;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2015-2024 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2015-2017, 2019-2021, 2023 Ludovic Courtès <ludo@gnu.org>
;;; Copyright © 2017 Mathieu Othacehe <m.othacehe@gmail.com>
;;; Copyright © 2020 Martin Becze <mjbecze@riseup.net>
;;; Copyright © 2021 Sarah Morgensen <iskarian@mgsn.dev>
;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2022 Hartmut Goebel <h.goebel@crazy-compilers.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 popen)
#: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 (srfi srfi-35)
#:use-module (srfi srfi-71)
#:use-module (web uri)
#:use-module (guix memoization)
#:use-module (guix http-client)
#:use-module (guix diagnostics)
#:use-module (guix hash)
#:use-module (guix i18n)
#: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
delete-file-recursively
with-directory-excursion))
#:use-module (guix utils)
#:use-module (guix git)
#:use-module ((guix build-system r) #:select (cran-uri bioconductor-uri))
#:use-module (guix upstream)
#:use-module (guix packages)
#:use-module (guix sets)
#:export (%input-style
%bioconductor-version
download
fetch-description
cran->guix-package
bioconductor->guix-package
cran-recursive-import
%cran-updater
%bioconductor-updater
%bioconductor-version
cran-package?
bioconductor-package?
bioconductor-data-package?
bioconductor-experiment-package?
description->alist
description->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 %input-style
(make-parameter 'variable)) ; or 'specification
(define (format-inputs inputs)
"Generate a sorted list of package inputs from a list of upstream inputs."
(map (lambda (input)
(case (%input-style)
((specification)
`(specification->package ,(upstream-input-downstream-name input)))
(else
((compose string->symbol
upstream-input-downstream-name)
input))))
(sort inputs
(lambda (a b)
(string-ci<? (upstream-input-name a)
(upstream-input-name b))))))
(define (string->licenses license-string license-prefix)
(let ((licenses
(map string-trim-both
(string-tokenize license-string
(char-set-complement (char-set #\|))))))
(string->license licenses license-prefix)))
(define (string->license license-string license-prefix)
(let ((prefix license-prefix))
(match license-string
("AGPL-3" (prefix 'agpl3))
("AGPL (>= 3)" (prefix 'agpl3+))
("Artistic-2.0" (prefix 'artistic2.0))
((or "Apache License 2.0"
"Apache License (== 2.0)"
"Apache License (>= 2.0)")
(prefix 'asl2.0))
("BSD_2_clause" (prefix 'bsd-2))
("BSD_2_clause + file LICENSE" (prefix 'bsd-2))
("BSD_3_clause" (prefix 'bsd-3))
("BSD_3_clause + file LICENSE" (prefix 'bsd-3))
("CC0" (prefix 'cc0))
("CC BY-SA 4.0" (prefix 'cc-by-sa4.0))
("CeCILL" (prefix 'cecill))
((or "GPL"
"GNU General Public License")
`(list ,(prefix 'gpl2+) ,(prefix 'gpl3+)))
((or "GPL (>= 2)"
"GPL (>= 2.0)")
(prefix 'gpl2+))
((or "GPL (> 2)"
"GPL (>= 3)"
"GPL (>= 3.0)"
"GPL (>=3)"
"GNU General Public License (>= 3)")
(prefix 'gpl3+))
((or "GPL-2"
"GNU General Public License version 2")
(prefix 'gpl2))
((or "GPL-3"
"GNU General Public License version 3")
(prefix 'gpl3))
((or "GNU Lesser General Public License"
"LGPL")
(prefix 'lgpl2.0+))
("LGPL-2" (prefix 'lgpl2.0))
("LGPL-2.1" (prefix 'lgpl2.1))
("LGPL-3" (prefix 'lgpl3))
((or "LGPL (>= 2)"
"LGPL (>= 2.0)")
(prefix 'lgpl2.0+))
("LGPL (>= 2.1)" (prefix 'lgpl2.1+))
("LGPL (>= 3)" (prefix 'lgpl3+))
("MIT" (prefix 'expat))
("MIT + file LICENSE" (prefix 'expat))
("file LICENSE"
`(,(prefix 'fsdg-compatible) "file://LICENSE"))
((x) (string->license x license-prefix))
((lst ...) `(list ,@(map (cut string->license <> license-prefix) lst)))
(unknown `(,(prefix 'fsdg-compatible) ,unknown)))))
(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* (maybe-inputs package-inputs #:optional (input-type 'inputs))
"Given a list of PACKAGE-INPUTS, tries to generate the TYPE field of a
package definition."
