From 26d6bcdc2a4cd04beb9410d798096088c2e4b718 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sun, 15 Oct 2023 11:33:21 +0300
Subject: [PATCH] r-alabaster.matrix: init

---
 BioArchLinux/r-alabaster.matrix/PKGBUILD   | 50 ++++++++++++++++++++++
 BioArchLinux/r-alabaster.matrix/lilac.py   | 14 ++++++
 BioArchLinux/r-alabaster.matrix/lilac.yaml | 18 ++++++++
 3 files changed, 82 insertions(+)
 create mode 100644 BioArchLinux/r-alabaster.matrix/PKGBUILD
 create mode 100644 BioArchLinux/r-alabaster.matrix/lilac.py
 create mode 100644 BioArchLinux/r-alabaster.matrix/lilac.yaml

diff --git a/BioArchLinux/r-alabaster.matrix/PKGBUILD b/BioArchLinux/r-alabaster.matrix/PKGBUILD
new file mode 100644
index 0000000000..e2b73cacd2
--- /dev/null
+++ b/BioArchLinux/r-alabaster.matrix/PKGBUILD
@@ -0,0 +1,50 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=alabaster.matrix
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Load and Save Artifacts from File"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(MIT)
+depends=(
+  r-alabaster.base
+  r-delayedarray
+  r-hdf5array
+  r-rhdf5
+)
+checkdepends=(
+  r-chihaya
+  r-testthat
+)
+optdepends=(
+  r-biocgenerics
+  r-biocstyle
+  r-chihaya
+  r-knitr
+  r-s4vectors
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('4b93a993b0f4a9b3333da48a8f49ad36')
+sha256sums=('637424bdb91f4f286cc1ed64405c5ef43c8ae96f849b038477536054344e1550')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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" "$pkgdir/usr/lib/R/library"
+
+  install -d "$pkgdir/usr/share/licenses/$pkgname"
+  ln -s "/usr/lib/R/library/$_pkgname/LICENSE" "$pkgdir/usr/share/licenses/$pkgname"
+}
diff --git a/BioArchLinux/r-alabaster.matrix/lilac.py b/BioArchLinux/r-alabaster.matrix/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-alabaster.matrix/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-alabaster.matrix/lilac.yaml b/BioArchLinux/r-alabaster.matrix/lilac.yaml
new file mode 100644
index 0000000000..07877e910f
--- /dev/null
+++ b/BioArchLinux/r-alabaster.matrix/lilac.yaml
@@ -0,0 +1,18 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-alabaster.base
+- r-delayedarray
+- r-hdf5array
+- r-rhdf5
+repo_makedepends:
+- r-chihaya
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: alabaster.matrix
+  repo: bioc
+  md5: true
+- alias: r