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Re: [PATCH] R build system and CRAN importer (updated)
|
From: |
Ricardo Wurmus |
|
Subject: |
Re: [PATCH] R build system and CRAN importer (updated) |
|
Date: |
Wed, 26 Aug 2015 18:05:51 +0200 |
> I’ll send a new patch once I’ve written a couple of tests
> for all this.
Attached is the latest version of this patch set. I tried to
incorporate all suggestions and also added tests for the CRAN importer.
I have not implemented the suggested procedure ‘cran-uri’ that generates
URLs for tarballs offered through CRAN, because I couldn’t determine
whether all packages really use the same URL prefix.
~~ Ricardo
>From 1c726be7746021f5d967d12154c057391e24585d Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 24 Jul 2015 16:49:57 +0200
Subject: [PATCH 1/2] import: Add 'cran' importer.
* guix/import/cran.scm: New file.
* guix/scripts/import.scm: Add "cran" to 'importers'.
* guix/scripts/import/cran.scm: New file.
* tests/cran.scm: New file.
* Makefile.am (MODULES): Add 'guix/import/cran.scm' and
'guix/scripts/import/cran.scm'.
(SCM_TESTS): Add 'tests/cran.scm'.
* doc/guix.texi (Invoking guix import): Document it.
* po/guix/POTFILES.in: Add 'guix/scripts/import/cran.scm'.
---
Makefile.am | 3 +
doc/guix.texi | 15 ++++
guix/import/cran.scm | 193 +++++++++++++++++++++++++++++++++++++++++++
guix/scripts/import.scm | 2 +-
guix/scripts/import/cran.scm | 92 +++++++++++++++++++++
tests/cran.scm | 178 +++++++++++++++++++++++++++++++++++++++
6 files changed, 482 insertions(+), 1 deletion(-)
create mode 100644 guix/import/cran.scm
create mode 100644 guix/scripts/import/cran.scm
create mode 100644 tests/cran.scm
diff --git a/Makefile.am b/Makefile.am
index ada4cbe..8f25145 100644
--- a/Makefile.am
+++ b/Makefile.am
@@ -98,6 +98,7 @@ MODULES = \
guix/import/gnu.scm \
guix/import/snix.scm \
guix/import/cabal.scm \
+ guix/import/cran.scm \
guix/import/hackage.scm \
guix/import/elpa.scm \
guix/scripts/download.scm \
@@ -113,6 +114,7 @@ MODULES = \
guix/scripts/refresh.scm \
guix/scripts/system.scm \
guix/scripts/lint.scm \
+ guix/scripts/import/cran.scm \
guix/scripts/import/gnu.scm \
guix/scripts/import/nix.scm \
guix/scripts/import/hackage.scm \
@@ -191,6 +193,7 @@ SCM_TESTS = \
tests/packages.scm \
tests/snix.scm \
tests/hackage.scm \
+ tests/cran.scm \
tests/elpa.scm \
tests/store.scm \
tests/monads.scm \
diff --git a/doc/guix.texi b/doc/guix.texi
index f05376e..8774607 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -3891,6 +3891,21 @@ Perl module:
guix import cpan Acme::Boolean
@end example
address@hidden cran
address@hidden CRAN
+Import meta-data from @uref{http://cran.r-project.org/, CRAN}, the
+central repository for the @uref{http://r-project.org, address@hidden
+statistical and graphical environment}.
+
+Information is extracted from the HTML package description.
+
+The command command below imports meta-data for the @code{Cairo}
+R package:
+
address@hidden
+guix import cran Cairo
address@hidden example
+
@item nix
Import meta-data from a local copy of the source of the
@uref{http://nixos.org/nixpkgs/, Nixpkgs address@hidden
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
new file mode 100644
index 0000000..7d5a82f
--- /dev/null
+++ b/guix/import/cran.scm
@@ -0,0 +1,193 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 Ricardo Wurmus <address@hidden>
+;;;
+;;; 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 import cran)
+ #:use-module (ice-9 match)
+ #:use-module (ice-9 regex)
+ #:use-module (srfi srfi-1)
+ #:use-module (sxml simple)
+ #:use-module (sxml match)
+ #:use-module (sxml xpath)
+ #:use-module (guix http-client)
+ #:use-module (guix hash)
+ #:use-module (guix store)
+ #:use-module (guix base32)
+ #:use-module ((guix download) #:select (download-to-store))
+ #:use-module (guix import utils)
+ #:export (cran->guix-package))
+
+;;; Commentary:
+;;;
+;;; Generate a package declaration template for the latest version of an R
+;;; package on CRAN, using the HTML description downloaded from
+;;; cran.r-project.org.
