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;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015, 2016, 2017 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
;;;
;;; 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 import cran)
#:use-module (ice-9 match)
#:use-module (ice-9 regex)
#:use-module ((ice-9 rdelim) #:select (read-string read-line))
#:use-module (srfi srfi-1)
#:use-module (srfi srfi-26)
#:use-module (srfi srfi-34)
#:use-module (ice-9 receive)
#:use-module (web uri)
#:use-module (guix memoization)
#:use-module (guix http-client)
#:use-module (gcrypt hash)
#:use-module (guix store)
#:use-module (guix base32)
#:use-module ((guix download) #:select (download-to-store))
#:use-module (guix import utils)
#:use-module ((guix build utils) #:select (find-files))
#:use-module (guix utils)
#:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri))
#:use-module (guix upstream)
#:use-module (guix packages)
#:use-module (gnu packages)
#:export (cran->guix-package
bioconductor->guix-package
cran-recursive-import
%cran-updater
%bioconductor-updater
cran-package?
bioconductor-package?
bioconductor-data-package?
bioconductor-experiment-package?))
;;; Commentary:
;;;
;;; Generate a package declaration template for the latest version of an R
;;; package on CRAN, using the DESCRIPTION file downloaded from
;;; cran.r-project.org.
;;;
;;; Code:
(define string->license
(match-lambda
("AGPL-3" 'agpl3+)
("Artistic-2.0" 'artistic2.0)
("Apache License 2.0" 'asl2.0)
("BSD_2_clause" 'bsd-2)
("BSD_2_clause + file LICENSE" 'bsd-2)
("BSD_3_clause" 'bsd-3)
("BSD_3_clause + file LICENSE" 'bsd-3)
("GPL" '(list gpl2+ gpl3+))
("GPL (>= 2)" 'gpl2+)
("GPL (>= 3)" 'gpl3+)
("GPL-2" 'gpl2)
("GPL-3" 'gpl3)
("LGPL-2" 'lgpl2.0)
("LGPL-2.1" 'lgpl2.1)
("LGPL-3" 'lgpl3)
("LGPL (>= 2)" 'lgpl2.0+)
("LGPL (>= 3)" 'lgpl3+)
("MIT" 'expat)
("MIT + file LICENSE" 'expat)
((x) (string->license x))
((lst ...) `(list ,@(map string->license lst)))
(_ #f)))
(define (description->alist description)
"Convert a DESCRIPTION string into an alist."
(let ((lines (string-split description #\newline))
(parse (lambda (line acc)
(if (string-null? line) acc
;; Keys usually start with a capital letter and end with
;; ":". There are some exceptions, unfortunately (such
;; as "biocViews"). There are no blanks in a key.
(if (string-match "^[A-Za-z][^ :]+:( |\n|$)" line)
;; New key/value pair
(let* ((pos (string-index line #\:))
(key (string-take line pos))
(value (string-drop line (+ 1 pos))))
(cons (cons key
(string-trim-both value))
acc))
;; This is a continuation of the previous pair
(match-let ((((key . value) . rest) acc))
(cons (cons key (string-join
(list value
(string-trim-both line))))
rest)))))))
(fold parse '() lines)))
(define (format-inputs names)
"Generate a sorted list of package inputs from a list of package NAMES."
(map (lambda (name)
(list name (list 'unquote (string->symbol name))))
(sort names string-ci<?)))
(define* (maybe-inputs package-inputs #:optional (type 'inputs))
"Given a list of PACKAGE-INPUTS, tries to generate the TYPE field of a
package definition."
(match package-inputs
(()
'())
((package-inputs ...)
`((,type (,'quasiquote ,(format-inputs package-inputs)))))))
(define %cran-url "http://cran.r-project.org/web/packages/")
(define %bioconductor-url "https://bioconductor.org/packages/")
;; The latest Bioconductor release is 3.7. Bioconductor packages should be
;; updated together.
(define %bioconductor-version "3.7")
(define %bioconductor-packages-list-url
(string-append "https://bioconductor.org/packages/"
%bioconductor-version "/bioc/src/contrib/PACKAGES"))
(define (bioconductor-packages-list)
"Return the latest version of package NAME for the current bioconductor
release."
(let ((url (string->uri %bioconductor-packages-list-url)))
(guard (c ((http-get-error? c)
(format (current-error-port)
"error: failed to retrieve list of packages from ~s: ~a (~s)~%"
(uri->string (http-get-error-uri c))
(http-get-error-code c)
(http-get-error-reason c))
#f))
;; Split the big list on empty lines, then turn each chunk into an
;; alist of attributes.
