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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2017, 2018, 2024 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 format)
#:use-module (ice-9 ftw)
#:use-module (ice-9 popen)
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-26)
#:use-module (srfi srfi-34)
#: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* ((closed (close-pipe port))
(code (status:exit-val closed)))
(unless (zero? code)
(raise (condition ((@@ (guix build utils) &invoke-error)
(program "R")
(arguments (cons command params))
(exit-status code)
(term-signal (status:term-sig closed))
(stop-signal (status:stop-sig closed)))))))))
(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 test-types 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))
;; Skip tests that should be skipped on CI systems.
(setenv "CI" "1")
(setenv "NOT_CRAN" "skip")
(setenv "IS_BIOC_BUILD_MACHINE" "true")
(setenv "R_LIBS_SITE" site-path)
(guard (c ((invoke-error? c)
;; Dump the test suite log to facilitate debugging.
(display "\nTests failed, dumping logs.\n"
(current-error-port))
(gnu:dump-file-contents "." ".*\\.Rout\\.fail$")
(raise c)))
(pipe-to-r (string-append "quit(status=tools::testInstalledPackage(\"" pkg-name "\", "
"lib.loc = \"" libdir "\", "
"errorsAreFatal=TRUE, "
(if test-types
(format #false "types=c(~{\"~a\"~^,~})" test-types)
"types=c(\"tests\", \"vignettes\")")
"))")
'("--no-save" "--slave"))))))
(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
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