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
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
| | ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2021 Ludovic Courtès <ludo@gnu.org>
;;;
;;; 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 gexp)
#:use-module (guix monads)
#:use-module (guix search-paths)
#:use-module (guix build-system)
#:use-module (guix build-system gnu)
#:use-module (ice-9 match)
#:export (%r-build-system-modules
r-build
r-build-system
cran-uri
bioconductor-uri))
;; Commentary:
;;
;; Standard build procedure for R packages.
;;
;; Code:
(define (cran-uri name version)
"Return a list of URI strings for the R package archive on CRAN for the
release corresponding to NAME and VERSION. As only the most recent version is
available via the first URI, the second URI points to the archived version."
(list (string-append "mirror://cran/src/contrib/"
name "_" version ".tar.gz")
(string-append "mirror://cran/src/contrib/Archive/"
name "/" name "_" version ".tar.gz")))
(define* (bioconductor-uri name version #:optional type)
"Return a URI string for the R package archive on Bioconductor for the
release corresponding to NAME and VERSION."
(let ((type-url-part (match type
('annotation "/data/annotation")
('experiment "/data/experiment")
(_ "/bioc"))))
(list (string-append "https://bioconductor.org/packages/release"
type-url-part
"/src/contrib/"
name "_" version ".tar.gz")
;; TODO: use %bioconductor-version from (guix import cran)
(string-append "https://bioconductor.org/packages/3.17"
type-url-part
"/src/contrib/"
name "_" version ".tar.gz"))))
(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-minimal)))
(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
'(#:target #:r #: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 name inputs
#:key
source
(tests? #t)
(test-target "tests")
(configure-flags ''())
(phases '%standard-phases)
(outputs '("out"))
(search-paths '())
(system (%current-system))
(guile #f)
(substitutable? #t)
(imported-modules %r-build-system-modules)
(modules '((guix build r-build-system)
(guix build utils))))
"Build SOURCE with INPUTS."
(define builder
(with-imported-modules imported-modules
#~(begin
(use-modules #$@(sexp->gexp modules))
(r-build #:name #$name
#:source #+source
#:configure-flags #$configure-flags
#:system #$system
#:tests? #$tests?
#:test-target #$test-target
#:phases #$phases
#:outputs #$(outputs->gexp outputs)
#:search-paths '#$(sexp->gexp
(map search-path-specification->sexp
search-paths))
#:inputs #$(input-tuples->gexp inputs)))))
(mlet %store-monad ((guile (package->derivation (or guile (default-guile))
system #:graft? #f)))
(gexp->derivation name builder
#:system system
#:guile-for-build guile
#:substitutable? substitutable?)))
(define r-build-system
(build-system
(name 'r)
(description "The standard R build system")
(lower lower)))
;;; r.scm ends here
|