From 16b88b72eca69db46deb3bf1e293841431debda2 Mon Sep 17 00:00:00 2001
From: Guoyi Zhang <kuoi@bioarchlinux.org>
Date: Tue, 5 Mar 2024 23:37:02 +0800
Subject: [PATCH] r-ecoindr: init

---
 BioArchLinux/r-ecoindr/PKGBUILD   | 42 +++++++++++++++++++++++++++++++
 BioArchLinux/r-ecoindr/lilac.py   | 14 +++++++++++
 BioArchLinux/r-ecoindr/lilac.yaml | 16 ++++++++++++
 BioArchLinux/r-fd/PKGBUILD        | 33 ++++++++++++++++++++++++
 BioArchLinux/r-fd/lilac.py        | 14 +++++++++++
 BioArchLinux/r-fd/lilac.yaml      | 15 +++++++++++
 BioArchLinux/r-rarity/PKGBUILD    | 26 +++++++++++++++++++
 BioArchLinux/r-rarity/lilac.py    | 14 +++++++++++
 BioArchLinux/r-rarity/lilac.yaml  | 10 ++++++++
 9 files changed, 184 insertions(+)
 create mode 100644 BioArchLinux/r-ecoindr/PKGBUILD
 create mode 100644 BioArchLinux/r-ecoindr/lilac.py
 create mode 100644 BioArchLinux/r-ecoindr/lilac.yaml
 create mode 100644 BioArchLinux/r-fd/PKGBUILD
 create mode 100644 BioArchLinux/r-fd/lilac.py
 create mode 100644 BioArchLinux/r-fd/lilac.yaml
 create mode 100644 BioArchLinux/r-rarity/PKGBUILD
 create mode 100644 BioArchLinux/r-rarity/lilac.py
 create mode 100644 BioArchLinux/r-rarity/lilac.yaml

diff --git a/BioArchLinux/r-ecoindr/PKGBUILD b/BioArchLinux/r-ecoindr/PKGBUILD
new file mode 100644
index 0000000000..6e4a2c695a
--- /dev/null
+++ b/BioArchLinux/r-ecoindr/PKGBUILD
@@ -0,0 +1,42 @@
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+
+_pkgname=EcoIndR
+_pkgver=2.0
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//[:-]/.}
+pkgrel=0
+pkgdesc='Ecological Indicators'
+arch=('any')
+url="https://cran.r-project.org/package=${_pkgname}"
+license=('GPL-2.0-or-later')
+depends=(
+  r
+  r-fd
+  r-picante
+  r-rarity
+  r-splancs
+  r-vegan
+)
+optdepends=(
+  r-alphahull
+  r-geor
+  r-methods
+  r-mgcv
+  r-plotrix
+  r-raster
+  r-sf
+  r-shape
+  r-sp
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('a')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et:
diff --git a/BioArchLinux/r-ecoindr/lilac.py b/BioArchLinux/r-ecoindr/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-ecoindr/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-ecoindr/lilac.yaml b/BioArchLinux/r-ecoindr/lilac.yaml
new file mode 100644
index 0000000000..673489a84b
--- /dev/null
+++ b/BioArchLinux/r-ecoindr/lilac.yaml
@@ -0,0 +1,16 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: starsareintherose
+  email: kuoi@bioarchlinux.org
+repo_depends:
+- r-fd
+- r-picante
+- r-rarity
+- r-splancs
+- r-vegan
+update_on:
+- source: rpkgs
+  pkgname: EcoIndR
+  repo: cran
+  md5: true
+- alias: r
diff --git a/BioArchLinux/r-fd/PKGBUILD b/BioArchLinux/r-fd/PKGBUILD
new file mode 100644
index 0000000000..46ae746875
--- /dev/null
+++ b/BioArchLinux/r-fd/PKGBUILD
@@ -0,0 +1,33 @@
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+
+_pkgname=FD
+_pkgver=1.0-12.3
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//[:-]/.}
+pkgrel=0
+pkgdesc='Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology'
+arch=('x86_64')
+url="https://cran.r-project.org/package=${_pkgname}"
+license=('GPL-2.0-only')
+depends=(
+  r
+  r-ade4
+  r-ape
+  r-geometry
+  r-vegan
+)
+makedepends=(
+  gcc-fortran
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('a')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et:
diff --git a/BioArchLinux/r-fd/lilac.py b/BioArchLinux/r-fd/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-fd/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-fd/lilac.yaml b/BioArchLinux/r-fd/lilac.yaml
new file mode 100644
index 0000000000..2d4150adfe
--- /dev/null
+++ b/BioArchLinux/r-fd/lilac.yaml
@@ -0,0 +1,15 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: starsareintherose
+  email: kuoi@bioarchlinux.org
+repo_depends:
+- r-ade4
+- r-ape
+- r-geometry
+- r-vegan
+update_on:
+- source: rpkgs
+  pkgname: FD
+  repo: cran
+  md5: true
+- alias: r
diff --git a/BioArchLinux/r-rarity/PKGBUILD b/BioArchLinux/r-rarity/PKGBUILD
new file mode 100644
index 0000000000..706088de7a
--- /dev/null
+++ b/BioArchLinux/r-rarity/PKGBUILD
@@ -0,0 +1,26 @@
+# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
+
+_pkgname=Rarity
+_pkgver=1.3-8
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//[:-]/.}
+pkgrel=0
+pkgdesc='Calculation of Rarity Indices for Species and Assemblages of Species'
+arch=('any')
+url="https://cran.r-project.org/package=${_pkgname}"
+license=('GPL-2.0-or-later')
+depends=(
+  r
+)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('a')
+
+build() {
+  R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+  cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
+}
+# vim:set ts=2 sw=2 et:
diff --git a/BioArchLinux/r-rarity/lilac.py b/BioArchLinux/r-rarity/lilac.py
new file mode 100644
index 0000000000..b5cdb057c5
--- /dev/null
+++ b/BioArchLinux/r-rarity/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-rarity/lilac.yaml b/BioArchLinux/r-rarity/lilac.yaml
new file mode 100644
index 0000000000..44829c59dd
--- /dev/null
+++ b/BioArchLinux/r-rarity/lilac.yaml
@@ -0,0 +1,10 @@
+build_prefix: extra-x86_64
+maintainers:
+- github: starsareintherose
+  email: kuoi@bioarchlinux.org
+update_on:
+- source: rpkgs
+  pkgname: Rarity
+  repo: cran
+  md5: true
+- alias: r