From 36c6f470c9d0b73bc1b56dec2992f44e119ea502 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sun, 3 Dec 2023 17:02:01 +0200
Subject: [PATCH] r-phenomis: init

---
 BioArchLinux/r-phenomis/PKGBUILD   | 70 ++++++++++++++++++++++++++++++
 BioArchLinux/r-phenomis/lilac.py   | 14 ++++++
 BioArchLinux/r-phenomis/lilac.yaml | 34 +++++++++++++++
 lilac-extensions/lilac_r_utils.py  |  1 +
 4 files changed, 119 insertions(+)
 create mode 100644 BioArchLinux/r-phenomis/PKGBUILD
 create mode 100644 BioArchLinux/r-phenomis/lilac.py
 create mode 100644 BioArchLinux/r-phenomis/lilac.yaml

diff --git a/BioArchLinux/r-phenomis/PKGBUILD b/BioArchLinux/r-phenomis/PKGBUILD
new file mode 100644
index 0000000000..dab00c1cf0
--- /dev/null
+++ b/BioArchLinux/r-phenomis/PKGBUILD
@@ -0,0 +1,70 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=phenomis
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Postprocessing and univariate analysis of omics data"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=('CECILL-2.0')
+depends=(
+  r-biobase
+  r-biodb
+  r-biodbchebi
+  r-data.table
+  r-futile.logger
+  r-ggplot2
+  r-ggrepel
+  r-htmlwidgets
+  r-igraph
+  r-limma
+  r-multiassayexperiment
+  r-multidataset
+  r-plotly
+  r-pmcmrplus
+  r-ranger
+  r-rcolorbrewer
+  r-ropls
+  r-summarizedexperiment
+  r-tibble
+  r-tidyr
+  r-venndiagram
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocgenerics
+  r-biocstyle
+  r-biosigner
+  r-cll
+  r-knitr
+  r-omicade4
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
+        "$_pkgname-LICENSE::http://www.cecill.info/licences/Licence_CeCILL_V2-en.txt")
+md5sums=('6fc3be4aed9fead1f2038fb3d2837854'
+         '599cf91b33571e942d3ba5f9623b8011')
+sha256sums=('2f002955d854868a2fd87bcea8902662a4f7089f07d83b490403d00034e1d9fd'
+            '0451b634c56ded90b29cd5e40295bcf24bd5224f5ffd7c5f1458535eb90ba85f')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+
+  install -Dm644 "$_pkgname-LICENSE" "$pkgdir/usr/share/licenses/$pkgname/LICENSE"
+}
diff --git a/BioArchLinux/r-phenomis/lilac.py b/BioArchLinux/r-phenomis/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-phenomis/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()
diff --git a/BioArchLinux/r-phenomis/lilac.yaml b/BioArchLinux/r-phenomis/lilac.yaml
new file mode 100644
index 0000000000..faf88fef4e
--- /dev/null
+++ b/BioArchLinux/r-phenomis/lilac.yaml
@@ -0,0 +1,34 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biobase
+- r-biodb
+- r-biodbchebi
+- r-data.table
+- r-futile.logger
+- r-ggplot2
+- r-ggrepel
+- r-htmlwidgets
+- r-igraph
+- r-limma
+- r-multiassayexperiment
+- r-multidataset
+- r-plotly
+- r-pmcmrplus
+- r-ranger
+- r-rcolorbrewer
+- r-ropls
+- r-summarizedexperiment
+- r-tibble
+- r-tidyr
+- r-venndiagram
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: phenomis
+  repo: bioc
+  md5: true
+- alias: r
diff --git a/lilac-extensions/lilac_r_utils.py b/lilac-extensions/lilac_r_utils.py
index 9deb557b0d..a5724e3a8e 100644
--- a/lilac-extensions/lilac_r_utils.py
+++ b/lilac-extensions/lilac_r_utils.py
@@ -195,6 +195,7 @@ license_map = {
     "BSD_3_clause + file LICENSE": "BSD",
     "BSL-1.0": "Boost",
     "CC0": "CC0-1.0",
+    "CeCILL": "CECILL-2.0",
     "EPL": "EPL",
     "GPL": "GPL",
     "GPL (>= 2)": "GPL",