add r-timechange, fix revbayes

BioArchLinux/cctz/PKGBUILD

@@ -0,0 +1,46 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+pkgname=cctz
+pkgver=2.3
+pkgrel=2
+pkgdesc="A C++ library for translating between absolute and civil times using the rules of a time zone"
+arch=('x86_64')
+url="https://github.com/google/cctz"
+license=('Apache')
+depends=(gcc-libs)
+makedepends=(benchmark cmake gtest)
+source=("$pkgname-$pkgver.tar.gz::https://github.com/google/cctz/archive/v${pkgver}.tar.gz")
+sha512sums=('e688ddac1bff108e8315bf94cb61483b72b0d16f601e4e1eeb0fd5c064aefe5a573eee66e8903401aa4c2be71ea9f10dd6c9a9cdf8379f5bb6073248a21a83ff')
+
+prepare() {
+  cd "$pkgname-$pkgver"
+  # Set shared library version and soversion
+  sed -i '/set_target_properties(cctz/a\ \ VERSION ${VERSION}\n  SOVERSION ${SOVERSION}' \
+      CMakeLists.txt
+
+  # Use system zoneinfo data in tests
+  sed -i 's|TZDIR=${CMAKE_CURRENT_SOURCE_DIR}/testdata/zoneinfo|TZDIR=/usr/share/zoneinfo|' \
+      CMakeLists.txt
+}
+
+build() {
+  cmake -B build -S "$pkgname-$pkgver" \
+      -DCMAKE_BUILD_TYPE='None' \
+      -DCMAKE_CXX_FLAGS_INIT=-DNDEBUG \
+      -DCMAKE_INSTALL_PREFIX='/usr' \
+      -DBUILD_SHARED_LIBS=ON \
+      -DBUILD_EXAMPLES=OFF \
+      -DVERSION="$pkgver" \
+      -DSOVERSION="${pkgver%%.*}" \
+      -Wno-dev
+  cmake --build build
+}
+
+check() {
+  cd build
+  ctest --output-on-failure
+}
+
+package() {
+  DESTDIR="$pkgdir" cmake --install build
+}

BioArchLinux/cctz/lilac.yaml

@@ -0,0 +1,14 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: sukanka
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+post_build_script: |
+  git_add_files('PKGBUILD')
+  git_commit()
+update_on:
+  - source: github
+    github: google/cctz
+    use_latest_release: true
+    prefix: 'v'

BioArchLinux/r-timechange/PKGBUILD

@@ -0,0 +1,40 @@
+# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
+
+_pkgname=timechange
+_pkgver=0.1.1
+pkgname=r-${_pkgname,,}
+pkgver=${_pkgver//[:-]/.}
+pkgrel=1
+pkgdesc='Efficient Manipulation of Date-Times'
+arch=('x86_64')
+url="https://cran.r-project.org/package=${_pkgname}"
+license=('GPL')
+depends=(cctz r)
+makedepends=(r-cpp11)
+checkdepends=(r-testthat)
+optdepends=(r-testthat r-knitr)
+source=("https://cran.r-project.org/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
+sha256sums=('8503919d233d7d7b81fe47692f0f2d6742ff4cae7320a5522bf98f077f5d7f70')
+
+prepare() {
+  # build against system cctz
+  sed -i -e 's/$(SHLIB): libcctz.a/$(SHLIB):/' \
+      -e 's#PKG_CPPFLAGS= -I. -I./cctz/src/#PKG_CPPFLAGS= -I.#' \
+      "$_cranname/src/Makevars"
+}
+
+build() {
+  mkdir -p build
+  R CMD INSTALL "${_cranname}" -l "${srcdir}/build"
+}
+
+check() {
+  cd "${_cranname}/tests"
+  R_LIBS="${srcdir}/build" NOT_CRAN=true Rscript --vanilla testthat.R
+}
+
+package() {
+  install -dm0755 "${pkgdir}/usr/lib/R/library"
+
+  cp -a --no-preserve=ownership "build/${_cranname}" "${pkgdir}/usr/lib/R/library"
+}

BioArchLinux/r-timechange/lilac.yaml

@@ -0,0 +1,15 @@
+build_prefix: extra-x86_64
+maintainers:
+  - github: sukanka
+pre_build_script: |
+  update_pkgver_and_pkgrel(_G.newver.lstrip('v'))
+  run_cmd(['updpkgsums'])
+post_build_script: |
+  git_add_files('PKGBUILD')
+  git_commit()
+repo_depends:
+  - r-cpp11
+update_on:
+  - regex: timechange_([\d._-]+).tar.gz
+    source: regex
+    url: https://cran.r-project.org/package=timechange

BioArchLinux/revbayes-mpi/PKGBUILD

@@ -1,7 +1,7 @@
 pkgname=revbayes-mpi
 _pkgname=revbayes
 pkgver=1.2.0
-pkgrel=3
+pkgrel=4
 pkgdesc="Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language https://doi.org/10.1093/sysbio/syw021"
 arch=(x86_64)
 url="https://github.com/revbayes/revbayes"
@@ -9,6 +9,7 @@ license=(GPL3)
 depends=('gcc-libs' 'boost-libs' 'openlibm' 'openmpi')
 makedepends=('boost' 'meson' 'ninja' 'cmake' 'git')
 conflicts=('lrzsz' 'revbayes-mpi')
+provides=('revbayes')
 source=("git+$url.git#tag=v$pkgver")
 md5sums=('SKIP')
 
@@ -20,7 +21,9 @@ prepare() {
 
 build() {
   cd $srcdir/$_pkgname
-  arch-meson build -Dmpi=true
+  CXXFLAGS="${CXXFLAGS} -std=c++14" arch-meson build \
+  --buildtype      release \
+  -Dmpi=true
   ninja -C build
 }
 
@@ -28,5 +31,3 @@ package() {
   cd $srcdir/$_pkgname
   DESTDIR="${pkgdir}" ninja -C build install
 }
-
-

BioArchLinux/revbayes/PKGBUILD

@@ -1,6 +1,6 @@
 pkgname=revbayes
 pkgver=1.2.0
-pkgrel=4
+pkgrel=5
 pkgdesc="Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language https://doi.org/10.1093/sysbio/syw021"
 arch=(x86_64)
 url="https://github.com/revbayes/revbayes"
@@ -19,7 +19,8 @@ prepare() {
 
 build() {
   cd $srcdir/$pkgname
-  arch-meson build
+  CXXFLAGS="${CXXFLAGS} -std=c++14" arch-meson build \
+  --buildtype      release
   ninja -C build
 }
 
@@ -27,5 +28,3 @@ package() {
   cd $srcdir/$pkgname
   DESTDIR="${pkgdir}" ninja -C build install
 }
-
-