From 6bea5bd5719344ebdce37fb5c7702075757d5d87 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 5 Dec 2023 13:35:32 +0200
Subject: [PATCH] r-scmet: init

---
 BioArchLinux/r-logitnorm/PKGBUILD   | 42 +++++++++++++++++++
 BioArchLinux/r-logitnorm/lilac.py   | 14 +++++++
 BioArchLinux/r-logitnorm/lilac.yaml | 12 ++++++
 BioArchLinux/r-scmet/PKGBUILD       | 62 +++++++++++++++++++++++++++++
 BioArchLinux/r-scmet/lilac.py       | 17 ++++++++
 BioArchLinux/r-scmet/lilac.yaml     | 34 ++++++++++++++++
 6 files changed, 181 insertions(+)
 create mode 100644 BioArchLinux/r-logitnorm/PKGBUILD
 create mode 100644 BioArchLinux/r-logitnorm/lilac.py
 create mode 100644 BioArchLinux/r-logitnorm/lilac.yaml
 create mode 100644 BioArchLinux/r-scmet/PKGBUILD
 create mode 100644 BioArchLinux/r-scmet/lilac.py
 create mode 100644 BioArchLinux/r-scmet/lilac.yaml

diff --git a/BioArchLinux/r-logitnorm/PKGBUILD b/BioArchLinux/r-logitnorm/PKGBUILD
new file mode 100644
index 0000000000..c46fb53a42
--- /dev/null
+++ b/BioArchLinux/r-logitnorm/PKGBUILD
@@ -0,0 +1,42 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=logitnorm
+_pkgver=0.8.38
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Functions for the Logitnormal Distribution"
+arch=(any)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL2)
+depends=(
+  r
+)
+checkdepends=(
+  r-runit
+)
+optdepends=(
+  r-ggplot2
+  r-knitr
+  r-markdown
+  r-reshape2
+  r-runit
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('4a1f49249dcd7a212287a1ac6b4e1921')
+sha256sums=('38f55427955625d17ea5e92267d2549f3f2a21f3c3ee228d81c181dc80d05b07')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_pkgname" -l build
+}
+
+check() {
+  cd "$_pkgname/tests"
+  R_LIBS="$srcdir/build" Rscript --vanilla doRUnit.R
+}
+
+package() {
+  install -d "$pkgdir/usr/lib/R/library"
+  cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
+}
diff --git a/BioArchLinux/r-logitnorm/lilac.py b/BioArchLinux/r-logitnorm/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-logitnorm/lilac.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-logitnorm/lilac.yaml b/BioArchLinux/r-logitnorm/lilac.yaml
new file mode 100644
index 0000000000..5124fa846c
--- /dev/null
+++ b/BioArchLinux/r-logitnorm/lilac.yaml
@@ -0,0 +1,12 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_makedepends:
+- r-runit
+update_on:
+- source: rpkgs
+  pkgname: logitnorm
+  repo: cran
+  md5: true
+- alias: r
diff --git a/BioArchLinux/r-scmet/PKGBUILD b/BioArchLinux/r-scmet/PKGBUILD
new file mode 100644
index 0000000000..de8ef302c5
--- /dev/null
+++ b/BioArchLinux/r-scmet/PKGBUILD
@@ -0,0 +1,62 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=scMET
+_pkgver=1.4.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Bayesian modelling of cell-to-cell DNA methylation heterogeneity"
+arch=(x86_64)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(GPL3)
+depends=(
+  r-assertthat
+  r-biocstyle
+  r-coda
+  r-cowplot
+  r-data.table
+  r-dplyr
+  r-ggplot2
+  r-logitnorm
+  r-matrixstats
+  r-rcpp
+  r-rcppparallel
+  r-rstan
+  r-rstantools
+  r-s4vectors
+  r-singlecellexperiment
+  r-summarizedexperiment
+  r-vgam
+  r-viridis
+)
+makedepends=(
+  r-bh
+  r-rcppeigen
+  r-stanheaders
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-knitr
+  r-rmarkdown
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('6420a2af7464f67eb676f06d20f9d5a6')
+sha256sums=('b4908e98a14b2a3ed26b52648a5ae025711676d8d06ad30a16bbfd0cc5007f2a')
+
+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-scmet/lilac.py b/BioArchLinux/r-scmet/lilac.py
new file mode 100644
index 0000000000..6cfc1b802b
--- /dev/null
+++ b/BioArchLinux/r-scmet/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_systemrequirements = "GNU make",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-scmet/lilac.yaml b/BioArchLinux/r-scmet/lilac.yaml
new file mode 100644
index 0000000000..fe58a1d975
--- /dev/null
+++ b/BioArchLinux/r-scmet/lilac.yaml
@@ -0,0 +1,34 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-assertthat
+- r-biocstyle
+- r-coda
+- r-cowplot
+- r-data.table
+- r-dplyr
+- r-ggplot2
+- r-logitnorm
+- r-matrixstats
+- r-rcpp
+- r-rcppparallel
+- r-rstan
+- r-rstantools
+- r-s4vectors
+- r-singlecellexperiment
+- r-summarizedexperiment
+- r-vgam
+- r-viridis
+repo_makedepends:
+- r-bh
+- r-rcppeigen
+- r-stanheaders
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: scMET
+  repo: bioc
+  md5: true
+- alias: r