(match package-inputs
(()
'())
((package-inputs ...)
`((,input-type (list ,@(format-inputs package-inputs)))))))
(define %cran-url "https://cloud.r-project.org/web/packages/")
(define %cran-canonical-url "https://cran.r-project.org/package=")
(define %bioconductor-url "https://bioconductor.org/packages/")
;; The latest Bioconductor release is 3.19. Bioconductor packages should be
;; updated together.
(define %bioconductor-version "3.19")
(define* (bioconductor-packages-list-url #:optional type)
(string-append "https://bioconductor.org/packages/"
%bioconductor-version
(match type
('annotation "/data/annotation")
('experiment "/data/experiment")
(_ "/bioc"))
"/src/contrib/PACKAGES"))
(define* (bioconductor-packages-list #:optional type)
"Return the latest version of package NAME for the current bioconductor
release."
(let ((url (string->uri (bioconductor-packages-list-url type))))
(guard (c ((http-get-error? c)
(warning (G_ "failed to retrieve list of packages \
from ~a: ~a (~a)~%")
(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")))
(let* ((port (http-fetch/cached url))
(lines (read-lines port)))
(close-port port)
(chunk-lines lines))))))
(define* (latest-bioconductor-package-version name #:optional type)
"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 type))
(cut assoc-ref <> "Version")))
;; Little helper to download URLs only once.
(define download
(memoize
(lambda* (url #:key method (ref '()))
(with-store store
(cond
((eq? method 'git)
(latest-repository-commit store url #:ref ref))
((eq? method 'hg)
(call-with-temporary-directory
(lambda (dir)
(unless (zero? (system* "hg" "clone" url dir))
(leave (G_ "~A: hg download failed~%") url))
(with-directory-excursion dir
(let* ((port (open-pipe* OPEN_READ "hg" "id" "--id"))
(changeset (string-trim-right (read-string port))))
(close-pipe port)
(for-each delete-file-recursively
(find-files dir "^\\.hg$" #:directories? #t))
(let ((store-directory
(add-to-store store (basename url) #t "sha256" dir)))
(values store-directory changeset)))))))
(else
(match url
((? string?)
(download-to-store store url))
((urls ...)
;; Try all the URLs. A use case where this is useful is when one
;; of the URLs is the /Archive CRAN URL.
(any (cut download-to-store store <>) urls)))))))))
(define* (fetch-description-from-tarball url #:key (download download))
"Fetch the tarball at URL, extra its 'DESCRIPTION' file, parse it, and
return the resulting alist."
(match (download url)
(#f #f)
(tarball
(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
(call-with-input-file (string-append dir "/DESCRIPTION")
read-string)))))))))
(define* (fetch-description repository name #:optional version replacement-download)
"Return an alist of the contents of the DESCRIPTION file for the R package
NAME at VERSION in the given REPOSITORY, or #f in case of failure. NAME is
case-sensitive."
(case repository
((cran)
(guard (c ((http-get-error? c)
(warning (G_ "failed to retrieve package information \
from ~a: ~a (~a)~%")
(uri->string (http-get-error-uri c))
(http-get-error-code c)
(http-get-error-reason c))
#f))
;; When VERSION is true, we have to download the tarball to get at its
;; 'DESCRIPTION' file; only the latest one is directly accessible over
;; HTTP.
(if version
(let ((urls (list (string-append "mirror://cran/src/contrib/"
name "_" version ".tar.gz")
(string-append "mirror://cran/src/contrib/Archive/"
name "/"
name "_" version ".tar.gz"))))
(fetch-description-from-tarball
urls #:download (or replacement-download
download)))
(let* ((url (string-append %cran-url name "/DESCRIPTION"))
(port (http-fetch url))
(result (description->alist (read-string port))))
(close-port port)
result))))
((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* ((type (or
(and (latest-bioconductor-package-version name) #t)
(and (latest-bioconductor-package-version name 'annotation) 'annotation)
(and (latest-bioconductor-package-version name 'experiment) 'experiment)))
;; TODO: Honor VERSION.
