514 lines
20 KiB
Scheme
514 lines
20 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2015, 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
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;;; Copyright © 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
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;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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;;; GNU Guix is free software; you can redistribute it and/or modify it
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;;; under the terms of the GNU General Public License as published by
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;;; the Free Software Foundation; either version 3 of the License, or (at
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;;; your option) any later version.
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;;;
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;;; GNU Guix is distributed in the hope that it will be useful, but
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;;; WITHOUT ANY WARRANTY; without even the implied warranty of
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;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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;;; GNU General Public License for more details.
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;;;
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;;; You should have received a copy of the GNU General Public License
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;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
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(define-module (guix import cran)
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#:use-module (ice-9 match)
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#:use-module (ice-9 regex)
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#:use-module ((ice-9 rdelim) #:select (read-string read-line))
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#:use-module (srfi srfi-1)
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#:use-module (srfi srfi-2)
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#:use-module (srfi srfi-26)
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#:use-module (srfi srfi-34)
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#:use-module (ice-9 receive)
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#:use-module (web uri)
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#:use-module (guix memoization)
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#:use-module (guix http-client)
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#:use-module (gcrypt hash)
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#:use-module (guix store)
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#:use-module (guix base32)
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#:use-module ((guix download) #:select (download-to-store))
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#:use-module (guix import utils)
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#:use-module ((guix build utils) #:select (find-files))
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#:use-module (guix utils)
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#:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri))
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#:use-module (guix upstream)
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#:use-module (guix packages)
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#:use-module (gnu packages)
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#:export (cran->guix-package
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bioconductor->guix-package
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cran-recursive-import
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%cran-updater
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%bioconductor-updater
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cran-package?
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bioconductor-package?
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bioconductor-data-package?
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bioconductor-experiment-package?))
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;;; Commentary:
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;;;
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;;; Generate a package declaration template for the latest version of an R
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;;; package on CRAN, using the DESCRIPTION file downloaded from
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;;; cran.r-project.org.
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;;;
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;;; Code:
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(define string->license
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(match-lambda
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("AGPL-3" 'agpl3+)
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("Artistic-2.0" 'artistic2.0)
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("Apache License 2.0" 'asl2.0)
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("BSD_2_clause" 'bsd-2)
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("BSD_2_clause + file LICENSE" 'bsd-2)
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("BSD_3_clause" 'bsd-3)
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("BSD_3_clause + file LICENSE" 'bsd-3)
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("GPL" '(list gpl2+ gpl3+))
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("GPL (>= 2)" 'gpl2+)
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("GPL (>= 3)" 'gpl3+)
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("GPL-2" 'gpl2)
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("GPL-3" 'gpl3)
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("LGPL-2" 'lgpl2.0)
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("LGPL-2.1" 'lgpl2.1)
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("LGPL-3" 'lgpl3)
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("LGPL (>= 2)" 'lgpl2.0+)
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("LGPL (>= 3)" 'lgpl3+)
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("MIT" 'expat)
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("MIT + file LICENSE" 'expat)
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((x) (string->license x))
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((lst ...) `(list ,@(map string->license lst)))
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(_ #f)))
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(define (description->alist description)
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"Convert a DESCRIPTION string into an alist."
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(let ((lines (string-split description #\newline))
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(parse (lambda (line acc)
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(if (string-null? line) acc
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;; Keys usually start with a capital letter and end with
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;; ":". There are some exceptions, unfortunately (such
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;; as "biocViews"). There are no blanks in a key.
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(if (string-match "^[A-Za-z][^ :]+:( |\n|$)" line)
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;; New key/value pair
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(let* ((pos (string-index line #\:))
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(key (string-take line pos))
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(value (string-drop line (+ 1 pos))))
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(cons (cons key
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(string-trim-both value))
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acc))
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;; This is a continuation of the previous pair
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(match-let ((((key . value) . rest) acc))
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(cons (cons key (string-join
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(list value
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(string-trim-both line))))
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rest)))))))
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(fold parse '() lines)))
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(define (format-inputs names)
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"Generate a sorted list of package inputs from a list of package NAMES."
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(map (lambda (name)
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(list name (list 'unquote (string->symbol name))))
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(sort names string-ci<?)))
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(define* (maybe-inputs package-inputs #:optional (type 'inputs))
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"Given a list of PACKAGE-INPUTS, tries to generate the TYPE field of a
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package definition."
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(match package-inputs
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(()
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'())
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((package-inputs ...)
