r-affypara: fix build error. functionality: tested

add its indirect dependency

BioArchLinux/r-affypara/PKGBUILD

@@ -1,13 +1,13 @@
 
 _pkgname=affyPara
-_pkgver=1.34.0
+_pkgver=1.54.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//[:-]/.}
 pkgrel=1
 pkgdesc='Sample size for RNAseq studies'
 arch=('any')
 url="https://bioconductor.org/packages/${_pkgname}"
-license=('GPL')
+license=('GPL3')
 depends=(
   r
   r-affy
@@ -27,6 +27,18 @@ optdepends=(
 source=("git+https://git.bioconductor.org/packages/${_pkgname}.git")
 sha256sums=('SKIP')
 
+prepare(){
+  # remove 22c `assign(".affyParaInternalEnv", .affyParaInternalEnv, envir=topenv(parent.frame()))`
+  # adapted from
+  # https://github.com/tidyverse/ggplot2/blob/7ebb6bd9d664f58794078afdb5a8ff71d5edf96d/R/ggplot-global.R#L4
+  sed -i '/assign(".affyParaInternalEnv/d' ${_pkgname}/R/zzz.R
+
+  # mv .affyParaInternalEnv <- new.env(parent=emptyenv()) to top of the file.
+  grep -E '^\s+.affyParaInternalEnv' ${_pkgname}/R/zzz.R  > tmpzzz.R
+  grep -vE '^\s+.affyParaInternalEnv' ${_pkgname}/R/zzz.R >> tmpzzz.R
+  mv tmpzzz.R ${_pkgname}/R/zzz.R
+}
+
 build() {
   tar -zcvf ${_pkgname}.tar.gz  ${_pkgname}
   R CMD INSTALL ${_pkgname}.tar.gz -l "${srcdir}"

BioArchLinux/r-affypara/lilac.yaml

@@ -11,4 +11,4 @@ repo_depends:
 update_on:
 - regex: <td>(\d+.\d+.\d+)</td>
   source: regex
-  url: https://bioconductor.org/packages/affyPara
+  url: https://bioconductor.org/packages/3.14/bioc/html/affyPara.html

BioArchLinux/r-hgu95av2cdf/PKGBUILD

@@ -0,0 +1,27 @@
+# Maintainer: sukanka <su975853527@gmail.com>
+
+_pkgname=hgu95av2cdf
+_pkgver=2.18.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//[:-]/.}
+pkgrel=1
+pkgdesc='hgu95av2cdf'
+arch=('any')
+url="https://bioconductor.org/packages/${_pkgname}"
+license=('LGPL')
+depends=(
+  r
+  r-annotationdbi
+)
+source=("https://bioconductor.org/packages/release/data/annotation/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('d449a06a2f55a5a1f942710c8da2a37a81e20342b6e600669df94ecb55f1e1fe')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et:

BioArchLinux/r-hgu95av2cdf/lilac.py

@@ -0,0 +1,12 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+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('-', '.'))
+
+def post_build():
+    git_pkgbuild_commit()

BioArchLinux/r-hgu95av2cdf/lilac.yaml

@@ -0,0 +1,9 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: sukanka
+repo_depends:
+  - r-annotationdbi
+update_on:
+  - regex: hgu95av2cdf_([\d._-]+).tar.gz
+    source: regex
+    url: https://bioconductor.org/packages/hgu95av2cdf