+;;;
+;;; Code:
+
+(define string->license
+ (match-lambda
+ ("AGPL-3" 'agpl3)
+ ("Artistic-2.0" 'artistic2.0)
+ ("Apache License 2.0" 'asl2.0)
+ ("BSD_2_clause" 'bsd-2)
+ ("BSD_3_clause" 'bsd-3)
+ ("GPL-2" 'gpl2)
+ ("GPL-3" 'GPL3)
+ ("LGPL-2" 'lgpl2.0)
+ ("LGPL-2.1" 'lgpl2.1)
+ ("LGPL-3" 'lgpl3)
+ ("MIT" 'x11)
+ ((x) (string->license x))
+ ((lst ...) `(list ,@(map string->license lst)))
+ (_ #f)))
+
+(define (format-inputs names)
+ "Generate a sorted list of package inputs from a list of package NAMES."
+ (sort
+ (map (lambda (name)
+ (list name (list 'unquote (string->symbol name))))
+ names)
+ (lambda args
+ (match args
+ (((a _ ...) (b _ ...))
+ (string-ci<? a b))))))
+
+(define* (maybe-inputs package-inputs #:optional (type 'inputs))
+ "Given a list of PACKAGE-INPUTS, tries to generate the TYPE field of a
+package definition."
+ (match package-inputs
+ (()
+ '())
+ ((package-inputs ...)
+ `((,type (,'quasiquote ,(format-inputs package-inputs)))))))
+
+(define (table-datum tree label)
+ "Extract the datum node following a LABEL in the sxml table TREE. Only the
+first cell of a table row is considered a label cell."
+ ((node-pos 1)
+ ((sxpath `(xhtml:tr
+ (xhtml:td 1) ; only first cell can contain label
+ (equal? ,label)
+ ,(node-parent tree) ; go up to label cell
+ ,(node-parent tree) ; go up to matching row
+ (xhtml:td 2))) ; select second cell
+ tree)))
+
+(define %cran-url "http://cran.r-project.org/web/packages/";)
+
+(define (cran-fetch name)
+ "Return an sxml representation of the CRAN page for the R package NAME,
+or #f on failure. NAME is case-sensitive."
+ ;; This API always returns the latest release of the module.
+ (let ((cran-url (string-append %cran-url name)))
+ (false-if-exception
+ (xml->sxml (http-fetch cran-url)
+ #:trim-whitespace? #t
+ #:namespaces '((xhtml . "http://www.w3.org/1999/xhtml";))
+ #:default-entity-handler
+ (lambda (port name)
+ (case name
+ ((nbsp) " ")
+ ((ge) ">=")
+ ((gt) ">")
+ ((lt) "<")
+ (else
+ (format (current-warning-port)
+ "~a:~a:~a: undefined entitity: ~a\n"
+ cran-url (port-line port) (port-column port)
+ name)
+ (symbol->string name))))))))
+
+(define (cran-sxml->sexp sxml)
+ "Return the `package' s-expression for a CRAN package from the SXML
+representation of the package page."
+ (define (nodes->text nodeset)
+ (string-join ((sxpath '(// *text*)) nodeset) " "))
+
+ (define (guix-name name)
+ (if (string-prefix? "r-" name)
+ (string-downcase name)
+ (string-append "r-" (string-downcase name))))
+
+ (sxml-match-let*
+ (((*TOP* (xhtml:html
+ ,head
+ (xhtml:body
+ (xhtml:h2 ,name-and-synopsis)
+ (xhtml:p ,description)
+ ,summary
+ (xhtml:h4 "Downloads:") ,downloads
+ . ,rest)))
+ sxml))
+ (let* ((name (match:prefix (string-match ": " name-and-synopsis)))
+ (synopsis (match:suffix (string-match ": " name-and-synopsis)))
+ (version (nodes->text (table-datum summary "Version:")))
+ (license ((compose string->license nodes->text)
+ (table-datum summary "License:")))
+ (home-page (nodes->text ((sxpath '((xhtml:a 1)))
+ (table-datum summary "URL:"))))
+ (source-url (string-append "mirror://cran/"
+ ;; Remove double dots, because we want an
+ ;; absolute path.