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`((,type (,'quasiquote ,(format-inputs package-inputs)))))))
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(define %cran-url "https://cran.r-project.org/web/packages/")
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(define %bioconductor-url "https://bioconductor.org/packages/")
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;; The latest Bioconductor release is 3.9. Bioconductor packages should be
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;; updated together.
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(define %bioconductor-version "3.9")
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(define %bioconductor-packages-list-url
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(string-append "https://bioconductor.org/packages/"
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%bioconductor-version "/bioc/src/contrib/PACKAGES"))
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(define (bioconductor-packages-list)
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"Return the latest version of package NAME for the current bioconductor
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release."
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(let ((url (string->uri %bioconductor-packages-list-url)))
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(guard (c ((http-get-error? c)
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(format (current-error-port)
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"error: failed to retrieve list of packages from ~s: ~a (~s)~%"
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(uri->string (http-get-error-uri c))
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(http-get-error-code c)
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(http-get-error-reason c))
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#f))
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;; Split the big list on empty lines, then turn each chunk into an
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;; alist of attributes.
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(map (lambda (chunk)
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(description->alist (string-join chunk "\n")))
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(chunk-lines (read-lines (http-fetch/cached url)))))))
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(define (latest-bioconductor-package-version name)
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"Return the version string corresponding to the latest release of the
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bioconductor package NAME, or #F if the package is unknown."
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(and=> (find (lambda (meta)
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(string=? (assoc-ref meta "Package") name))
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(bioconductor-packages-list))
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(cut assoc-ref <> "Version")))
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;; Little helper to download URLs only once.
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(define download
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(memoize
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(lambda (url)
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(with-store store (download-to-store store url)))))
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(define (fetch-description repository name)
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"Return an alist of the contents of the DESCRIPTION file for the R package
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NAME in the given REPOSITORY, or #f in case of failure. NAME is
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case-sensitive."
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(case repository
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((cran)
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(let ((url (string-append %cran-url name "/DESCRIPTION")))
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(guard (c ((http-get-error? c)
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(format (current-error-port)
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"error: failed to retrieve package information \
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from ~s: ~a (~s)~%"
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(uri->string (http-get-error-uri c))
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(http-get-error-code c)
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(http-get-error-reason c))
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#f))
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(description->alist (read-string (http-fetch url))))))
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((bioconductor)
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;; Currently, the bioconductor project does not offer a way to access a
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;; package's DESCRIPTION file over HTTP, so we determine the version,
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;; download the source tarball, and then extract the DESCRIPTION file.
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(and-let* ((version (latest-bioconductor-package-version name))
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(url (car (bioconductor-uri name version)))
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(tarball (download url)))
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(call-with-temporary-directory
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(lambda (dir)
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(parameterize ((current-error-port (%make-void-port "rw+"))
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(current-output-port (%make-void-port "rw+")))
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(and (zero? (system* "tar" "--wildcards" "-x"
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"--strip-components=1"
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"-C" dir
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"-f" tarball "*/DESCRIPTION"))
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(description->alist (with-input-from-file
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(string-append dir "/DESCRIPTION") read-string))))))))))
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(define (listify meta field)
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"Look up FIELD in the alist META. If FIELD contains a comma-separated
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string, turn it into a list and strip off parenthetic expressions. Return the
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empty list when the FIELD cannot be found."
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(let ((value (assoc-ref meta field)))
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(if (not value)
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'()
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;; Strip off parentheses
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(let ((items (string-split (regexp-substitute/global
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#f "( *\\([^\\)]+\\)) *"
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value 'pre 'post)
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#\,)))
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(remove (lambda (item)
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(or (string-null? item)
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;; When there is whitespace inside of items it is
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;; probably because this was not an actual list to
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;; begin with.
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(string-any char-set:whitespace item)))
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(map string-trim-both items))))))
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(define default-r-packages
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(list "base"
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"compiler"
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"grDevices"
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"graphics"
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"grid"
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"methods"
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"parallel"
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"splines"
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"stats"
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"stats4"
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"tcltk"
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"tools"
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"translations"
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"utils"))
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;; The field for system dependencies is often abused to specify non-package
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;; dependencies (such as c++11). This list is used to ignore them.
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(define invalid-packages
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(list "c++11"))
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(define cran-guix-name (cut guix-name "r-" <>))
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(define (needs-fortran? tarball)
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"Check if the TARBALL contains Fortran source files."
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(define (check pattern)
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(parameterize ((current-error-port (%make-void-port "rw+"))
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(current-output-port (%make-void-port "rw+")))
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(zero? (system* "tar" "--wildcards" "--list" pattern "-f" tarball))))
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(or (check "*.f90")
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(check "*.f95")
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(check "*.f")))
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(define (tarball-files-match-pattern? tarball regexp . file-patterns)
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"Return #T if any of the files represented by FILE-PATTERNS in the TARBALL
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match the given REGEXP."
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(call-with-temporary-directory
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(lambda (dir)
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(let ((pattern (make-regexp regexp)))
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(parameterize ((current-error-port (%make-void-port "rw+")))
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(apply system* "tar"
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"xf" tarball "-C" dir
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`("--wildcards" ,@file-patterns)))
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(any (lambda (file)
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(call-with-input-file file
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(lambda (port)
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(let loop ()
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(let ((line (read-line port)))
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(cond
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((eof-object? line) #f)
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((regexp-exec pattern line) #t)
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(else (loop))))))))
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(find-files dir))))))
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(define (needs-zlib? tarball)
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"Return #T if any of the Makevars files in the src directory of the TARBALL
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contain a zlib linker flag."
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(tarball-files-match-pattern?
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tarball "-lz"
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"*/src/Makevars*" "*/src/configure*" "*/configure*"))
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(define (needs-pkg-config? tarball)
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"Return #T if any of the Makevars files in the src directory of the TARBALL
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reference the pkg-config tool."
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(tarball-files-match-pattern?
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tarball "pkg-config"
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"*/src/Makevars*" "*/src/configure*" "*/configure*"))
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(define (description->package repository meta)
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"Return the `package' s-expression for an R package published on REPOSITORY
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from the alist META, which was derived from the R package's DESCRIPTION file."
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(let* ((base-url (case repository
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((cran) %cran-url)
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((bioconductor) %bioconductor-url)))
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(uri-helper (case repository
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((cran) cran-uri)
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((bioconductor) bioconductor-uri)))
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(name (assoc-ref meta "Package"))
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(synopsis (assoc-ref meta "Title"))
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(version (assoc-ref meta "Version"))
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(license (string->license (assoc-ref meta "License")))
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;; Some packages have multiple home pages. Some have none.
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(home-page (match (listify meta "URL")
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((url rest ...) url)
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(_ (string-append base-url name))))
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(source-url (match (uri-helper name version)
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((url rest ...) url)
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((? string? url) url)
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(_ #f)))
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(tarball (download source-url))
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(sysdepends (append
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(if (needs-zlib? tarball) '("zlib") '())
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(filter (lambda (name)
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(not (member name invalid-packages)))
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(map string-downcase (listify meta "SystemRequirements")))))
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(propagate (filter (lambda (name)
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(not (member name (append default-r-packages
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invalid-packages))))
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(lset-union equal?
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(listify meta "Imports")
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(listify meta "LinkingTo")
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(delete "R"
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(listify meta "Depends"))))))
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(values
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`(package
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(name ,(cran-guix-name name))
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(version ,version)
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(source (origin
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(method url-fetch)
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(uri (,(procedure-name uri-helper) ,name version))
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(sha256
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(base32
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,(bytevector->nix-base32-string (file-sha256 tarball))))))
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,@(if (not (equal? (string-append "r-" name)
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(cran-guix-name name)))
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`((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
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'())
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(build-system r-build-system)
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,@(maybe-inputs sysdepends)
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,@(maybe-inputs (map cran-guix-name propagate) 'propagated-inputs)
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,@(maybe-inputs
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`(,@(if (needs-fortran? tarball)
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'("gfortran") '())
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,@(if (needs-pkg-config? tarball)
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'("pkg-config") '()))
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'native-inputs)
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(home-page ,(if (string-null? home-page)
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(string-append base-url name)
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home-page))
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(synopsis ,synopsis)
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(description ,(beautify-description (or (assoc-ref meta "Description")
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"")))
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(license ,license))
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propagate)))
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(define cran->guix-package
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(memoize
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(lambda* (package-name #:optional (repo 'cran))
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"Fetch the metadata for PACKAGE-NAME from REPO and return the `package'
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s-expression corresponding to that package, or #f on failure."
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(let ((description (fetch-description repo package-name)))
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(if (and (not description)
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(eq? repo 'bioconductor))
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;; Retry import from CRAN
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(cran->guix-package package-name 'cran)
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(and description
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(description->package repo description)))))))
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(define* (cran-recursive-import package-name #:optional (repo 'cran))
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(recursive-import package-name repo
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#:repo->guix-package cran->guix-package
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#:guix-name cran-guix-name))
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;;;
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;;; Updater.
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;;;
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(define (package->upstream-name package)
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"Return the upstream name of the PACKAGE."
