From 86bc0d63c6323f9c8bb60b82bdae5864cd58b2c0 Mon Sep 17 00:00:00 2001
From: Pekka Ristola <pekkarr@protonmail.com>
Date: Tue, 28 Nov 2023 21:03:02 +0200
Subject: [PATCH] r-scdesign3: init

---
 BioArchLinux/r-kde1d/PKGBUILD          | 46 +++++++++++++++++++
 BioArchLinux/r-kde1d/lilac.py          | 17 +++++++
 BioArchLinux/r-kde1d/lilac.yaml        | 17 +++++++
 BioArchLinux/r-rvinecopulib/PKGBUILD   | 50 ++++++++++++++++++++
 BioArchLinux/r-rvinecopulib/lilac.py   | 17 +++++++
 BioArchLinux/r-rvinecopulib/lilac.yaml | 21 +++++++++
 BioArchLinux/r-scdesign3/PKGBUILD      | 63 ++++++++++++++++++++++++++
 BioArchLinux/r-scdesign3/lilac.py      | 14 ++++++
 BioArchLinux/r-scdesign3/lilac.yaml    | 29 ++++++++++++
 BioArchLinux/r-wdm/PKGBUILD            | 46 +++++++++++++++++++
 BioArchLinux/r-wdm/lilac.py            | 14 ++++++
 BioArchLinux/r-wdm/lilac.yaml          | 16 +++++++
 12 files changed, 350 insertions(+)
 create mode 100644 BioArchLinux/r-kde1d/PKGBUILD
 create mode 100644 BioArchLinux/r-kde1d/lilac.py
 create mode 100644 BioArchLinux/r-kde1d/lilac.yaml
 create mode 100644 BioArchLinux/r-rvinecopulib/PKGBUILD
 create mode 100644 BioArchLinux/r-rvinecopulib/lilac.py
 create mode 100644 BioArchLinux/r-rvinecopulib/lilac.yaml
 create mode 100644 BioArchLinux/r-scdesign3/PKGBUILD
 create mode 100644 BioArchLinux/r-scdesign3/lilac.py
 create mode 100644 BioArchLinux/r-scdesign3/lilac.yaml
 create mode 100644 BioArchLinux/r-wdm/PKGBUILD
 create mode 100644 BioArchLinux/r-wdm/lilac.py
 create mode 100644 BioArchLinux/r-wdm/lilac.yaml

diff --git a/BioArchLinux/r-kde1d/PKGBUILD b/BioArchLinux/r-kde1d/PKGBUILD
new file mode 100644
index 0000000000..ddf2b02fe7
--- /dev/null
+++ b/BioArchLinux/r-kde1d/PKGBUILD
@@ -0,0 +1,46 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=kde1d
+_pkgver=1.0.5
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Univariate Kernel Density Estimation"
+arch=(x86_64)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(MIT)
+depends=(
+  r-randtoolbox
+  r-rcpp
+)
+makedepends=(
+  r-bh
+  r-rcppeigen
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('72ac5e9cd260b9f2792ec2ae9186dfe8')
+sha256sums=('b5fab76a394a7819deee10afdff39ac64fccdb844735adfe51c92043016f2468')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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-kde1d/lilac.py b/BioArchLinux/r-kde1d/lilac.py
new file mode 100644
index 0000000000..b8fd4ff762
--- /dev/null
+++ b/BioArchLinux/r-kde1d/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 = "C++11",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-kde1d/lilac.yaml b/BioArchLinux/r-kde1d/lilac.yaml
new file mode 100644
index 0000000000..8f6a8fb71c
--- /dev/null
+++ b/BioArchLinux/r-kde1d/lilac.yaml
@@ -0,0 +1,17 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-randtoolbox
+- r-rcpp
+repo_makedepends:
+- r-bh
+- r-rcppeigen
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: kde1d
+  repo: cran
+  md5: true
+- alias: r
diff --git a/BioArchLinux/r-rvinecopulib/PKGBUILD b/BioArchLinux/r-rvinecopulib/PKGBUILD
new file mode 100644
index 0000000000..03a8b3a479
--- /dev/null
+++ b/BioArchLinux/r-rvinecopulib/PKGBUILD
@@ -0,0 +1,50 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=rvinecopulib
+_pkgver=0.6.3.1.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="High Performance Algorithms for Vine Copula Modeling"
+arch=(x86_64)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(GPL3)
+depends=(
+  r-assertthat
+  r-kde1d
+  r-rcpp
+)
+makedepends=(
+  r-bh
+  r-rcppeigen
+  r-rcppthread
+  r-wdm
+)
+checkdepends=(
+  r-ggraph
+  r-testthat
+)
+optdepends=(
+  r-ggplot2
+  r-ggraph
+  r-igraph
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('a4b38ea99d4a5a6dc167a34b84028b15')
+sha256sums=('df95d007552e7fa30aefad90a86acf5e14f6fe1e363ed4c71a74d501a08cbf32')
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "$_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" "$pkgdir/usr/lib/R/library"
+}
diff --git a/BioArchLinux/r-rvinecopulib/lilac.py b/BioArchLinux/r-rvinecopulib/lilac.py
new file mode 100644
index 0000000000..b5d481821a
--- /dev/null
+++ b/BioArchLinux/r-rvinecopulib/lilac.py