(version (latest-bioconductor-package-version name type))
(url (car (bioconductor-uri name version type)))
(meta (fetch-description-from-tarball
url #:download (or replacement-download
download))))
(if (boolean? type)
meta
(cons `(bioconductor-type . ,type) meta))))
((git)
(and (string-prefix? "http" name)
;; Download the git repository at "NAME"
(call-with-values
(lambda () (download name #:method 'git))
(lambda (dir commit)
(and=> (description->alist (with-input-from-file
(string-append dir "/DESCRIPTION") read-string))
(lambda (meta)
(cons* `(git . ,name)
`(git-commit . ,commit)
meta)))))))
((hg)
(and (string-prefix? "http" name)
;; Download the mercurial repository at "NAME"
(call-with-values
(lambda () (download name #:method 'hg))
(lambda (dir changeset)
(and=> (description->alist (with-input-from-file
(string-append dir "/DESCRIPTION") read-string))
(lambda (meta)
(cons* `(hg . ,name)
`(hg-changeset . ,changeset)
meta)))))))))
(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))))))
;; Trick Guile 3 so that it keeps the 'listify' binding accessible *and*
;; private even though this module is declarative.
(set! listify listify)
(define default-r-packages
(list "base"
"compiler"
"datasets"
"grDevices"
"graphics"
"grid"
"methods"
"parallel"
"splines"
"stats"
"stats4"
"tcltk"
"tools"
"translations"
"utils"))
;; The field for system dependencies is often abused to specify non-package
;; dependencies (such as c++11). This list is used to ignore them.
(define invalid-packages
(list "build-essential"
"c++"
"c++11"
"c++14"
"c++17"
"c99"
"getopt::long"
"gnu"
"posix.1-2001"
"linux"
"libR"
"none"
"rtools"
"unix"
"use_c17"
"windows"
"xcode"
"xquartz"))
(define (transform-sysname sysname)
"Return a Guix package name for the common package name SYSNAME."
(match sysname
("booktabs" "texlive-booktabs")
("bowtie2" "bowtie")
("cat" "coreutils")
("java" "openjdk")
("exiftool" "perl-image-exiftool")
("fftw3" "fftw")
("freetype2" "freetype")
("gettext" "gnu-gettext")
("gmake" "gnu-make")
("h5py" "python-h5py")
("hmmer3" "hmmer")
("leidenalg" "python-leidenalg")
("libarchive-devel" "libarchive")
("libarchive_dev" "libarchive")
("libbz2" "bzip2")
("libexpat" "expat")
("libjpeg" "libjpeg-turbo")
("liblz4" "lz4")
("liblzma" "xz")
("libssl-dev" "openssl")
("libssl_dev" "openssl")
("libzstd" "zstd")
("libxml2-devel" "libxml2")
("libxml2-dev" "libxml2")
("libz" "zlib")
("libz-dev" "zlib")
("mariadb-devel" "mariadb")
("mysql56_dev" "mariadb")
("nodejs" "node")
("numpy" "python-numpy")
("openssl-devel" "openssl")
("openssl@1.1" "openssl-1.1")
("packaging" "python-packaging")
("pandas" "python-pandas")
("pandoc-citeproc" "pandoc")
("python3" "python-3")
("pytorch" "python-pytorch")
("scikit-learn" "python-scikit-learn")
("scipy" "python-scipy")
("sklearn" "python-scikit-learn")
("sqlite3" "sqlite")
("svn" "subversion")
("tcl/tk" "tcl")
("udunits-2" "udunits")
("whoami" "coreutils")
("x11" "libx11")
("xml2" "libxml2")
("zlib-devel" "zlib")
("zlib1g-dev" "zlib")
(_ sysname)))
(define cran-guix-name (cut guix-name "r-" <>))
(define (directory-needs-fortran? dir)
"Check if the directory DIR contains Fortran source files."
(match (find-files dir "\\.f(90|95)?$")
(() #f)
(_ #t)))
(define (directory-needs-esbuild? dir)
"Check if the directory DIR contains minified JavaScript files and thus
needs a JavaScript compiler."