+ (regexp-substitute/global
+ #f "\\.\\./"
+ (string-join
+ ((sxpath '((xhtml:a 1) @ href *text*))
+ (table-datum downloads
+ " Package source: ")))
+ 'pre 'post)))
+ (tarball (with-store store (download-to-store store source-url)))
+ (sysdepends (map match:substring
+ (list-matches
+ "[^ ]+"
+ ;; Strip off comma and parenthetical
+ ;; expressions.
+ (regexp-substitute/global
+ #f "(,|\\([^\\)]+\\))"
+ (nodes->text (table-datum summary
+ "SystemRequirements:"))
+ 'pre 'post))))
+ (imports (map guix-name
+ ((sxpath '(// xhtml:a *text*))
+ (table-datum summary "Imports:")))))
+ `(package
+ (name ,(guix-name name))
+ (version ,version)
+ (source (origin
+ (method url-fetch)
+ (uri (string-append ,@(factorize-uri source-url version)))
+ (sha256
+ (base32
+ ,(bytevector->nix-base32-string (file-sha256 tarball))))))
+ (build-system r-build-system)
+ ,@(maybe-inputs sysdepends)
+ ,@(maybe-inputs imports 'propagated-inputs)
+ (home-page ,(if (string-null? home-page)
+ (string-append %cran-url name)
+ home-page))
+ (synopsis ,synopsis)
+ ;; Use double spacing
+ (description ,(regexp-substitute/global #f "\\. \\b" description
+ 'pre ". " 'post))
+ (license ,license)))))
+
+(define (cran->guix-package package-name)
+ "Fetch the metadata for PACKAGE-NAME from cran.r-project.org, and return the
+`package' s-expression corresponding to that package, or #f on failure."
+ (let ((module-meta (cran-fetch package-name)))
+ (and=> module-meta cran-sxml->sexp)))
diff --git a/guix/scripts/import.scm b/guix/scripts/import.scm
index d0bdec1..9d8e5cb 100644
--- a/guix/scripts/import.scm
+++ b/guix/scripts/import.scm
@@ -73,7 +73,7 @@ rather than \\n."
;;; Entry point.
;;;
-(define importers '("gnu" "nix" "pypi" "cpan" "hackage" "elpa"))
+(define importers '("gnu" "nix" "pypi" "cpan" "hackage" "elpa" "cran"))
(define (resolve-importer name)
(let ((module (resolve-interface
diff --git a/guix/scripts/import/cran.scm b/guix/scripts/import/cran.scm
new file mode 100644
index 0000000..f11fa10
--- /dev/null
+++ b/guix/scripts/import/cran.scm
@@ -0,0 +1,92 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2014 Eric Bavier <address@hidden>
+;;; Copyright © 2015 Ricardo Wurmus <address@hidden>
+;;;
+;;; 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 scripts import cran)
+ #:use-module (guix ui)
+ #:use-module (guix utils)
+ #:use-module (guix import cran)
+ #:use-module (guix scripts import)
+ #:use-module (srfi srfi-1)
+ #:use-module (srfi srfi-11)
+ #:use-module (srfi srfi-37)
+ #:use-module (ice-9 match)
+ #:use-module (ice-9 format)
+ #:export (guix-import-cran))
+
+
+;;;
+;;; Command-line options.
+;;;
+
+(define %default-options
+ '())
+
+(define (show-help)
+ (display (_ "Usage: guix import cran PACKAGE-NAME
+Import and convert the CRAN package for PACKAGE-NAME.\n"))
+ (display (_ "
+ -h, --help display this help and exit"))
+ (display (_ "
+ -V, --version display version information and exit"))
+ (newline)
+ (show-bug-report-information))
+
+(define %options
+ ;; Specification of the command-line options.
+ (cons* (option '(#\h "help") #f #f
+ (lambda args
+ (show-help)
+ (exit 0)))
+ (option '(#\V "version") #f #f
+ (lambda args
+ (show-version-and-exit "guix import cran")))
+ %standard-import-options))
+
+
+;;;
+;;; Entry point.
+;;;
+
+(define (guix-import-cran . args)
+ (define (parse-options)
+ ;; Return the alist of option values.
