build: Add R build system.
* guix/build-system/r.scm: New file. * guix/build/r-build-system: New file. * Makefile.am (MODULES): Add new files. * doc/guix.texi (Build Systems): Document r-build-system.
This commit is contained in:
Ricardo Wurmus
parent
e1248602f9
commit
f8f3bef6aa
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@ -58,6 +58,7 @@ MODULES = \
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guix/build-system/perl.scm \
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guix/build-system/python.scm \
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guix/build-system/waf.scm \
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guix/build-system/r.scm \
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guix/build-system/ruby.scm \
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guix/build-system/trivial.scm \
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guix/ftp-client.scm \
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@ -77,6 +78,7 @@ MODULES = \
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guix/build/gnu-dist.scm \
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guix/build/perl-build-system.scm \
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guix/build/python-build-system.scm \
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guix/build/r-build-system.scm \
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guix/build/ruby-build-system.scm \
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guix/build/waf-build-system.scm \
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guix/build/haskell-build-system.scm \
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@ -2491,6 +2491,16 @@ passes flags specified by the @code{#:make-maker-flags} or
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Which Perl package is used can be specified with @code{#:perl}.
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@end defvr
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@defvr {Scheme Variable} r-build-system
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This variable is exported by @code{(guix build-system r)}. It
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implements the build procedure used by @uref{http://r-project.org, R}
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packages, which essentially is little more than running @code{R CMD
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INSTALL --library=/gnu/store/@dots{}} in an environment where
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@code{R_LIBS_SITE} contains the paths to all R package inputs. Tests
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are run after installation using the R function
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@code{tools::testInstalledPackage}.
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@end defvr
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@defvr {Scheme Variable} ruby-build-system
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This variable is exported by @code{(guix build-system ruby)}. It
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implements the RubyGems build procedure used by Ruby packages, which
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@ -0,0 +1,134 @@
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (guix build-system r)
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#:use-module (guix store)
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#:use-module (guix utils)
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#:use-module (guix packages)
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#:use-module (guix derivations)
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#:use-module (guix search-paths)
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#:use-module (guix build-system)
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#:use-module (guix build-system gnu)
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#:use-module (ice-9 match)
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#:use-module (srfi srfi-26)
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#:export (%r-build-system-modules
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r-build
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r-build-system))
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;; Commentary:
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;;
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;; Standard build procedure for R packages.
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;;
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;; Code:
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(define %r-build-system-modules
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;; Build-side modules imported by default.
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`((guix build r-build-system)
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,@%gnu-build-system-modules))
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(define (default-r)
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"Return the default R package."
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;; Lazily resolve the binding to avoid a circular dependency.
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(let ((r-mod (resolve-interface '(gnu packages statistics))))
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(module-ref r-mod 'r)))
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(define* (lower name
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#:key source inputs native-inputs outputs system target
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(r (default-r))
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#:allow-other-keys
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#:rest arguments)
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"Return a bag for NAME."
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(define private-keywords
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'(#:source #:target #:inputs #:native-inputs))
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(and (not target) ;XXX: no cross-compilation
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(bag
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(name name)
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(system system)
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(host-inputs `(,@(if source
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`(("source" ,source))
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'())
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,@inputs
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;; Keep the standard inputs of 'gnu-build-system'.
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,@(standard-packages)))
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(build-inputs `(("r" ,r)
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,@native-inputs))
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(outputs outputs)
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(build r-build)
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(arguments (strip-keyword-arguments private-keywords arguments)))))
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(define* (r-build store name inputs
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#:key
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(tests? #t)
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(test-target "tests")
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(configure-flags ''())
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(phases '(@ (guix build r-build-system)
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%standard-phases))
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(outputs '("out"))
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(search-paths '())
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(system (%current-system))
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(guile #f)
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(imported-modules %r-build-system-modules)
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(modules '((guix build r-build-system)
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(guix build utils))))
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"Build SOURCE with INPUTS."
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(define builder
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`(begin
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(use-modules ,@modules)
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(r-build #:name ,name
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#:source ,(match (assoc-ref inputs "source")
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(((? derivation? source))
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(derivation->output-path source))
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((source)
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source)
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(source
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source))
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#:configure-flags ,configure-flags
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#:system ,system
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#:tests? ,tests?
