r-gdsfmt: use metadata checks

BioArchLinux/r-gdsfmt/PKGBUILD

@@ -1,16 +1,25 @@
-# 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=gdsfmt
 _pkgver=1.36.1
 pkgname=r-${_pkgname,,}
-pkgver=1.36.1
+pkgver=${_pkgver//-/.}
 pkgrel=1
-pkgdesc='R Interface to CoreArray Genomic Data Structure (GDS) Files'
+pkgdesc="R Interface to CoreArray Genomic Data Structure (GDS) Files"
-arch=('x86_64')
+arch=(x86_64)
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('LGPL')
+license=(LGPL3)
 depends=(
+  lz4
   r
+  xz
+  zlib
+)
+checkdepends=(
+  r-biocgenerics
+  r-digest
+  r-runit
 )
 optdepends=(
   r-biocgenerics
@@ -18,20 +27,32 @@ optdepends=(
   r-digest
   r-knitr
   r-markdown
-  r-matrix
-  r-parallel
   r-rmarkdown
   r-runit
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
-sha256sums=('a753d15c43d4d8618f6751b6ec87f1d8439a9eb3a1e2d4c1f2fbdb6fbf581187')
+        "system-libs.patch")
+md5sums=('7e54216f1539f908f188665986552ab5'
+         'bffd05eba8706aacc469c69a3b0eeada')
+sha256sums=('a753d15c43d4d8618f6751b6ec87f1d8439a9eb3a1e2d4c1f2fbdb6fbf581187'
+            'a30cf43b5d8f07f19e88cc26fc2ccf6d88ab491e21ab3eb5b656d5258272af85')
+
+prepare() {
+  # use system lz4, xz and zlib
+  patch -Np1 -i system-libs.patch
+}
 
 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" Rscript --vanilla runTests.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-gdsfmt/lilac.py

@@ -1,12 +1,13 @@
 #!/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(_G)
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-gdsfmt/lilac.yaml

@@ -1,9 +1,28 @@
 build_prefix: extra-x86_64
 maintainers:
-- github: starsareintherose
+- github: pekkarr
-  email: kuoi@bioarchlinux.org
+  email: pekkarr@protonmail.com
+repo_makedepends:
+- r-biocgenerics
+- r-digest
+- r-runit
 update_on:
-- regex: gdsfmt_([\d._-]+).tar.gz
+- source: rpkgs
-  source: regex
+  pkgname: gdsfmt
-  url: https://bioconductor.org/packages/gdsfmt
+  repo: bioc
+  md5: true
 - alias: r
+- source: alpmfiles
+  pkgname: lz4
+  filename: usr/lib/liblz4\.so\.([^.]+)
+  repo: core
+- source: alpm
+  alpm: xz
+  repo: core
+  provided: liblzma.so
+  strip_release: true
+- source: alpm
+  alpm: zlib
+  repo: core
+  provided: libz.so
+  strip_release: true

BioArchLinux/r-gdsfmt/system-libs.patch

@@ -0,0 +1,42 @@
+diff --git a/gdsfmt/src/Makevars b/gdsfmt/src/Makevars
+index 0140469..3d4d197 100755
+--- a/gdsfmt/src/Makevars
++++ b/gdsfmt/src/Makevars
+@@ -6,7 +6,7 @@
+ PKG_CPPFLAGS = -DUSING_R -D_FILE_OFFSET_BITS=64 -I../inst/include -ICoreArray
+ 
+ # to set flags for the linker
+-PKG_LIBS = ./liblzma.a -lpthread
++PKG_LIBS = -lz -llz4 -llzma -lpthread
+ 
+ SOURCES = \
+ 	R_CoreArray.cpp \
+@@ -65,27 +65,11 @@ OBJECTS = \
+ 	CoreArray/dStream.o \
+ 	CoreArray/dStruct.o \
+ 	CoreArray/dSparse.o \
+-	CoreArray/dVLIntGDS.o \
+-	ZLIB/adler32.o \
+-	ZLIB/compress.o \
+-	ZLIB/crc32.o \
+-	ZLIB/deflate.o \
+-	ZLIB/infback.o \
+-	ZLIB/inffast.o \
+-	ZLIB/inflate.o \
+-	ZLIB/inftrees.o \
+-	ZLIB/trees.o \
+-	ZLIB/uncompr.o \
+-	ZLIB/zutil.o \
+-	LZ4/lz4.o \
+-	LZ4/lz4hc.o \
+-	LZ4/lz4frame.o \
+-	LZ4/xxhash.o
++	CoreArray/dVLIntGDS.o
+ 
+ 
+ all: $(SHLIB)
+ 
+-$(SHLIB): liblzma.a
+ 
+ 
+ ZLIB/adler32.o: