From a507010723ba8a8ca618e90b17b073f811e5c4d0 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sun, 17 Sep 2023 13:09:24 +0300
Subject: [PATCH] r-mvabund: init, checkdependency of r-glmmtmb

---
 BioArchLinux/r-mvabund/PKGBUILD   | 44 +++++++++++++++++++++++++++++++
 BioArchLinux/r-mvabund/lilac.py   | 14 ++++++++++
 BioArchLinux/r-mvabund/lilac.yaml | 21 +++++++++++++++
 3 files changed, 79 insertions(+)
 create mode 100644 BioArchLinux/r-mvabund/PKGBUILD
 create mode 100644 BioArchLinux/r-mvabund/lilac.py
 create mode 100644 BioArchLinux/r-mvabund/lilac.yaml

diff --git a/BioArchLinux/r-mvabund/PKGBUILD b/BioArchLinux/r-mvabund/PKGBUILD
new file mode 100644
index 0000000000..5fe22408db
--- /dev/null
+++ b/BioArchLinux/r-mvabund/PKGBUILD
@@ -0,0 +1,44 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=mvabund
+_pkgver=4.2.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Statistical Methods for Analysing Multivariate Abundance Data"
+arch=(x86_64)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(LGPL)
+depends=(
+  gsl
+  r-rcpp
+  r-statmod
+  r-tweedie
+)
+makedepends=(
+  r-rcppgsl
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('5ff7cf64b64e2d8ca4df9c3d198d3cf4')
+sha256sums=('ed6946c95609443584081100cd38624d2309f7f5d210fd4b8ec12ad25bd27a06')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-mvabund/lilac.py b/BioArchLinux/r-mvabund/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-mvabund/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-mvabund/lilac.yaml b/BioArchLinux/r-mvabund/lilac.yaml
new file mode 100644
index 0000000000..faf995124b
--- /dev/null
+++ b/BioArchLinux/r-mvabund/lilac.yaml
@@ -0,0 +1,21 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-rcpp
+- r-statmod
+- r-tweedie
+repo_makedepends:
+- r-rcppgsl
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: mvabund
+  repo: cran
+  md5: true
+- alias: r
+- source: alpmfiles
+  pkgname: gsl
+  filename: usr/lib/libgsl\.so\.([^.]+)
+  repo: extra