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#:test-target ,test-target
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#:phases ,phases
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#:outputs %outputs
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#:search-paths ',(map search-path-specification->sexp
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search-paths)
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#:inputs %build-inputs)))
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(define guile-for-build
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(match guile
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((? package?)
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(package-derivation store guile system #:graft? #f))
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(#f ; the default
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(let* ((distro (resolve-interface '(gnu packages commencement)))
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(guile (module-ref distro 'guile-final)))
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(package-derivation store guile system #:graft? #f)))))
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(build-expression->derivation store name builder
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#:inputs inputs
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#:system system
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#:modules imported-modules
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#:outputs outputs
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#:guile-for-build guile-for-build))
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(define r-build-system
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(build-system
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(name 'r)
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(description "The standard R build system")
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(lower lower)))
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;;; r.scm ends here
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@ -0,0 +1,112 @@
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015 Ricardo Wurmus <rekado@elephly.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (guix build r-build-system)
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#:use-module ((guix build gnu-build-system) #:prefix gnu:)
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#:use-module (guix build utils)
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#:use-module (ice-9 match)
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#:use-module (ice-9 ftw)
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#:use-module (ice-9 popen)
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#:use-module (srfi srfi-1)
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#:use-module (srfi srfi-26)
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#:export (%standard-phases
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r-build))
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;; Commentary:
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;;
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;; Builder-side code of the standard build procedure for R packages.
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;;
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;; Code:
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(define (invoke-r command params)
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(zero? (apply system* "R" "CMD" command params)))
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(define (pipe-to-r command params)
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(let ((port (apply open-pipe* OPEN_WRITE "R" params)))
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(display command port)
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(zero? (status:exit-val (close-pipe port)))))
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(define (generate-site-path inputs)
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(string-join (map (match-lambda
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((_ . path)
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(string-append path "/site-library")))
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;; Restrict to inputs beginning with "r-".
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(filter (match-lambda
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((name . _)
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(string-prefix? "r-" name)))
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inputs))
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":"))
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(define* (check #:key test-target inputs outputs tests? #:allow-other-keys)
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"Run the test suite of a given R package."
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(let* ((libdir (string-append (assoc-ref outputs "out") "/site-library/"))
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;; R package names are case-sensitive and cannot be derived from the
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;; Guix package name. The exact package name is required as an
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;; argument to ‘tools::testInstalledPackage’, which runs the tests
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;; for a package given its name and the path to the “library” (a
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;; location for a collection of R packages) containing it.
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;; Since there can only be one R package in any collection (=
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;; “library”), the name of the only directory in the collection path
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;; is the original name of the R package.
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(pkg-name (car (scandir libdir (negate (cut member <> '("." ".."))))))
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(testdir (string-append libdir pkg-name "/" test-target))
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(site-path (string-append libdir ":" (generate-site-path inputs))))
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(if (and tests? (file-exists? testdir))
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(begin
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(setenv "R_LIBS_SITE" site-path)
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(pipe-to-r (string-append "tools::testInstalledPackage(\"" pkg-name "\", "
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"lib.loc = \"" libdir "\")")
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'("--no-save" "--slave")))
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#t)))
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(define* (install #:key outputs inputs (configure-flags '())
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#:allow-other-keys)
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"Install a given R package."
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(let* ((out (assoc-ref outputs "out"))
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(site-library (string-append out "/site-library/"))
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(params (append configure-flags
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(list "--install-tests"
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(string-append "--library=" site-library)
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".")))
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(site-path (string-append site-library ":"
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(generate-site-path inputs))))
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;; If dependencies cannot be found at install time, R will refuse to
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;; install the package.
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(setenv "R_LIBS_SITE" site-path)
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;; Some R packages contain a configure script for which the CONFIG_SHELL
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;; variable should be set.
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(setenv "CONFIG_SHELL" (which "bash"))
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(mkdir-p site-library)
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(invoke-r "INSTALL" params)))
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(define %standard-phases
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(modify-phases gnu:%standard-phases
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(delete 'configure)
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(delete 'build)
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(delete 'check) ; tests must be run after installation
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(replace 'install install)
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(add-after 'install 'check check)))
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(define* (r-build #:key inputs (phases %standard-phases)
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#:allow-other-keys #:rest args)
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"Build the given R package, applying all of PHASES in order."
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(apply gnu:gnu-build #:inputs inputs #:phases phases args))
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;;; r-build-system.scm ends here
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