diff --git a/BioArchLinux/cctz/PKGBUILD b/BioArchLinux/cctz/PKGBUILD new file mode 100644 index 0000000000..b13a1981a4 --- /dev/null +++ b/BioArchLinux/cctz/PKGBUILD @@ -0,0 +1,46 @@ +# Maintainer: Pekka Ristola + +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="$pkgdir" cmake --install build +} diff --git a/BioArchLinux/cctz/lilac.yaml b/BioArchLinux/cctz/lilac.yaml new file mode 100644 index 0000000000..501dda9388 --- /dev/null +++ b/BioArchLinux/cctz/lilac.yaml @@ -0,0 +1,14 @@ +build_prefix: extra-x86_64 +maintainers: + - github: sukanka +pre_build_script: | + update_pkgver_and_pkgrel(_G.newver.lstrip('v')) + run_cmd(['updpkgsums']) +post_build_script: | + git_add_files('PKGBUILD') + git_commit() +update_on: + - source: github + github: google/cctz + use_latest_release: true + prefix: 'v' diff --git a/BioArchLinux/r-timechange/PKGBUILD b/BioArchLinux/r-timechange/PKGBUILD new file mode 100644 index 0000000000..e910bcef36 --- /dev/null +++ b/BioArchLinux/r-timechange/PKGBUILD @@ -0,0 +1,40 @@ +# Maintainer: Pekka Ristola + +_pkgname=timechange +_pkgver=0.1.1 +pkgname=r-${_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" +} diff --git a/BioArchLinux/r-timechange/lilac.yaml b/BioArchLinux/r-timechange/lilac.yaml new file mode 100644 index 0000000000..65ecd93155 --- /dev/null +++ b/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 diff --git a/BioArchLinux/revbayes-mpi/PKGBUILD b/BioArchLinux/revbayes-mpi/PKGBUILD index 6431ab383a..b008ccbbc5 100644 --- a/BioArchLinux/revbayes-mpi/PKGBUILD +++ b/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 } - - diff --git a/BioArchLinux/revbayes/PKGBUILD b/BioArchLinux/revbayes/PKGBUILD index 6f526e77a9..02191ece88 100644 --- a/BioArchLinux/revbayes/PKGBUILD +++ b/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 } - -