diff options
| -rw-r--r-- | Makefile.am | 2 | ||||
| -rw-r--r-- | doc/guix.texi | 10 | ||||
| -rw-r--r-- | guix/build-system/r.scm | 134 | ||||
| -rw-r--r-- | guix/build/r-build-system.scm | 112 |
4 files changed, 258 insertions, 0 deletions
diff --git a/Makefile.am b/Makefile.am index af41ea57c8..711181b7cf 100644 --- a/Makefile.am +++ b/Makefile.am @@ -58,6 +58,7 @@ MODULES = \ guix/build-system/perl.scm \ guix/build-system/python.scm \ guix/build-system/waf.scm \ + guix/build-system/r.scm \ guix/build-system/ruby.scm \ guix/build-system/trivial.scm \ guix/ftp-client.scm \ @@ -77,6 +78,7 @@ MODULES = \ guix/build/gnu-dist.scm \ guix/build/perl-build-system.scm \ guix/build/python-build-system.scm \ + guix/build/r-build-system.scm \ guix/build/ruby-build-system.scm \ guix/build/waf-build-system.scm \ guix/build/haskell-build-system.scm \ diff --git a/doc/guix.texi b/doc/guix.texi index 4dbedb15ec..c42aedbbb0 100644 --- a/doc/guix.texi +++ b/doc/guix.texi @@ -2491,6 +2491,16 @@ passes flags specified by the @code{#:make-maker-flags} or Which Perl package is used can be specified with @code{#:perl}. @end defvr +@defvr {Scheme Variable} r-build-system +This variable is exported by @code{(guix build-system r)}. It +implements the build procedure used by @uref{http://r-project.org, R} +packages, which essentially is little more than running @code{R CMD +INSTALL --library=/gnu/store/@dots{}} in an environment where +@code{R_LIBS_SITE} contains the paths to all R package inputs. Tests +are run after installation using the R function +@code{tools::testInstalledPackage}. +@end defvr + @defvr {Scheme Variable} ruby-build-system This variable is exported by @code{(guix build-system ruby)}. It implements the RubyGems build procedure used by Ruby packages, which diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm new file mode 100644 index 0000000000..4daec5eb66 --- /dev/null +++ b/guix/build-system/r.scm @@ -0,0 +1,134 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2015 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-system r) + #:use-module (guix store) + #:use-module (guix utils) + #:use-module (guix packages) + #:use-module (guix derivations) + #:use-module (guix search-paths) + #:use-module (guix build-system) + #:use-module (guix build-system gnu) + #:use-module (ice-9 match) + #:use-module (srfi srfi-26) + #:export (%r-build-system-modules + r-build + r-build-system)) + +;; Commentary: +;; +;; Standard build procedure for R packages. +;; +;; Code: + +(define %r-build-system-modules + ;; Build-side modules imported by default. + `((guix build r-build-system) + ,@%gnu-build-system-modules)) + +(define (default-r) + "Return the default R package." + ;; Lazily resolve the binding to avoid a circular dependency. + (let ((r-mod (resolve-interface '(gnu packages statistics)))) + (module-ref r-mod 'r))) + +(define* (lower name + #:key source inputs native-inputs outputs system target + (r (default-r)) + #:allow-other-keys + #:rest arguments) + "Return a bag for NAME." + (define private-keywords + '(#:source #:target #:inputs #:native-inputs)) + + (and (not target) ;XXX: no cross-compilation + (bag + (name name) + (system system) + (host-inputs `(,@(if source + `(("source" ,source)) + '()) + ,@inputs + + ;; Keep the standard inputs of 'gnu-build-system'. + ,@(standard-packages))) + (build-inputs `(("r" ,r) + ,@native-inputs)) + (outputs outputs) + (build r-build) + (arguments (strip-keyword-arguments private-keywords arguments))))) + +(define* (r-build store name inputs + #:key + (tests? #t) + (test-target "tests") + (configure-flags ''()) + (phases '(@ (guix build r-build-system) + %standard-phases)) + (outputs '("out")) + (search-paths '()) + (system (%current-system)) + (guile #f) + (imported-modules %r-build-system-modules) + (modules '((guix build r-build-system) + (guix build utils)))) + "Build SOURCE with INPUTS." + (define builder + `(begin + (use-modules ,@modules) + (r-build #:name ,name + #:source ,(match (assoc-ref inputs "source") + (((? derivation? source)) + (derivation->output-path source)) + ((source) + source) + (source + source)) + #:configure-flags ,configure-flags + #:system ,system + #:tests? ,tests? + #:test-target ,test-target + #:phases ,phases + #:outputs %outputs + #:search-paths ',(map search-path-specification->sexp + search-paths) + #:inputs %build-inputs))) + + (define guile-for-build + (match guile + ((? package?) + (package-derivation store guile system #:graft? #f)) + (#f ; the default + (let* ((distro (resolve-interface '(gnu packages commencement))) + (guile (module-ref distro 'guile-final))) + (package-derivation store guile system #:graft? #f))))) + + (build-expression->derivation store name builder + #:inputs inputs + #:system system + #:modules imported-modules + #:outputs outputs + #:guile-for-build guile-for-build)) + +(define r-build-system + (build-system + (name 'r) + (description "The standard R build system") + (lower lower))) + +;;; r.scm ends here diff --git a/guix/build/r-build-system.scm b/guix/build/r-build-system.scm new file mode 100644 index 0000000000..3fc13eb835 --- /dev/null +++ b/guix/build/r-build-system.scm @@ -0,0 +1,112 @@ +;;; GNU Guix --- Functional package management for GNU +;;; Copyright © 2015 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) + #:export (%standard-phases + r-build)) + +;; Commentary: +;; +;; Builder-side code of the standard build procedure for R packages. +;; +;; Code: + +(define (invoke-r command params) + (zero? (apply system* "R" "CMD" command params))) + +(define (pipe-to-r command params) + (let ((port (apply open-pipe* OPEN_WRITE "R" params))) + (display command port) + (zero? (status:exit-val (close-pipe port))))) + +(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)))) + (if (and tests? (file-exists? testdir)) + (begin + (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) + "."))) + (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 + (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 |