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r-cytolib: use metadata checks
This commit is contained in:
Pekka Ristola
parent
ba82312638
commit
57c8f02a66
4 changed files with 143 additions and 28 deletions
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@ -1,37 +1,53 @@
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# system requirements: GNU make, C++11
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# Maintainer: Guoyi Zhang <guoyizhang at malacology dot net>
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# Maintainer: Pekka Ristola <pekkarr [at] protonmail [dot] com>
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# Contributor: Guoyi Zhang <guoyizhang at malacology dot net>
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_pkgname=cytolib
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_pkgver=2.12.1
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pkgname=r-${_pkgname,,}
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pkgver=2.12.1
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pkgver=${_pkgver//-/.}
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pkgrel=1
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pkgdesc='C++ infrastructure for representing and interacting with the gated cytometry data'
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arch=('x86_64')
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pkgdesc="C++ infrastructure for representing and interacting with the gated cytometry data"
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arch=(x86_64)
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url="https://bioconductor.org/packages/${_pkgname}"
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license=('custom')
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license=(AGPL3)
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depends=(
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gcc
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make
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r
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boost-libs
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hdf5
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lapack
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protobuf
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r-rprotobuflib
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)
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makedepends=(
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boost
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r-bh
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r-rhdf5lib
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r-rprotobuflib
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)
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optdepends=(
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r-knitr
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r-rmarkdown
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)
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source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz")
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sha256sums=('1fcf5c4f45411321fd4fd8b8a0ace9955ab195c8f1a3fdcf037f8b345311db55')
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source=("https://bioconductor.org/packages/release/bioc/src/contrib/${_pkgname}_${_pkgver}.tar.gz"
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"shared-cytolib.patch")
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md5sums=('0d7e3b666779431c8cd3dc79e507cef3'
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'0447368b51efaea7ab68b056b4c2b602')
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sha256sums=('1fcf5c4f45411321fd4fd8b8a0ace9955ab195c8f1a3fdcf037f8b345311db55'
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'3fd80ac3109153df3619d0b481aa5797b9393300b6f82babb721dea8a2c55b45')
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prepare() {
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# build cytolib as a shared library
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patch -Np1 -i shared-cytolib.patch
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}
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build() {
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R CMD INSTALL ${_pkgname}_${_pkgver}.tar.gz -l "${srcdir}"
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mkdir -p build
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R CMD INSTALL "$_pkgname" -l build
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}
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package() {
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install -dm0755 "${pkgdir}/usr/lib/R/library"
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cp -a --no-preserve=ownership "${_pkgname}" "${pkgdir}/usr/lib/R/library"
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install -Dm644 "${_pkgname}/LICENSE" -t "${pkgdir}/usr/share/licenses/${pkgname}"
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install -d "$pkgdir/usr/lib/R/library"
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cp -a --no-preserve=ownership "build/$_pkgname" "$pkgdir/usr/lib/R/library"
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# install shared library
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install -Dm755 -t "$pkgdir/usr/lib" "$_pkgname/src/libcytolib.so.$_pkgver"
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ln -s "libcytolib.so.$_pkgver" "$pkgdir/usr/lib/libcytolib.so"
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}
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# vim:set ts=2 sw=2 et:
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@ -1,12 +1,17 @@
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#!/usr/bin/env python3
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from lilaclib import *
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import os
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import sys
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sys.path.append(os.path.normpath(f'{__file__}/../../../lilac-extensions'))
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from lilac_r_utils import r_pre_build
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def pre_build():
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for line in edit_file('PKGBUILD'):
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if line.startswith('_pkgver='):
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line = f'_pkgver={_G.newver}'
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print(line)
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update_pkgver_and_pkgrel(_G.newver.replace(':', '.').replace('-', '.'))
