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author | BioArchLinuxBot | 2023-10-20 18:06:09 +0000 |
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committer | BioArchLinuxBot | 2023-10-20 18:06:09 +0000 |
commit | 156306be5bac4fbc643dc15c895c23b95e595c26 (patch) | |
tree | 9129aff926218664c60657c5f93f3631e8314744 | |
parent | 52dea2d0975bba465d7e73fe28384a271a0188aa (diff) | |
download | aur-156306be5bac4fbc643dc15c895c23b95e595c26.tar.gz |
[lilac] updated to 2.12.2-2
-rw-r--r-- | .SRCINFO | 20 | ||||
-rw-r--r-- | PKGBUILD | 58 | ||||
-rw-r--r-- | fix-build.patch | 21 |
3 files changed, 69 insertions, 30 deletions
@@ -1,21 +1,20 @@ pkgbase = r-flowcore pkgdesc = flowCore: Basic structures for flow cytometry data pkgver = 2.12.2 - pkgrel = 1 + pkgrel = 2 url = https://bioconductor.org/packages/flowCore arch = x86_64 license = Artistic2.0 - depends = gcc - depends = make - depends = r - depends = r-bh + checkdepends = r-flowworkspacedata + checkdepends = r-testthat + makedepends = r-bh + makedepends = r-cpp11 + makedepends = r-rprotobuflib depends = r-biobase depends = r-biocgenerics - depends = r-cpp11 depends = r-cytolib depends = r-matrixstats depends = r-rcpp - depends = r-rprotobuflib depends = r-s4vectors optdepends = r-flowstats optdepends = r-flowviz @@ -27,10 +26,11 @@ pkgbase = r-flowcore optdepends = r-opencyto optdepends = r-rgraphviz optdepends = r-testthat - options = !lto - options = !buildflags - options = staticlibs source = https://bioconductor.org/packages/release/bioc/src/contrib/flowCore_2.12.2.tar.gz + source = fix-build.patch + md5sums = 92bb3f604d43aef47d1b8d4ecbb5f28d + md5sums = 219c62c718ad269fd5e832397a354e83 sha256sums = 1064a2941dbca4a25ff129ca8d62c9341b545aa070d6221987b2edeac3d57dfc + sha256sums = 73e075b8ce2f0e9f3dea2e8778c6174586b71fb3c2b64c6ded4e5fb50ccd350c pkgname = r-flowcore @@ -1,29 +1,33 @@ -# system requirements: GNU make, C++11 -# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net> +# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com> +# Contributor: Guoyi Zhang <guoyizhang at malacology dot net> +# Contributor: Nick B <Shirakawasuna at gmail _dot_com> _pkgname=flowCore _pkgver=2.12.2 pkgname=r-${_pkgname,,} -pkgver=2.12.2 -pkgrel=1 -pkgdesc='flowCore: Basic structures for flow cytometry data' -arch=('x86_64') +pkgver=${_pkgver//-/.} +pkgrel=2 +pkgdesc="flowCore: Basic structures for flow cytometry data" +arch=(x86_64) url="https://bioconductor.org/packages/${_pkgname}" -license=('Artistic2.0') +license=(Artistic2.0) depends=( - gcc - make - r - r-bh r-biobase r-biocgenerics - r-cpp11 r-cytolib r-matrixstats r-rcpp - r-rprotobuflib r-s4vectors ) +makedepends=( + r-bh + r-cpp11 + r-rprotobuflib +) +checkdepends=( + r-flowworkspacedata + r-testthat +) optdepends=( r-flowstats r-flowviz @@ -36,15 +40,29 @@ optdepends=( r-rgraphviz r-testthat ) -source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz") -sha256sums=('1064a2941dbca4a25ff129ca8d62c9341b545aa070d6221987b2edeac3d57dfc') -options=(!lto !buildflags staticlibs) +source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz" + "fix-build.patch") +md5sums=('92bb3f604d43aef47d1b8d4ecbb5f28d' + '219c62c718ad269fd5e832397a354e83') +sha256sums=('1064a2941dbca4a25ff129ca8d62c9341b545aa070d6221987b2edeac3d57dfc' + '73e075b8ce2f0e9f3dea2e8778c6174586b71fb3c2b64c6ded4e5fb50ccd350c') + +prepare() { + # fix build and remove unnecessary import from tests + patch -Np1 -i fix-build.patch +} + build() { - R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}" + mkdir -p build + R CMD INSTALL "$_pkgname" -l build +} + +check() { + cd "$_pkgname/tests" + R_LIBS="$srcdir/build" NOT_CRAN=true Rscript --vanilla testthat.R } package() { - install -dm0755 "${pkgdir}/usr/lib/R/library" - cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library" + install -d "$pkgdir/usr/lib/R/library" + cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library" } -# vim:set ts=2 sw=2 et: diff --git a/fix-build.patch b/fix-build.patch new file mode 100644 index 000000000000..feadcb4d3359 --- /dev/null +++ b/fix-build.patch @@ -0,0 +1,21 @@ +diff --git a/flowCore/src/Makevars b/flowCore/src/Makevars +index ec6344b..f04c475 100644 +--- a/flowCore/src/Makevars ++++ b/flowCore/src/Makevars +@@ -1,4 +1,4 @@ +-CXX_STD = CXX11 ++CXX_STD = CXX17 + + PKG_LIBS = `${R_HOME}/bin/Rscript -e "cytolib:::cytolib_LdFlags()"` + +diff --git a/flowCore/tests/testthat.R b/flowCore/tests/testthat.R +index c979b0d..6d81483 100644 +--- a/flowCore/tests/testthat.R ++++ b/flowCore/tests/testthat.R +@@ -1,6 +1,5 @@ + library(testthat) + library(flowCore) +-library(flowStats) + + + test_check("flowCore") |