(map (lambda (chunk)
(description->alist (string-join chunk "\n")))
(chunk-lines (read-lines (http-fetch/cached url)))))))
(define (latest-bioconductor-package-version name)
"Return the version string corresponding to the latest release of the
bioconductor package NAME, or #F if the package is unknown."
(and=> (find (lambda (meta)
(string=? (assoc-ref meta "Package") name))
(bioconductor-packages-list))
(cut assoc-ref <> "Version")))
(define (fetch-description repository name)
"Return an alist of the contents of the DESCRIPTION file for the R package
NAME in the given REPOSITORY, or #f in case of failure. NAME is
case-sensitive."
(case repository
((cran)
(let ((url (string-append %cran-url name "/DESCRIPTION")))
(guard (c ((http-get-error? c)
(format (current-error-port)
"error: failed to retrieve package information \
from ~s: ~a (~s)~%"
(uri->string (http-get-error-uri c))
(http-get-error-code c)
(http-get-error-reason c))
#f))
(description->alist (read-string (http-fetch url))))))
((bioconductor)
;; Currently, the bioconductor project does not offer a way to access a
;; package's DESCRIPTION file over HTTP, so we determine the version,
;; download the source tarball, and then extract the DESCRIPTION file.
(let* ((version (latest-bioconductor-package-version name))
(url (car (bioconductor-uri name version)))
(tarball (with-store store (download-to-store store url))))
(call-with-temporary-directory
(lambda (dir)
(parameterize ((current-error-port (%make-void-port "rw+"))
(current-output-port (%make-void-port "rw+")))
(and (zero? (system* "tar" "--wildcards" "-x"
"--strip-components=1"
"-C" dir
"-f" tarball "*/DESCRIPTION"))
(description->alist (with-input-from-file
(string-append dir "/DESCRIPTION") read-string))))))))))
(define (listify meta field)
"Look up FIELD in the alist META. If FIELD contains a comma-separated
string, turn it into a list and strip off parenthetic expressions. Return the
empty list when the FIELD cannot be found."
(let ((value (assoc-ref meta field)))
(if (not value)
'()
;; Strip off parentheses
(let ((items (string-split (regexp-substitute/global
#f "( *\\([^\\)]+\\)) *"
value 'pre 'post)
#\,)))
(remove (lambda (item)
(or (string-null? item)
;; When there is whitespace inside of items it is
;; probably because this was not an actual list to
;; begin with.
(string-any char-set:whitespace item)))
(map string-trim-both items))))))
(define default-r-packages
(list "base"
"compiler"
"grDevices"
"graphics"
"grid"
"methods"
"parallel"
"splines"
"stats"
"stats4"
"tcltk"
"tools"
"translations"
"utils"))
(define cran-guix-name (cut guix-name "r-" <>))
(define (needs-fortran? tarball)
"Check if the TARBALL contains Fortran source files."
(define (check pattern)
(parameterize ((current-error-port (%make-void-port "rw+"))
(current-output-port (%make-void-port "rw+")))
(zero? (system* "tar" "--wildcards" "--list" pattern "-f" tarball))))
(or (check "*.f90")
(check "*.f95")
(check "*.f")))
(define (tarball-files-match-pattern? tarball regexp . file-patterns)
"Return #T if any of the files represented by FILE-PATTERNS in the TARBALL
match the given REGEXP."
(call-with-temporary-directory
(lambda (dir)
(let ((pattern (make-regexp regexp)))
(parameterize ((current-error-port (%make-void-port "rw+")))
(apply system* "tar"
"xf" tarball "-C" dir
`("--wildcards" ,@file-patterns)))
(any (lambda (file)
(call-with-input-file file
(lambda (port)
(let loop ()
(let ((line (read-line port)))
(cond
((eof-object? line) #f)
((regexp-exec pattern line) #t)
(else (loop))))))))
(find-files dir))))))
(define (needs-zlib? tarball)
"Return #T if any of the Makevars files in the src directory of the TARBALL
contain a zlib linker flag."
(tarball-files-match-pattern?
tarball "-lz"
"*/src/Makevars*" "*/src/configure*" "*/configure*"))
(define (needs-pkg-config? tarball)
"Return #T if any of the Makevars files in the src directory of the TARBALL
reference the pkg-config tool."
(tarball-files-match-pattern?
tarball "pkg-config"
"*/src/Makevars*" "*/src/configure*" "*/configure*"))
(define (description->package repository meta)
"Return the `package' s-expression for an R package published on REPOSITORY
from the alist META, which was derived from the R package's DESCRIPTION file."
