAKEFLAGS+=" -j1"
+  R CMD INSTALL -l build "$_pkgname"
 }
 
 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-rnadecay/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,
+        extra_r_makedepends = ["r-rcppeigen"],
+    )
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-rnadecay/lilac.yaml

@@ -8,8 +8,11 @@ repo_depends:
 - r-nloptr
 - r-scales
 - r-tmb
+repo_makedepends:
+- r-rcppeigen
 update_on:
-- regex: RNAdecay_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/RNAdecay
+- source: rpkgs
+  pkgname: RNAdecay
+  repo: bioc
+  md5: true
 - alias: r

lilac-extensions/lilac_r_utils.py

@@ -243,6 +243,7 @@ class CheckConfig:
         expect_systemrequirements: str = None,
         expect_title: str = None,
         extra_r_depends_cb = None,
+        extra_r_makedepends = [],
         ignore_fortran_files: bool = False,
     ):
         self.expect_license = expect_license
@@ -250,6 +251,7 @@ class CheckConfig:
         self.expect_systemrequirements = expect_systemrequirements
         self.expect_title = expect_title
         self.extra_r_depends_cb = extra_r_depends_cb
+        self.extra_r_makedepends = extra_r_makedepends
         self.ignore_fortran_files = ignore_fortran_files
 
 def check_default_pkgs(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
@@ -294,10 +296,10 @@ def check_depends(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
 def check_makedepends(pkg: Pkgbuild, desc: Description, cfg: CheckConfig):
     errors = []
     for dep in pkg.makedepends:
-        if dep in pkg.depends or (dep.startswith("r-") and dep not in desc.linkingto):
+        if dep in pkg.depends or (dep.startswith("r-") and (dep not in desc.linkingto and dep not in cfg.extra_r_makedepends)):
             errors.append(f"Unnecessary make dependency: {dep}")
 
-    for dep in desc.linkingto:
+    for dep in desc.linkingto + cfg.extra_r_makedepends:
         if (dep not in cfg.default_r_pkgs) and (dep not in desc.depends) and (dep not in desc.imports) and (dep not in pkg.makedepends):
             errors.append(f"Missing make dependency: {dep}")