(match (find-files dir "\\.min.js$")
(() #f)
(_ #t)))
(define (files-match-pattern? directory regexp . file-patterns)
"Return #T if any of the files matching FILE-PATTERNS in the DIRECTORY match
the given REGEXP."
(let ((pattern (make-regexp regexp)))
(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))))))))
(apply find-files directory file-patterns))))
(define packages-for-matches
'(("-lcrypto" . "openssl")
("-lcurl" . "curl")
("-lgit2" . "libgit2")
("-lpcre" . "pcre2")
("-lssh" . "openssh")
("-lssl" . "openssl")
("-ltbb" . "tbb")
("-lz" . "zlib")
("gsl-config" . "gsl")
("xml2-config" . "libxml2")
("CURL_LIBS" . "curl")))
(define libraries-pattern
(make-regexp
(string-append "("
(string-join
(map (compose regexp-quote first) packages-for-matches) "|")
")")))
(define (needed-libraries-in-directory dir)
"Return a list of package names that correspond to libraries that are
referenced in build system files."
(set->list
(fold
(lambda (file packages)
(call-with-input-file file
(lambda (port)
(let loop ((packages packages))
(let ((line (read-line port)))
(cond
((eof-object? line) packages)
(else
(loop
(fold (lambda (match acc)
(or (and=> (assoc-ref packages-for-matches
(match:substring match))
(cut set-insert <> acc))
acc))
packages
(list-matches libraries-pattern line))))))))))
(set)
(find-files dir "(Makevars(.in.*)?|configure.*)"))))
(define (directory-needs-pkg-config? dir)
"Return #T if any of the Makevars files in the src directory DIR reference
the pkg-config tool."
(files-match-pattern? dir "pkg-config"
"(Makevars.*|configure.*)"))
(define (source-dir->dependencies dir)
"Guess dependencies of R package source in DIR and return a list of
<upstream-input> corresponding to the dependencies guessed from source files
in DIR."
(define (native name)
(upstream-input
(name name)
(downstream-name name)
(type 'native)))
(append (map (lambda (name)
(upstream-input
(name name)
(downstream-name name)))
(needed-libraries-in-directory dir))
(if (directory-needs-esbuild? dir)
(list (native "esbuild"))
'())
(if (directory-needs-pkg-config? dir)
(list (native "pkg-config"))
'())
(if (directory-needs-fortran? dir)
(list (native "gfortran"))
'())))
(define (source->dependencies source tarball?)
"SOURCE-DIR->DEPENDENCIES, but for directories and tarballs as indicated
by TARBALL?"
(if tarball?
(call-with-temporary-directory
(lambda (dir)
(parameterize ((current-error-port (%make-void-port "rw+")))
(system* "tar" "xf" source "-C" dir))
(source-dir->dependencies dir)))
(source-dir->dependencies source)))
(define (vignette-builders meta)
(map (lambda (name)
(upstream-input
(name name)
(downstream-name (cran-guix-name name))
(type 'native)))
(listify meta "VignetteBuilder")))
(define (uri-helper repository)
(match repository
('cran cran-uri)
('bioconductor bioconductor-uri)
('git #f)
('hg #f)))
(define (cran-package-source-url meta repository)
"Return the URL of the source code referred to by META, a package in
REPOSITORY."
(case repository
((git) (assoc-ref meta 'git))
((hg) (assoc-ref meta 'hg))
(else
(match (apply (uri-helper repository)
(assoc-ref meta "Package")
(assoc-ref meta "Version")
(case repository
((bioconductor)
(list (assoc-ref meta 'bioconductor-type)))
(else '())))
((urls ...) urls)
((? string? url) url)
(_ #f)))))
(define (cran-package-propagated-inputs meta)
"Return the list of <upstream-input> derived from dependency information in
META."
(filter-map (lambda (name)
(and (not (member name
(append default-r-packages invalid-packages)))
(upstream-input
(name name)
(downstream-name (cran-guix-name name))
(type 'propagated))))
(lset-union equal?
(listify meta "Imports")
(listify meta "LinkingTo")
(delete "R" (listify meta "Depends")))))
(define* (cran-package-inputs meta repository
#:key (download-source download))
"Return the list of <upstream-input> corresponding to all the dependencies
of META, a package in REPOSITORY."
