02/04: build: Add R build system.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit f8f3bef6aac4ed96bfd236567536c4b039b7bd31
Author: Ricardo Wurmus <address@hidden>
Date:   Fri Jul 31 14:47:34 2015 +0200

    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(+), 0 deletions(-)

diff --git a/Makefile.am b/Makefile.am
index af41ea5..711181b 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 4dbedb1..c42aedb 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
 
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..3fc13eb
--- /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 (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