Mirror of GNU Guix
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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 (srfi srfi-41)
#:use-module (ice-9 receive)
#:use-module (web uri)
#:use-module (guix memoization)
#:use-module (guix http-client)
#:use-module (guix 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
recursive-import
%cran-updater
%bioconductor-updater))
;;; 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 "http://bioconductor.org/packages/")
;; The latest Bioconductor release is 3.5. Bioconductor packages should be
;; updated together.
(define (bioconductor-mirror-url name)
(string-append "https://raw.githubusercontent.com/Bioconductor-mirror/"
name "/release-3.5"))
(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."
;; This API always returns the latest release of the module.
(let ((url (string-append (case repository
((cran) (string-append %cran-url name))
((bioconductor) (bioconductor-mirror-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))))))
(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 (guix-name name)
"Return a Guix package name for a given R package name."
(string-append "r-" (string-map (match-lambda
(#\_ #\-)
(#\. #\-)
(chr (char-downcase chr)))
name)))
(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 (needs-zlib? tarball)
"Return #T if any of the Makevars files in the src directory of the TARBALL
contain a zlib linker flag."
(call-with-temporary-directory
(lambda (dir)
(let ((pattern (make-regexp "-lz")))
(parameterize ((current-error-port (%make-void-port "rw+")))
(system* "tar"
"xf" tarball "-C" dir
"--wildcards"
"*/src/Makevars*" "*/src/configure*" "*/configure*"))
(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)))))))
#t)
(find-files dir))))))
(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 ,(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)
(guix-name name)))
`((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
'())
(build-system r-build-system)
,@(maybe-inputs sysdepends)
,@(maybe-inputs (map guix-name propagate) 'propagated-inputs)
,@(if (needs-fortran? tarball)
`((native-inputs (,'quasiquote
,(list "gfortran"
(list 'unquote 'gfortran)))))
'())
(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* (recursive-import package-name #:optional (repo 'cran))
"Generate a stream of package expressions for PACKAGE-NAME and all its
dependencies."
(receive (package . dependencies)
(cran->guix-package package-name repo)
(if (not package)
stream-null
;; Generate a lazy stream of package expressions for all unknown
;; dependencies in the graph.
(let* ((make-state (lambda (queue done)
(cons queue done)))
(next (match-lambda
(((next . rest) . done) next)))
(imported (match-lambda
((queue . done) done)))
(done? (match-lambda
((queue . done)
(zero? (length queue)))))
(unknown? (lambda* (dependency #:optional (done '()))
(and (not (member dependency
done))
(null? (find-packages-by-name
(guix-name dependency))))))
(update (lambda (state new-queue)
(match state
(((head . tail) . done)
(make-state (lset-difference
equal?
(lset-union equal? new-queue tail)
done)
(cons head done)))))))
(stream-cons
package
(stream-unfold
;; map: produce a stream element
(lambda (state)
(cran->guix-package (next state) repo))
;; predicate
(negate done?)
;; generator: update the queue
(lambda (state)
(receive (package . dependencies)
(cran->guix-package (next state) repo)
(if package
(update state (filter (cut unknown? <>
(cons (next state)
(imported state)))
(car dependencies)))
;; TODO: Try the other archives before giving up
(update state (imported state)))))
;; initial state
(make-state (filter unknown? (car dependencies))
(list package-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 meta
(fetch-description 'bioconductor upstream-name))
(and meta
(let ((version (assoc-ref meta "Version")))
;; Bioconductor does not provide signatures.
(upstream-source
(package (package-name package))
(version version)
(urls (list (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? "http://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? "http://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 %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