(let* ((url (cran-package-source-url meta repository))
(name (assoc-ref meta "Package"))
(source (download-source url
#:method
(cond ((assoc-ref meta 'git) 'git)
((assoc-ref meta 'hg) 'hg)
(else #f))))
(tarball? (not (or (assoc-ref meta 'git)
(assoc-ref meta 'hg)))))
(sort (filter
;; Prevent tight cycles.
(lambda (input)
((negate string=?) name (upstream-input-name input)))
(append (source->dependencies source tarball?)
(filter-map (lambda (name)
(and (not (member name invalid-packages))
(upstream-input
(name name)
(downstream-name
(transform-sysname name)))))
(map string-downcase
(listify meta "SystemRequirements")))
(cran-package-propagated-inputs meta)
(vignette-builders meta)))
(lambda (input1 input2)
(string<? (upstream-input-downstream-name input1)
(upstream-input-downstream-name input2))))))
(define (phases-for-inputs input-names)
"Generate a list of build phases based on the provided INPUT-NAMES, a list
of package names for all input packages."
(let ((rules
(list (lambda ()
(and (any (lambda (name)
(member name '("styler" "ExperimentHub")))
input-names)
'(add-after 'unpack 'set-HOME
(lambda _ (setenv "HOME" "/tmp")))))
(lambda ()
(and (member "esbuild" input-names)
'(add-after 'unpack 'process-javascript
(lambda* (#:key inputs #:allow-other-keys)
(with-directory-excursion "inst/"
(for-each (match-lambda
((source . target)
(minify source #:target target)))
'())))))))))
(fold (lambda (rule phases)
(let ((new-phase (rule)))
(if new-phase (cons new-phase phases) phases)))
(list)
rules)))
(define (maybe-arguments inputs)
"Generate a list for the arguments field that can be spliced into a package
S-expression."
(let ((input-names (map upstream-input-name inputs))
(esbuild-modules '(#:modules
'((guix build r-build-system)
(guix build minify-build-system)
(guix build utils)
(ice-9 match))
#:imported-modules
`(,@%r-build-system-modules
(guix build minify-build-system)))))
(match (phases-for-inputs input-names)
(() '())
(phases
`((arguments
(list
,@(if (member "esbuild" input-names)
esbuild-modules '())
#:phases
'(modify-phases %standard-phases
,@phases))))))))
(define* (description->package repository meta #:key (license-prefix identity)
(download-source download))
"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)
((git) #f)
((hg) #f)))
(canonical-url-base (case repository
((cran) %cran-canonical-url)
((bioconductor) %bioconductor-url)
((git) #f)))
(name (assoc-ref meta "Package"))
(synopsis (assoc-ref meta "Title"))
(version (assoc-ref meta "Version"))
(license (string->licenses (assoc-ref meta "License") license-prefix))
;; Some packages have multiple home pages. Some have none.
(home-page (case repository
((git) (assoc-ref meta 'git))
((hg) (assoc-ref meta 'hg))
(else (match (listify meta "URL")
((url rest ...) url)
(_ (string-append canonical-url-base name))))))
(source-url (cran-package-source-url meta repository))
(git? (if (assoc-ref meta 'git) #true #false))
(hg? (if (assoc-ref meta 'hg) #true #false))
(source (download-source source-url #:method (cond
(git? 'git)
(hg? 'hg)
(else #f))))
(uri-helper (uri-helper repository))
(inputs (cran-package-inputs meta repository
#:download-source download-source))
(package
`(package
(name ,(cran-guix-name name))
(version ,(cond
(git?
`(git-version ,version revision commit))
(hg?
`(string-append ,version "-" revision "." changeset))
(else version)))
(source (origin
(method ,(cond
(git? 'git-fetch)
(hg? 'hg-fetch)
(else 'url-fetch)))
(uri ,(cond
(git?
`(git-reference
(url ,(assoc-ref meta 'git))
(commit commit)))
(hg?