@@ -0,0 +1,17 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(
+        _G,
+        expect_license = "GPL-3 | file LICENSE",
+    )
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-rvinecopulib/lilac.yaml b/BioArchLinux/r-rvinecopulib/lilac.yaml
new file mode 100644
index 0000000000..2191983f2a
--- /dev/null
+++ b/BioArchLinux/r-rvinecopulib/lilac.yaml
@@ -0,0 +1,21 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-assertthat
+- r-kde1d
+- r-rcpp
+repo_makedepends:
+- r-bh
+- r-rcppeigen
+- r-rcppthread
+- r-wdm
+- r-ggraph
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: rvinecopulib
+  repo: cran
+  md5: true
+- alias: r
diff --git a/BioArchLinux/r-scdesign3/PKGBUILD b/BioArchLinux/r-scdesign3/PKGBUILD
new file mode 100644
index 0000000000..b9eb511dc9
--- /dev/null
+++ b/BioArchLinux/r-scdesign3/PKGBUILD
@@ -0,0 +1,63 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=scDesign3
+_pkgver=1.0.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics"
+arch=(any)
+url="https://bioconductor.org/packages/${_pkgname}"
+license=(MIT)
+depends=(
+  r-biocparallel
+  r-dplyr
+  r-gamlss
+  r-gamlss.dist
+  r-ggplot2
+  r-irlba
+  r-matrixstats
+  r-mclust
+  r-mvtnorm
+  r-pbmcapply
+  r-rvinecopulib
+  r-singlecellexperiment
+  r-summarizedexperiment
+  r-tibble
+  r-umap
+  r-viridis
+)
+checkdepends=(
+  r-testthat
+)
+optdepends=(
+  r-biocstyle
+  r-igraph
+  r-knitr
+  r-mvnfast
+  r-refmanager
+  r-rmarkdown
+  r-sessioninfo
+  r-testthat
+)
+source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('84c2f07635607b2167f24750f952745a')
+sha256sums=('229a556fd77e2ec861d1b4e1f915b0fe4e1095095cad380319680a32a1b4d5dc')
+
+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/$pkgname"
+}
diff --git a/BioArchLinux/r-scdesign3/lilac.py b/BioArchLinux/r-scdesign3/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-scdesign3/lilac.py
@@ -0,0 +1,14 @@
+#!/usr/bin/env python3
+from lilaclib import *
+
+import os
+import sys
+sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
+from lilac_r_utils import r_pre_build
+
+def pre_build():
+    r_pre_build(_G)
+
+def post_build():
+    git_pkgbuild_commit()
+    update_aur_repo()
diff --git a/BioArchLinux/r-scdesign3/lilac.yaml b/BioArchLinux/r-scdesign3/lilac.yaml
new file mode 100644
index 0000000000..bd55a08f2a
--- /dev/null
+++ b/BioArchLinux/r-scdesign3/lilac.yaml
@@ -0,0 +1,29 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-biocparallel
+- r-dplyr
+- r-gamlss
+- r-gamlss.dist
+- r-ggplot2
+- r-irlba
+- r-matrixstats
+- r-mclust
+- r-mvtnorm
+- r-pbmcapply
+- r-rvinecopulib
+- r-singlecellexperiment
+- r-summarizedexperiment
+- r-tibble
+- r-umap
+- r-viridis
+repo_makedepends:
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: scDesign3
+  repo: bioc
+  md5: true
+- alias: r
diff --git a/BioArchLinux/r-wdm/PKGBUILD b/BioArchLinux/r-wdm/PKGBUILD
new file mode 100644
index 0000000000..baf523c397
--- /dev/null
+++ b/BioArchLinux/r-wdm/PKGBUILD
@@ -0,0 +1,46 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=wdm
+_pkgver=0.2.4
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//-/.}
+pkgrel=1
+pkgdesc="Weighted Dependence Measures"
+arch=(x86_64)
+url="https://cran.r-project.org/package=${_pkgname}"
+license=(MIT)
+depends=(
+  r-rcpp
+)
+checkdepends=(
+  r-copula
+  r-hmisc
+  r-testthat
+)
+optdepends=(
+  r-copula
+  r-covr
+  r-hmisc
+  r-testthat
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+md5sums=('53467d0a74a2b78738d526fe078996d9')
+sha256sums=('e2d19c04ea2fb9394cc2b61899c7fd21ae7c6d5825bfdcb74822c7243cd335d3')
+
+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-wdm/lilac.py b/BioArchLinux/r-wdm/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-wdm/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-wdm/lilac.yaml b/BioArchLinux/r-wdm/lilac.yaml
new file mode 100644
index 0000000000..07f63912c7
--- /dev/null
+++ b/BioArchLinux/r-wdm/lilac.yaml
@@ -0,0 +1,16 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: pekkarr
+  email: pekkarr@protonmail.com
+repo_depends:
+- r-rcpp
+repo_makedepends:
+- r-copula
+- r-hmisc
+- r-testthat
+update_on:
+- source: rpkgs
+  pkgname: wdm
+  repo: cran
+  md5: true
+- alias: r