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authorRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-07-31 14:47:34 +0200
committerRicardo Wurmus <ricardo.wurmus@mdc-berlin.de>2015-08-31 15:39:34 +0200
commitf8f3bef6aac4ed96bfd236567536c4b039b7bd31 (patch)
treebe52127c468938d127a229a035615815a28c3607 /guix
parente1248602f92c45a731e47e74d3612bee03eaa0da (diff)
downloadgnu-guix-f8f3bef6aac4ed96bfd236567536c4b039b7bd31.tar
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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.
Diffstat (limited to 'guix')
-rw-r--r--guix/build-system/r.scm134
-rw-r--r--guix/build/r-build-system.scm112
2 files changed, 246 insertions, 0 deletions
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