From ae0b9d706fc5578655b8659f6b708946484cf59e Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 28 Nov 2023 13:45:21 +0200
Subject: [PATCH] r-qtlexperiment: init

---
 BioArchLinux/r-qtlexperiment/PKGBUILD   | 52 +++++++++++++++++++++++++
 BioArchLinux/r-qtlexperiment/lilac.py   | 14 +++++++
 BioArchLinux/r-qtlexperiment/lilac.yaml | 24 ++++++++++++
 3 files changed, 90 insertions(+)
 create mode 100644 BioArchLinux/r-qtlexperiment/PKGBUILD
 create mode 100644 BioArchLinux/r-qtlexperiment/lilac.py
 create mode 100644 BioArchLinux/r-qtlexperiment/lilac.yaml

diff --git a/BioArchLinux/r-qtlexperiment/PKGBUILD b/BioArchLinux/r-qtlexperiment/PKGBUILD
new file mode 100644
index 0000000000..19f6d4955f
--- /dev/null
+++ b/BioArchLinux/r-qtlexperiment/PKGBUILD
@@ -0,0 +1,52 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=QTLExperiment
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="S4 classes for QTL summary statistics and metadata"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-ashr
+  r-biocgenerics
+  r-checkmate
+  r-collapse
+  r-dplyr
+  r-rlang
+  r-s4vectors
+  r-summarizedexperiment
+  r-tibble
+  r-tidyr
+  r-vroom
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-covr
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('fe7642e0952c4c68e5417906dfb66fb3')
+sha256sums=('9d216fb41c637fa3118d42f4475638fab0f5d3a3b6e1e1ecf6244d78388ecc74')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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"
+}
diff --git a/BioArchLinux/r-qtlexperiment/lilac.py b/BioArchLinux/r-qtlexperiment/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-qtlexperiment/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-qtlexperiment/lilac.yaml b/BioArchLinux/r-qtlexperiment/lilac.yaml
new file mode 100644
index 0000000000..730c24ca2d
--- /dev/null
+++ b/BioArchLinux/r-qtlexperiment/lilac.yaml
@@ -0,0 +1,24 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-ashr
+- r-biocgenerics
+- r-checkmate
+- r-collapse
+- r-dplyr
+- r-rlang
+- r-s4vectors
+- r-summarizedexperiment
+- r-tibble
+- r-tidyr
+- r-vroom
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: QTLExperiment
+  repo: bioc
+  md5: true
+- alias: r