guix-devel/guix/build/r-build-system.scm

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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (guix build r-build-system)
#:use-module ((guix build gnu-build-system) #:prefix gnu:)
#:use-module (guix build utils)
#:use-module (ice-9 match)
#:use-module (ice-9 ftw)
#:use-module (ice-9 popen)
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-26)
#:use-module (srfi srfi-35)
#:export (%standard-phases
r-build))
;; Commentary:
;;
;; Builder-side code of the standard build procedure for R packages.
;;
;; Code:
(define (invoke-r command params)
(apply invoke "R" "CMD" command params))
(define (pipe-to-r command params)
(let ((port (apply open-pipe* OPEN_WRITE "R" params)))
(display command port)
(let ((code (status:exit-val (close-pipe port))))
(unless (zero? code)
(raise (condition ((@@ (guix build utils) &invoke-error)
(program "R")
(arguments (cons command params))
(exit-status (status:exit-val code))
(term-signal (status:term-sig code))
(stop-signal (status:stop-sig code)))))))))
(define (generate-site-path inputs)
(string-join (map (match-lambda
((_ . path)
(string-append path "/site-library")))
;; Restrict to inputs beginning with "r-".
(filter (match-lambda
((name . _)
(string-prefix? "r-" name)))
inputs))
":"))
(define* (check #:key test-target inputs outputs tests? #:allow-other-keys)
"Run the test suite of a given R package."
(let* ((libdir (string-append (assoc-ref outputs "out") "/site-library/"))
;; R package names are case-sensitive and cannot be derived from the
;; Guix package name. The exact package name is required as an
;; argument to tools::testInstalledPackage, which runs the tests
;; for a package given its name and the path to the “library” (a
;; location for a collection of R packages) containing it.
;; Since there can only be one R package in any collection (=
;; “library”), the name of the only directory in the collection path
;; is the original name of the R package.
(pkg-name (car (scandir libdir (negate (cut member <> '("." ".."))))))
(testdir (string-append libdir pkg-name "/" test-target))
(site-path (string-append libdir ":" (generate-site-path inputs))))
(when (and tests? (file-exists? testdir))
(setenv "R_LIBS_SITE" site-path)
(pipe-to-r (string-append "tools::testInstalledPackage(\"" pkg-name "\", "
"lib.loc = \"" libdir "\")")
'("--no-save" "--slave")))
#t))
(define* (install #:key outputs inputs (configure-flags '())
#:allow-other-keys)
"Install a given R package."
(let* ((out (assoc-ref outputs "out"))
(site-library (string-append out "/site-library/"))
(params (append configure-flags
(list "--install-tests"
(string-append "--library=" site-library)
"--built-timestamp=1970-01-01"
".")))
(site-path (string-append site-library ":"
(generate-site-path inputs))))
;; If dependencies cannot be found at install time, R will refuse to
;; install the package.
(setenv "R_LIBS_SITE" site-path)
;; Some R packages contain a configure script for which the CONFIG_SHELL
;; variable should be set.
(setenv "CONFIG_SHELL" (which "bash"))
(mkdir-p site-library)
(invoke-r "INSTALL" params)))
(define %standard-phases
(modify-phases gnu:%standard-phases
build-system/gnu: Add 'bootstrap' phase. This factorizes what has become a widespread idiom. * guix/build/gnu-build-system.scm (%bootstrap-scripts): New variable. (bootstrap): New procedure. (%standard-phases): Add it after 'unpack'. * guix/build/ant-build-system.scm (%standard-phases): Delete 'bootstrap. * guix/build/asdf-build-system.scm (%standard-phases/source) (%standard-phases): Likewise. * guix/build/cargo-build-system.scm (%standard-phases): Likewise. * guix/build/cmake-build-system.scm (%standard-phases): Likewise. * guix/build/dub-build-system.scm (%standard-phases): Likewise. * guix/build/emacs-build-system.scm (%standard-phases): Likewise. * guix/build/font-build-system.scm (%standard-phases): Likewise. * guix/build/go-build-system.scm (%standard-phases): Likewise. * guix/build/haskell-build-system.scm (%standard-phases): Likewise. * guix/build/minify-build-system.scm (%standard-phases): Likewise. * guix/build/ocaml-build-system.scm (%standard-phases): Likewise. * guix/build/perl-build-system.scm (%standard-phases): Likewise. * guix/build/python-build-system.scm (%standard-phases): Likewise. * guix/build/r-build-system.scm (%standard-phases): Likewise. * guix/build/ruby-build-system.scm (%standard-phases): Likewise. * guix/build/scons-build-system.scm (%standard-phases): Likewise. * guix/build/texlive-build-system.scm (%standard-phases): Likewise. * guix/build/waf-build-system.scm (%standard-phases): Likewise. * gnu/packages/audio.scm (faad2)[arguments]: Replace 'bootstrap. (soundtouch, cuetools, bluez-alsa): Remove 'arguments'. (cava)[arguments]: Replace 'bootstrap. * gnu/packages/backup.scm (rdup): Remove 'bootstrap. * gnu/packages/bioinformatics.scm (seek)[arguments]: Replace 'bootstrap. * gnu/packages/bioinformatics.scm (htslib-for-sambamba): Remove 'arguments'. * gnu/packages/ci.scm (hydra, cuirass): Remove 'bootstrap'. * gnu/packages/crypto.scm (libb2): Remove #:phases. * gnu/packages/databases.scm (guile-wiredtiger): Likewise. * gnu/packages/debug.scm (stress-make): Remove 'bootstrap'. * gnu/packages/documentation.scm (asciidoc): Likewise. * gnu/packages/fontutils.scm (libuninameslist): Remove 'arguments'. * gnu/packages/ftp.scm (weex): Remove 'arguments'. * gnu/packages/game-development.scm (ois): Remove 'arguments'. * gnu/packages/games.scm (pioneer): Remove 'bootstrap. * gnu/packages/gnome.scm (vte-ng, byzanz): Replace 'bootstrap. (arc-theme): Remove 'arguments'. (faba-icon-theme): Remove 'bootstrap. (arc-icon-theme): Remove 'arguments'. * gnu/packages/gnunet.scm (guile-gnunet): Likewise. * gnu/packages/gtk.scm (guile-rsvg): Likewise. * gnu/packages/guile.scm (mcron2): Remove 'bootstrap. (guile-bash): Remove #:phases. (guile-git): Remove 'bootstrap. (guile-syntax-highlight): Remove 'arguments'. (guile-sjson): Likewise. * gnu/packages/java.scm (classpath-devel): Remove 'bootstrap. * gnu/packages/kodi.scm (libdvdnav/kodi) (libdvdread/kodi, libdvdcss/kodi): Likewise. * gnu/packages/libreoffice.scm (hunspell): Remove 'arguments'. * gnu/packages/libusb.scm (hidapi): Likewise. * gnu/packages/linux.scm (bridge-utils): Rename 'bootstrap' to 'patch-stuff'; move it before 'bootstrap', without autoreconf invocation. (eudev): Rename 'bootstrap' to 'patch-file-names', without 'autogen.sh' invocation; move it before 'bootstrap. (gpm): Replace 'bootstrap'. (f2fs-tools): Remove 'arguments'. (rng-tools): Remove #:phases. * gnu/packages/messaging.scm (hexchat): Rename 'bootstrap' to 'copy-intltool-makefile'; remove "autoreconf" invocation and move before 'bootstrap'. (libmesode): Remove 'arguments'. (libstrophe): Likewise. * gnu/packages/microcom.scm (microcom): Likewise. * gnu/packages/networking.scm (libnet): Remove 'bootstrap. * gnu/packages/onc-rpc.scm (libnsl): Remove 'arguments'. * gnu/packages/package-management.scm (guix): Replace 'bootstrap. * gnu/packages/sawfish.scm (librep): Remove 'arguments'. * gnu/packages/version-control.scm (findnewest): Likewise. * gnu/packages/video.scm (liba52, handbrake, motion): Replace 'bootstrap. * gnu/packages/web.scm (fcgiwrap): Remove #:phases. (tidy): Replace 'bootstrap. (gumbo-parser): Remove #:phases. * gnu/packages/wget.scm (wget2): Replace 'bootstrap. * gnu/packages/wm.scm (i3lock-color): Remove #:phases. * gnu/packages/xdisorg.scm (xclip): Likewise. * gnu/packages/xml.scm (libxls): Replace 'bootstrap'. * gnu/packages/xorg.scm (xf86-video-freedreno) (xf86-video-intel): Remove #:phases. * gnu/packages/zile.scm (zile-on-guile): Replace 'bootstrap.
2018-03-11 21:46:30 +01:00
(delete 'bootstrap)
(delete 'configure)
(delete 'build)
(delete 'check) ; tests must be run after installation
(replace 'install install)
(add-after 'install 'check check)))
(define* (r-build #:key inputs (phases %standard-phases)
#:allow-other-keys #:rest args)
"Build the given R package, applying all of PHASES in order."
(apply gnu:gnu-build #:inputs inputs #:phases phases args))
;;; r-build-system.scm ends here