blob: 2c0b322da9eb139ea42b337199f01837f072ac5b (
about) (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
|
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2017, 2018 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)
#:use-module (srfi srfi-35)
#:export (%standard-phases
r-build))
;; Commentary:
;;
;; Builder-side code of the standard build procedure for R packages.
;;
;; Code:
(define (invoke-r command params)
(apply invoke "R" "CMD" command params))
(define (pipe-to-r command params)
(let ((port (apply open-pipe* OPEN_WRITE "R" params)))
(display command port)
(let ((code (status:exit-val (close-pipe port))))
(unless (zero? code)
(raise (condition ((@@ (guix build utils) &invoke-error)
(program "R")
(arguments (cons command params))
(exit-status (status:exit-val code))
(term-signal (status:term-sig code))
(stop-signal (status:stop-sig code)))))))))
(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))))
(when (and tests? (file-exists? testdir))
(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)
"--built-timestamp=1970-01-01"
".")))
(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 'bootstrap)
(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
|
