r-rhisat2: fix depends, use metadata checks

BioArchLinux/r-rhisat2/PKGBUILD

@@ -1,21 +1,19 @@
-# system requirements: GNU make
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 # Contributor: Viktor Drobot (aka dviktor) linux776 [at] gmail [dot] com
 
 _pkgname=Rhisat2
-_pkgver=1.18.0
+_pkgver=1.20.0
 pkgname=r-${_pkgname,,}
-pkgver=1.18.0
-pkgrel=2
-pkgdesc='R Wrapper for HISAT2 Aligner'
-arch=('x86_64')
-url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+pkgver=${_pkgver//-/.}
+pkgrel=0
+pkgdesc="R Wrapper for HISAT2 Aligner"
+arch=(x86_64)
+url="https://bioconductor.org/packages/$_pkgname"
+license=('GPL-3.0-only')
 depends=(
-  r
-  r-genomicfeatures
   r-genomicranges
   r-sgseq
+  r-txdbmaker
 )
 optdepends=(
   r-biocstyle
@@ -23,17 +21,26 @@ optdepends=(
   r-rmarkdown
   r-testthat
 )
-source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-sha256sums=('5830fa5e23b6d8e38614dd71ecabf364a40212663b79aec30231b6f531bfb4df')
-# parallel compilation leads to the race conditions and installation fail
-options=(!makeflags)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "fix-build.patch")
+md5sums=('40eeced68deeadf6506e97eb53e4a831'
+         '3f45bc291d0db4e626db5336680b2f73')
+b2sums=('f289e764d5085458a8248154e2aa8bc790c76c3e23866153757ba5e86a157b62b1d20f65732952a6a7fd0a8098b3c8289afcdd043c54fb691e69673fc07c35e0'
+        'f3d4cc8719124604b7d295c6143d38187901cbca50da949f4c49edac0d43e818cde3ab03cc05ad77425091db705979b1d9b381c751c0fada90b48796b54fee2c')
+
+prepare() {
+  # fix compiler flags
+  patch -Np1 -i fix-build.patch
+}
 
 build() {
-  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+  mkdir build
+  # parallel compilation fails
+  MAKEFLAGS+=" -j1"
+  R CMD INSTALL -l build "$_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-rhisat2/fix-build.patch

@@ -0,0 +1,22 @@
+diff --git a/Rhisat2/src/Makefile b/Rhisat2/src/Makefile
+index 005d756..87ef966 100644
+--- a/Rhisat2/src/Makefile
++++ b/Rhisat2/src/Makefile
+@@ -217,7 +217,7 @@ endif
+ 
+ DEBUG_FLAGS    = -O0 -g3 $(BITS_FLAG) $(SSE_FLAG)
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
+-RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3
++RELEASE_FLAGS  = $(CXXFLAGS) $(LDFLAGS) $(BITS_FLAG) -funroll-loops -g3
+ RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
+ NOASSERT_FLAGS = -DNDEBUG
+ FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+@@ -298,7 +298,7 @@ BIN_PKG_LIST = $(GENERAL_LIST)
+ .PHONY: all allall both both-debug
+ 
+ all: $(HISAT2_BIN_LIST) ../inst/hisat2
+-	$(CXX) -shared -fPIC -o Rhisat2.so get_info.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -shared -fPIC -o Rhisat2.so get_info.cpp
+ 
+ allall: $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)
+ 

BioArchLinux/r-rhisat2/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'):
-        if line.startswith('_pkgver='):
-            line = f'_pkgver={_G.newver}'
-        print(line)
-    update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
+    r_pre_build(_G)
 
 def post_build():
     git_pkgbuild_commit()

BioArchLinux/r-rhisat2/lilac.yaml

@@ -3,11 +3,12 @@ maintainers:
 - github: starsareintherose
   email: kuoi@bioarchlinux.org
 repo_depends:
-- r-genomicfeatures
 - r-genomicranges
 - r-sgseq
+- r-txdbmaker
 update_on:
-- regex: Rhisat2_([\d._-]+).tar.gz
-  source: regex
-  url: https://bioconductor.org/packages/Rhisat2
+- source: rpkgs
+  pkgname: Rhisat2
+  repo: bioc
+  md5: true
 - alias: r