r-autonomics: fix depends

BioArchLinux/r-autonomics/PKGBUILD

@@ -1,27 +1,25 @@
 # Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
 
 _pkgname=autonomics
-_pkgver=1.10.2
+_pkgver=1.12.0
 pkgname=r-${_pkgname,,}
 pkgver=${_pkgver//-/.}
-pkgrel=3
-pkgdesc="Generifying and intuifying cross-platform omics analysis"
+pkgrel=0
+pkgdesc="Unified statistal Modeling of Omics Data"
 arch=(any)
 url="https://bioconductor.org/packages/$_pkgname"
 license=('GPL-3.0-only')
 depends=(
   r-abind
-  r-assertive.base
-  r-assertive.files
-  r-assertive.numbers
-  r-assertive.sets
   r-biocfilecache
   r-biocgenerics
   r-bit64
+  r-codingmatrices
   r-colorspace
   r-data.table
   r-dplyr
   r-edger
+  r-ggforce
   r-ggplot2
   r-ggrepel
   r-gridextra
@@ -29,9 +27,8 @@ depends=(
   r-magrittr
   r-matrixstats
   r-multiassayexperiment
-  r-pcamethods
   r-r.utils
-  r-rappdirs
+  r-rcolorbrewer
   r-readxl
   r-rlang
   r-s4vectors
@@ -39,37 +36,57 @@ depends=(
   r-stringi
   r-summarizedexperiment
   r-tidyr
+  r-tidyselect
+  r-vsn
 )
 optdepends=(
   r-affy
   r-annotationdbi
+  r-annotationhub
+  r-apcluster
   r-biocmanager
   r-biocstyle
+  r-biostrings
+  r-dbi
   r-diagram
+  r-ensembldb
+  r-fpc
+  r-genomicdatacommons
   r-genomicranges
   r-geoquery
   r-hgu95av2.db
   r-icsnp
+  r-jsonlite
   r-knitr
   r-lme4
   r-lmertest
   r-mixomics
   r-mpm
+  r-olinkanalyze
   r-org.hs.eg.db
   r-org.mm.eg.db
+  r-pcamethods
+  r-pheatmap
+  r-progeny
+  r-propagate
   r-rcurl
+  r-readods
   r-remotes
   r-rmarkdown
   r-ropls
+  r-rsqlite
   r-rsubread
   r-rtracklayer
-  r-seqinr
   r-statmod
+  r-survminer
   r-testthat
+  r-uniprot.ws
+  r-writexl
+  r-xml
 )
 source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
-md5sums=('9034c755764d54d8bf0eb0e330f4e54f')
-b2sums=('ed49786ceee54208e06c3447dc00f6babcafbc68c339f2bbd2fabc632f9311a0173abf5ba7353f128d42f95710e3dfc25465a606ad1c889200e3132b4329ac57')
+md5sums=('c7bff80077a4a5113d328ccd01f5b115')
+b2sums=('ada10202f89010d9a7dc6255860f1e4d886bdeae777510488c7e9d568de6b60ba919d2bc57ad947b12219b6a64f794e08edbab148c7a3541cd9106c56c7c1269')
 
 build() {
   mkdir build

BioArchLinux/r-autonomics/lilac.yaml

@@ -4,17 +4,15 @@ maintainers:
   email: kuoi@bioarchlinux.org
 repo_depends:
 - r-abind
-- r-assertive.base
-- r-assertive.files
-- r-assertive.numbers
-- r-assertive.sets
 - r-biocfilecache
 - r-biocgenerics
 - r-bit64
+- r-codingmatrices
 - r-colorspace
 - r-data.table
 - r-dplyr
 - r-edger
+- r-ggforce
 - r-ggplot2
 - r-ggrepel
 - r-gridextra
@@ -22,9 +20,8 @@ repo_depends:
 - r-magrittr
 - r-matrixstats
 - r-multiassayexperiment
-- r-pcamethods
 - r-r.utils
-- r-rappdirs
+- r-rcolorbrewer
 - r-readxl
 - r-rlang
 - r-s4vectors
@@ -32,6 +29,8 @@ repo_depends:
 - r-stringi
 - r-summarizedexperiment
 - r-tidyr
+- r-tidyselect
+- r-vsn
 update_on:
 - source: rpkgs
   pkgname: autonomics

BioArchLinux/r-codingmatrices/PKGBUILD

@@ -0,0 +1,34 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=codingMatrices
+_pkgver=0.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Alternative Factor Coding Matrices for Linear Model Formulae"
+arch=(any)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
+depends=(
+  r-fractional
+)
+optdepends=(
+  r-car
+  r-dplyr
+  r-ggplot2
+  r-knitr
+  r-xtable
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('b7d15a0ce93cab8e8fb032ef8f4bc0e3')
+b2sums=('2ef7720cae7b1886c9c7554985b57f39d3c51f995f6f9eb6514ce786e61728bef292699aac2080fa96aa8dcf557de301c3b2fb55a5c8de0d76314832f3cec7a5')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-codingmatrices/lilac.py

@@ -0,0 +1,14 @@
+#!/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():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-codingmatrices/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-fractional
+update_on:
+- source: rpkgs
+  pkgname: codingMatrices
+  repo: cran
+  md5: true
+- alias: r

BioArchLinux/r-fractional/PKGBUILD

@@ -0,0 +1,33 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=fractional
+_pkgver=0.1.3
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Vulgar Fractions in R"
+arch=(x86_64)
+url="https://cran.r-project.org/package=$_pkgname"
+license=('GPL-2.0-or-later')
+depends=(
+  r-rcpp
+)
+optdepends=(
+  r-dplyr
+  r-ggplot2
+  r-knitr
+  r-rmarkdown
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('e33165a29333e4a8ac11b3e9db006907')
+b2sums=('8b94e9312f115311e6a8ab38359a37d02b4e8af33a2bbb035db9c8d2d3dcdbc580cfe8e0acc32f4b11dd52e9da0f032688270c52909025b3ff8bf95d686ba353')
+
+build() {
+  mkdir build
+  R CMD INSTALL -l build "$_pkgname"
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}

BioArchLinux/r-fractional/lilac.py

@@ -0,0 +1,14 @@
+#!/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():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()

BioArchLinux/r-fractional/lilac.yaml

@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-rcpp
+update_on:
+- source: rpkgs
+  pkgname: fractional
+  repo: cran
+  md5: true
+- alias: r