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(let* ((properties (package-properties package))
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(upstream-name (and=> properties
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(cut assoc-ref <> 'upstream-name))))
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(if upstream-name
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upstream-name
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(match (package-source package)
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((? origin? origin)
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(match (origin-uri origin)
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((or (? string? url) (url _ ...))
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(let ((end (string-rindex url #\_))
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(start (string-rindex url #\/)))
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;; The URL ends on
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;; (string-append "/" name "_" version ".tar.gz")
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(and start end (substring url (+ start 1) end))))
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(_ #f)))
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(_ #f)))))
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(define (latest-cran-release pkg)
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"Return an <upstream-source> for the latest release of the package PKG."
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(define upstream-name
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(package->upstream-name pkg))
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(define meta
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(fetch-description 'cran upstream-name))
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(and meta
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(let ((version (assoc-ref meta "Version")))
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;; CRAN does not provide signatures.
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(upstream-source
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(package (package-name pkg))
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(version version)
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(urls (cran-uri upstream-name version))
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(input-changes
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(changed-inputs pkg
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(description->package 'cran meta)))))))
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(define (latest-bioconductor-release pkg)
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"Return an <upstream-source> for the latest release of the package PKG."
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(define upstream-name
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(package->upstream-name pkg))
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(define version
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(latest-bioconductor-package-version upstream-name))
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(and version
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;; Bioconductor does not provide signatures.
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(upstream-source
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(package (package-name pkg))
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(version version)
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(urls (bioconductor-uri upstream-name version))
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(input-changes
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(changed-inputs
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pkg
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(cran->guix-package upstream-name 'bioconductor))))))
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(define (cran-package? package)
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"Return true if PACKAGE is an R package from CRAN."
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(and (string-prefix? "r-" (package-name package))
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;; Check if the upstream name can be extracted from package uri.
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(package->upstream-name package)
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;; Check if package uri(s) are prefixed by "mirror://cran".
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(match (and=> (package-source package) origin-uri)
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((? string? uri)
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(string-prefix? "mirror://cran" uri))
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((? list? uris)
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(any (cut string-prefix? "mirror://cran" <>) uris))
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(_ #f))))
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(define (bioconductor-package? package)
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"Return true if PACKAGE is an R package from Bioconductor."
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(let ((predicate (lambda (uri)
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(and (string-prefix? "https://bioconductor.org" uri)
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;; Data packages are neither listed in SVN nor on
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;; the Github mirror, so we have to exclude them
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;; from the set of bioconductor packages that can be
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;; updated automatically.
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(not (string-contains uri "/data/annotation/"))
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;; Experiment packages are in a separate repository.
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(not (string-contains uri "/data/experiment/"))))))
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(and (string-prefix? "r-" (package-name package))
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(match (and=> (package-source package) origin-uri)
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((? string? uri)
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(predicate uri))
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((? list? uris)
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(any predicate uris))
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(_ #f)))))
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(define (bioconductor-data-package? package)
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||
"Return true if PACKAGE is an R data package from Bioconductor."
|
||
(let ((predicate (lambda (uri)
|
||
(and (string-prefix? "https://bioconductor.org" uri)
|
||
(string-contains uri "/data/annotation/")))))
|
||
(and (string-prefix? "r-" (package-name package))
|
||
(match (and=> (package-source package) origin-uri)
|
||
((? string? uri)
|
||
(predicate uri))
|
||
((? list? uris)
|
||
(any predicate uris))
|
||
(_ #f)))))
|
||
|
||
(define (bioconductor-experiment-package? package)
|
||
"Return true if PACKAGE is an R experiment package from Bioconductor."
|
||
(let ((predicate (lambda (uri)
|
||
(and (string-prefix? "https://bioconductor.org" uri)
|
||
(string-contains uri "/data/experiment/")))))
|
||
(and (string-prefix? "r-" (package-name package))
|
||
(match (and=> (package-source package) origin-uri)
|
||
((? string? uri)
|
||
(predicate uri))
|
||
((? list? uris)
|
||
(any predicate uris))
|
||
(_ #f)))))
|
||
|
||
(define %cran-updater
|
||
(upstream-updater
|
||
(name 'cran)
|
||
(description "Updater for CRAN packages")
|
||
(pred cran-package?)
|
||
(latest latest-cran-release)))
|
||
|
||
(define %bioconductor-updater
|
||
(upstream-updater
|
||
(name 'bioconductor)
|
||
(description "Updater for Bioconductor packages")
|
||
(pred bioconductor-package?)
|
||
(latest latest-bioconductor-release)))
|
||
|
||
;;; cran.scm ends here
|