+ (args-fold* args %options
+ (lambda (opt name arg result)
+ (leave (_ "~A: unrecognized option~%") name))
+ (lambda (arg result)
+ (alist-cons 'argument arg result))
+ %default-options))
+
+ (let* ((opts (parse-options))
+ (args (filter-map (match-lambda
+ (('argument . value)
+ value)
+ (_ #f))
+ (reverse opts))))
+ (match args
+ ((package-name)
+ (let ((sexp (cran->guix-package package-name)))
+ (unless sexp
+ (leave (_ "failed to download description for package '~a'~%")
+ package-name))
+ sexp))
+ (()
+ (leave (_ "too few arguments~%")))
+ ((many ...)
+ (leave (_ "too many arguments~%"))))))
diff --git a/tests/cran.scm b/tests/cran.scm
new file mode 100644
index 0000000..c9cb5f6
--- /dev/null
+++ b/tests/cran.scm
@@ -0,0 +1,178 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 Ricardo Wurmus <address@hidden>
+;;;
+;;; 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 (test-cran)
+ #:use-module (guix import cran)
+ #:use-module (guix tests)
+ #:use-module (srfi srfi-64)
+ #:use-module (ice-9 match))
+
+(define sxml
+ '(*TOP* (xhtml:html
+ (xhtml:head
+ (xhtml:title "CRAN - Package my-example-sxml"))
+ (xhtml:body
+ (xhtml:h2 "my-example-sxml: Short description")
+ (xhtml:p "Long description")
+ (xhtml:table
+ (@ (summary "Package my-example-sxml summary"))
+ (xhtml:tr
+ (xhtml:td "Version:")
+ (xhtml:td "1.2.3"))
+ (xhtml:tr
+ (xhtml:td "Depends:")
+ (xhtml:td "R (>= 3.1.0)"))
+ (xhtml:tr
+ (xhtml:td "SystemRequirements:")
+ (xhtml:td "cairo (>= 1.2 http://www.cairographics.org/)"))
+ (xhtml:tr
+ (xhtml:td "Imports:")
+ (xhtml:td
+ (xhtml:a (@ (href "../scales/index.html"))
+ "scales")
+ " (>= 0.2.3), "
+ (xhtml:a (@ (href "../proto/index.html"))
+ "proto")
+ ", "
+ (xhtml:a (@ (href "../Rcpp/index.html")) "Rcpp")
+ " (>= 0.11.0)"))
+ (xhtml:tr
+ (xhtml:td "Suggests:")
+ (xhtml:td
+ (xhtml:a (@ (href "../some/index.html"))
+ "some")
+ ", "
+ (xhtml:a (@ (href "../suggestions/index.html"))
+ "suggestions")))
+ (xhtml:tr
+ (xhtml:td "License:")
+ (xhtml:td
+ (xhtml:a (@ (href "../../licenses/MIT")) "MIT")))
+ (xhtml:tr
+ (xhtml:td "URL:")
+ (xhtml:td
+ (xhtml:a (@ (href "http://gnu.org/s/my-example-sxml";))
+ "http://gnu.org/s/my-example-sxml";)
+ ", "
+ (xhtml:a (@ (href "http://alternative/home/page";))
+ "http://alternative/home/page";))))
+ (xhtml:h4 "Downloads:")
+ (xhtml:table
+ (@ (summary "Package my-example-sxml downloads"))
+ (xhtml:tr
+ (xhtml:td " Reference manual: ")
+ (xhtml:td
+ (xhtml:a (@ (href "my-example-sxml.pdf"))
+ " my-example-sxml.pdf ")))
+ (xhtml:tr
+ (xhtml:td " Package source: ")
+ (xhtml:td
+ (xhtml:a
+ (@ (href "../../../src/contrib/my-example-sxml_1.2.3.tar.gz"))
+ " my-example-sxml_1.2.3.tar.gz "))))
+ (xhtml:h4 "Reverse dependencies:")
+ (xhtml:table
+ (@ (summary "Package my-example-sxml reverse dependencies"))
+ (xhtml:tr
+ (xhtml:td "Reverse depends:")
+ (xhtml:td "Too many."))
+ (xhtml:tr
+ (xhtml:td "Reverse imports:")
+ (xhtml:td "Likewise."))
+ (xhtml:tr
+ (xhtml:td "Reverse suggests:")
+ (xhtml:td "Uncountable.")))))))
