499 lines
19 KiB
Scheme
499 lines
19 KiB
Scheme
;;; GNU Guix --- Functional package management for GNU
|
||
;;; Copyright © 2015, 2016, 2017, 2018 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-2)
|
||
#: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 "https://cran.r-project.org/web/packages/")
|
||
(define %bioconductor-url "https://bioconductor.org/packages/")
|
||
|
||
;; The latest Bioconductor release is 3.8. Bioconductor packages should be
|
||
;; updated together.
|
||
(define %bioconductor-version "3.8")
|
||
|
||
(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")))
|
||
|
||
;; Little helper to download URLs only once.
|
||
(define download
|
||
(memoize
|
||
(lambda (url)
|
||
(with-store store (download-to-store store url)))))
|
||
|
||
(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.
|
||
(and-let* ((version (latest-bioconductor-package-version name))
|
||
(url (car (bioconductor-uri name version)))
|
||
(tarball (download 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 (download 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."
|
||
(let ((description (fetch-description repo package-name)))
|
||
(if (and (not description)
|
||
(eq? repo 'bioconductor))
|
||
;; Retry import from CRAN
|
||
(cran->guix-package package-name 'cran)
|
||
(and description
|
||
(description->package repo description)))))))
|
||
|
||
(define* (cran-recursive-import package-name #:optional (repo 'cran))
|
||
(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
|