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r_pre_build(
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_G,
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expect_license = "AGPL-3.0-only",
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expect_systemrequirements = "GNU make, C++11",
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)
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def post_build():
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git_pkgbuild_commit()
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@ -1,13 +1,39 @@
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build_prefix: extra-x86_64
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maintainers:
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- github: starsareintherose
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email: kuoi@bioarchlinux.org
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- github: pekkarr
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email: pekkarr@protonmail.com
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repo_depends:
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- r-rprotobuflib
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repo_makedepends:
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- r-bh
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- r-rhdf5lib
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- r-rprotobuflib
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update_on:
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- regex: cytolib_([\d._-]+).tar.gz
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source: regex
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url: https://bioconductor.org/packages/cytolib
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- source: rpkgs
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pkgname: cytolib
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repo: bioc
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md5: true
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- alias: r
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- source: alpm
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alpm: boost-libs
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repo: extra
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provided: libboost_filesystem.so
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strip_release: true
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- source: alpmfiles
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pkgname: hdf5
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filename: usr/lib/libhdf5\.so\.([^.]+)
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repo: extra
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- source: alpmfiles
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pkgname: hdf5
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filename: usr/lib/libhdf5_cpp\.so\.([^.]+)
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repo: extra
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- source: alpmfiles
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pkgname: lapack
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filename: usr/lib/liblapack\.so\.([^.]+)
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repo: extra
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- source: alpm
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alpm: protobuf
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repo: extra
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provided: libprotobuf.so
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strip_release: true
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update_on_build:
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- pkgbase: r-rprotobuflib
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68
BioArchLinux/r-cytolib/shared-cytolib.patch
Normal file
68
BioArchLinux/r-cytolib/shared-cytolib.patch
Normal file
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@ -0,0 +1,68 @@
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diff --git a/cytolib/R/build.R b/cytolib/R/build.R
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index 779fb83..6e42d7a 100644
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--- a/cytolib/R/build.R
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+++ b/cytolib/R/build.R
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@@ -20,10 +20,7 @@ CxxFlags <- function() {
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#' @export
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#' @importFrom RProtoBufLib LdFlags
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cytolib_LdFlags <- function() {
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- libDir <- "lib/"
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- if (.Platform$OS.type == "windows")
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- libDir <- paste(libDir, .Platform$r_arch, "/", sep="")
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- cat(asBuildPath(system.file(paste(libDir, "libcytolib.a", sep = ""), package = "cytolib")))
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+ cat("-lcytolib -lboost_filesystem -lboost_system")
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}
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diff --git a/cytolib/src/Makevars.in b/cytolib/src/Makevars.in
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index 6d806e4..5888f8c 100644
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--- a/cytolib/src/Makevars.in
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+++ b/cytolib/src/Makevars.in
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@@ -8,40 +8,25 @@ ifneq (,)
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This makefile requires GNU Make.
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endif
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-
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-CXX_STD = CXX11
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-boost_sys_src=${wildcard boost/libs/system/src/*.cpp}
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-boost_sys_objs=${boost_sys_src:.cpp=.o}
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-boost_fs_src=${wildcard boost/libs/filesystem/src/*.cpp}
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-boost_fs_objs=${boost_fs_src:.cpp=.o}
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+CXX_STD = CXX17
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PKG_CPPFLAGS =-DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED #the last to flagsare needed to compile bundled boost file system library 1.78
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cytolib_src=${wildcard *.cpp}
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cytolib_objs=${cytolib_src:.cpp=.o}
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-BOOSTFSLIB = libboost_fs.a
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-USERDIR = ${R_PACKAGE_DIR}/lib${R_ARCH}
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-USERLIB = ${USERDIR}/libcytolib.a
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+USERLIB = libcytolib.so.@CYTOLIB_VERSION@
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OBJECTS=dummy.o
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-#needs to wrap in $(shell) to strip the quotes returned by rhdf5lib::pkgconfig
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-FSLIB = ${boost_fs_objs} ${boost_sys_objs}
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+CLINK_CPPFLAGS := -I/usr/lib/R/library/RProtoBufLib/include
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+RPROTOBUF_LIBS := $(shell Rscript -e "RProtoBufLib::LdFlags()")
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+all: $(SHLIB) $(USERLIB)
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-all: $(SHLIB)
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-
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-$(SHLIB): $(USERLIB)
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-
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-$(USERLIB): ${boost_fs_objs} ${cytolib_objs}
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- mkdir -p "${USERDIR}"
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- $(AR) rs "${USERLIB}" ${cytolib_objs} ${boost_fs_objs} ${boost_sys_objs}
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-
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-$(boost_fs_objs): ${boost_sys_objs}
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-
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+$(USERLIB): $(cytolib_objs)
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+ $(CC) -shared $(LDFLAGS) -Wl,-soname=$(USERLIB) -o $@ $^ -lboost_filesystem -lboost_system -lhdf5_cpp -lhdf5 -llapack $(RPROTOBUF_LIBS) $(LIBR)
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clean:
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rm -f $(OBJECTS) ${cytolib_objs} ${boost_fs_objs} ${boost_sys_objs} $(SHLIB)
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-
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