From 78c1c67723a146763ef0c17d0bb2a8102186825d Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Sun, 22 Oct 2023 16:38:36 +0300
Subject: [PATCH] r-intact: init

---
 BioArchLinux/r-intact/PKGBUILD   | 43 ++++++++++++++++++++++++++++++++
 BioArchLinux/r-intact/lilac.py   | 17 +++++++++++++
 BioArchLinux/r-intact/lilac.yaml | 16 ++++++++++++
 3 files changed, 76 insertions(+)
 create mode 100644 BioArchLinux/r-intact/PKGBUILD
 create mode 100644 BioArchLinux/r-intact/lilac.py
 create mode 100644 BioArchLinux/r-intact/lilac.yaml

diff --git a/BioArchLinux/r-intact/PKGBUILD b/BioArchLinux/r-intact/PKGBUILD
new file mode 100644
index 0000000000..5bf77ffa38
--- /dev/null
+++ b/BioArchLinux/r-intact/PKGBUILD
@@ -0,0 +1,43 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=INTACT
+_pkgver=1.0.2
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-bdsmatrix
+  r-numderiv
+  r-squarem
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('1a64972b6c12f98b3246e1ec19e4a36d')
+sha256sums=('aa03f9c665530c65e4bef5866f13f38c561bbfc34f86dceff4dec0e26bfb68ee')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-intact/lilac.py b/BioArchLinux/r-intact/lilac.py
new file mode 100644
index 0000000000..c08ad6cea8
--- /dev/null
+++ b/BioArchLinux/r-intact/lilac.py
@@ -0,0 +1,17 @@
+#!/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,
+        expect_license = "GPL-3 + file LICENSE",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-intact/lilac.yaml b/BioArchLinux/r-intact/lilac.yaml
new file mode 100644
index 0000000000..61d3e39988
--- /dev/null
+++ b/BioArchLinux/r-intact/lilac.yaml
@@ -0,0 +1,16 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-bdsmatrix
+- r-numderiv
+- r-squarem
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: INTACT
+  repo: bioc
+  md5: true
+- alias: r