+
+(define simple-table
+ '(xhtml:table
+ (xhtml:tr
+ (xhtml:td "Numbers")
+ (xhtml:td "123"))
+ (xhtml:tr
+ (@ (class "whatever"))
+ (xhtml:td (@ (class "unimportant")) "Letters")
+ (xhtml:td "abc"))
+ (xhtml:tr
+ (xhtml:td "Letters")
+ (xhtml:td "xyz"))
+ (xhtml:tr
+ (xhtml:td "Single"))
+ (xhtml:tr
+ (xhtml:td "not a value")
+ (xhtml:td "not a label")
+ (xhtml:td "also not a label"))))
+
+(test-begin "cran")
+
+(test-equal "table-datum: return list of first table cell matching label"
+ '((xhtml:td "abc"))
+ ((@@ (guix import cran) table-datum) simple-table "Letters"))
+
+(test-equal "table-datum: return empty list if no match"
+ '()
+ ((@@ (guix import cran) table-datum) simple-table "Astronauts"))
+
+(test-equal "table-datum: only consider the first cell as a label cell"
+ '()
+ ((@@ (guix import cran) table-datum) simple-table "not a label"))
+
+
+(test-assert "cran-sxml->sexp"
+ ;; Replace network resources with sample data.
+ (mock ((guix build download) url-fetch
+ (lambda* (url file-name #:key (mirrors '()))
+ (with-output-to-file file-name
+ (lambda ()
+ (display
+ (match url
+ ("mirror://cran/src/contrib/my-example-sxml_1.2.3.tar.gz"
+ "source")
+ (_ (error "Unexpected URL: " url))))))))
+ (match ((@@ (guix import cran) cran-sxml->sexp) sxml)
+ (('package
+ ('name "r-my-example-sxml")
+ ('version "1.2.3")
+ ('source ('origin
+ ('method 'url-fetch)
+ ('uri ('string-append
"mirror://cran/src/contrib/my-example-sxml_"
+ 'version ".tar.gz"))
+ ('sha256
+ ('base32
+ (? string? hash)))))
+ ('build-system 'r-build-system)
+ ('inputs
+ ('quasiquote
+ (("cairo" ('unquote 'cairo)))))
+ ('propagated-inputs
+ ('quasiquote
+ (("r-proto" ('unquote 'r-proto))
+ ("r-rcpp" ('unquote 'r-rcpp))
+ ("r-scales" ('unquote 'r-scales)))))
+ ('home-page "http://gnu.org/s/my-example-sxml";)
+ ('synopsis "Short description")
+ ('description "Long description")
+ ('license 'x11)))
+ (x
+ (begin
+ (format #t "~s\n" x)
+ (pk 'fail x #f))))))
+
+(test-end "cran")
+
+
+(exit (= (test-runner-fail-count (test-runner-current)) 0))
--
2.1.0
>From 8271e8a5e7d237693e8d4b7b34e4a484b9a1fc22 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <address@hidden>
Date: Fri, 31 Jul 2015 14:47:34 +0200
Subject: [PATCH 2/2] 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.
---
Makefile.am | 2 +
doc/guix.texi | 10 ++++
guix/build-system/r.scm | 134 ++++++++++++++++++++++++++++++++++++++++++
guix/build/r-build-system.scm | 112 +++++++++++++++++++++++++++++++++++
4 files changed, 258 insertions(+)
create mode 100644 guix/build-system/r.scm
create mode 100644 guix/build/r-build-system.scm
diff --git a/Makefile.am b/Makefile.am
index 8f25145..ab00485 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 8774607..3a40c98 100644
--- a/doc/guix.texi
+++ b/doc/guix.texi
@@ -2481,6 +2481,16 @@ passes flags specified by the @code{#:make-maker-flags}
or
Which Perl package is used can be specified with @code{#:perl}.
@end defvr
address@hidden {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
address@hidden contains the paths to all R package inputs. Tests
+are run after installation using the R function
address@hidden::testInstalledPackage}.
address@hidden 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 0000000..4daec5e
--- /dev/null
+++ b/guix/build-system/r.scm
@@ -0,0 +1,134 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 Ricardo Wurmus <address@hidden>
+;;;
+;;; 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 0000000..81e2de9
--- /dev/null
+++ b/guix/build/r-build-system.scm
@@ -0,0 +1,112 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2015 Ricardo Wurmus <address@hidden>
+;;;
+;;; 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 (call-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)
+ (call-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
--
2.1.0