(let* ((base-url (case repository
((cran) %cran-url)
((bioconductor) %bioconductor-url)))
(uri-helper (case repository
((cran) cran-uri)
((bioconductor) bioconductor-uri)))
(name (assoc-ref meta "Package"))
(synopsis (assoc-ref meta "Title"))
(version (assoc-ref meta "Version"))
(license (string->license (assoc-ref meta "License")))
;; Some packages have multiple home pages. Some have none.
(home-page (match (listify meta "URL")
((url rest ...) url)
(_ (string-append base-url name))))
(source-url (match (uri-helper name version)
((url rest ...) url)
((? string? url) url)
(_ #f)))
(tarball (with-store store (download-to-store store source-url)))
(sysdepends (append
(if (needs-zlib? tarball) '("zlib") '())
(map string-downcase (listify meta "SystemRequirements"))))
(propagate (filter (lambda (name)
(not (member name default-r-packages)))
(lset-union equal?
(listify meta "Imports")
(listify meta "LinkingTo")
(delete "R"
(listify meta "Depends"))))))
(values
`(package
(name ,(cran-guix-name name))
(version ,version)
(source (origin
(method url-fetch)
(uri (,(procedure-name uri-helper) ,name version))
(sha256
(base32
,(bytevector->nix-base32-string (file-sha256 tarball))))))
,@(if (not (equal? (string-append "r-" name)
(cran-guix-name name)))
`((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
'())
(build-system r-build-system)
,@(maybe-inputs sysdepends)
,@(maybe-inputs (map cran-guix-name propagate) 'propagated-inputs)
,@(maybe-inputs
`(,@(if (needs-fortran? tarball)
'("gfortran") '())
,@(if (needs-pkg-config? tarball)
'("pkg-config") '()))
'native-inputs)
(home-page ,(if (string-null? home-page)
(string-append base-url name)
home-page))
(synopsis ,synopsis)
(description ,(beautify-description (or (assoc-ref meta "Description")
"")))
(license ,license))
propagate)))
(define cran->guix-package
(memoize
(lambda* (package-name #:optional (repo 'cran))
"Fetch the metadata for PACKAGE-NAME from REPO and return the `package'
s-expression corresponding to that package, or #f on failure."
(and=> (fetch-description repo package-name)
(cut description->package repo <>)))))
(define* (cran-recursive-import package-name #:optional (repo 'gnu))
(recursive-import package-name repo
#:repo->guix-package cran->guix-package
#:guix-name cran-guix-name))
;;;
;;; Updater.
;;;
(define (package->upstream-name package)
"Return the upstream name of the PACKAGE."
(let* ((properties (package-properties package))
(upstream-name (and=> properties
(cut assoc-ref <> 'upstream-name))))
(if upstream-name
upstream-name
(match (package-source package)
((? origin? origin)
(match (origin-uri origin)
((or (? string? url) (url _ ...))
(let ((end (string-rindex url #\_))
(start (string-rindex url #\/)))
;; The URL ends on
;; (string-append "/" name "_" version ".tar.gz")
(and start end (substring url (+ start 1) end))))
(_ #f)))
(_ #f)))))
(define (latest-cran-release package)
"Return an <upstream-source> for the latest release of PACKAGE."
(define upstream-name
(package->upstream-name package))
(define meta
(fetch-description 'cran upstream-name))
(and meta
(let ((version (assoc-ref meta "Version")))
;; CRAN does not provide signatures.
(upstream-source
(package (package-name package))
(version version)
(urls (cran-uri upstream-name version))))))
(define (latest-bioconductor-release package)
"Return an <upstream-source> for the latest release of PACKAGE."
(define upstream-name
(package->upstream-name package))
(define version
(latest-bioconductor-package-version upstream-name))
(and version
;; Bioconductor does not provide signatures.
(upstream-source
(package (package-name package))
(version version)
(urls (bioconductor-uri upstream-name version)))))
(define (cran-package? package)
"Return true if PACKAGE is an R package from CRAN."
(and (string-prefix? "r-" (package-name package))
;; Check if the upstream name can be extracted from package uri.
(package->upstream-name package)
;; Check if package uri(s) are prefixed by "mirror://cran".
(match (and=> (package-source package) origin-uri)
((? string? uri)
(string-prefix? "mirror://cran" uri))
((? list? uris)
(any (cut string-prefix? "mirror://cran" <>) uris))
(_ #f))))
(define (bioconductor-package? package)
"Return true if PACKAGE is an R package from Bioconductor."
(let ((predicate (lambda (uri)
(and (string-prefix? "https://bioconductor.org" uri)
;; Data packages are neither listed in SVN nor on
;; the Github mirror, so we have to exclude them
;; from the set of bioconductor packages that can be
;; updated automatically.
(not (string-contains uri "/data/annotation/"))
;; Experiment packages are in a separate repository.
(not (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 (bioconductor-data-package? package)
"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