`(hg-reference
(url ,(assoc-ref meta 'hg))
(changeset changeset)))
(else
`(,(procedure-name uri-helper) ,name version
,@(or (and=> (assoc-ref meta 'bioconductor-type)
(lambda (type)
(list (list 'quote type))))
'())))))
,@(cond
(git?
'((file-name (git-file-name name version))))
(hg?
'((file-name (string-append name "-" version "-checkout"))))
(else '()))
(sha256
(base32
,(bytevector->nix-base32-string
(file-hash* source #:recursive? (or git? hg?)))))))
,@(if (not (and git? hg?
(equal? (string-append "r-" name)
(cran-guix-name name))))
`((properties ,`(,'quasiquote ((,'upstream-name . ,name)))))
'())
(build-system r-build-system)
,@(maybe-arguments inputs)
,@(maybe-inputs (filter (upstream-input-type-predicate 'regular)
inputs)
'inputs)
,@(maybe-inputs (filter (upstream-input-type-predicate
'propagated)
inputs)
'propagated-inputs)
,@(maybe-inputs (filter (upstream-input-type-predicate 'native)
inputs)
'native-inputs)
(home-page ,(if (string-null? home-page)
(string-append base-url name)
home-page))
(synopsis ,(beautify-synopsis synopsis))
(description ,(beautify-description (or (assoc-ref meta "Description")
"")))
(license ,license))))
(values
(cond
(git?
`(let ((commit ,(assoc-ref meta 'git-commit))
(revision "1"))
,package))
(hg?
`(let ((changeset ,(assoc-ref meta 'hg-changeset))
(revision "1"))
,package))
(else package))
(filter-map (lambda (input)
(and (eq? 'propagated (upstream-input-type input))
(upstream-input-name input)))
inputs))))
(define cran->guix-package
(memoize
(lambda* (package-name #:key (repo 'cran) version (license-prefix identity)
(fetch-description fetch-description)
(download-source download)
#:allow-other-keys)
"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 version)))
(if description
(description->package repo description
#:license-prefix license-prefix
#:download-source download-source)
(case repo
((git)
;; Retry import from Bioconductor
(cran->guix-package package-name #:repo 'bioconductor
#:license-prefix license-prefix))
((hg)
;; Retry import from Bioconductor
(cran->guix-package package-name #:repo 'bioconductor
#:license-prefix license-prefix))
((bioconductor)
;; Retry import from CRAN
(cran->guix-package package-name #:repo 'cran
#:license-prefix license-prefix))
(else
(values #f '()))))))))
(define* (cran-recursive-import package-name #:key (repo 'cran) version
(license-prefix identity))
(recursive-import package-name
#:version version
#:repo repo
#:repo->guix-package cran->guix-package
#:guix-name cran-guix-name
#:license-prefix license-prefix))
;;;
;;; 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 pkg #:key (version #f))
"Return an <upstream-source> for the latest release of the package PKG."
(when version
(error
(formatted-message
(G_ "~a provides only the latest version of each package, sorry.")
"CRAN")))
(define upstream-name
(package->upstream-name pkg))
(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 pkg))
(version version)
(urls (cran-uri upstream-name version))
(inputs (cran-package-inputs meta 'cran))))))
(define* (latest-bioconductor-release pkg #:key (version #f))
"Return an <upstream-source> for the latest release of the package PKG."
(when version
(error
(formatted-message
(G_ "~a provides only the latest version of each package, sorry.")
"bioconductor.org")))
(define upstream-name
(package->upstream-name pkg))
(define type
(cond
((bioconductor-data-package? pkg)
'annotation)
((bioconductor-experiment-package? pkg)
'experiment)
((bioconductor-package? pkg)
#true)
(else #false)))
(define latest-version
(latest-bioconductor-package-version upstream-name type))
(and latest-version
;; Bioconductor does not provide signatures.
(upstream-source
(package (package-name pkg))
(version latest-version)
(urls (bioconductor-uri upstream-name latest-version type))
(inputs
(let ((meta (fetch-description 'bioconductor upstream-name)))
(cran-package-inputs meta 'bioconductor))))))
(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".
((url-predicate (cut string-prefix? "mirror://cran" <>)) package)))
(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))
((url-predicate predicate) package))))
(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))
((url-predicate predicate) package))))
(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))
((url-predicate predicate) package))))
(define %cran-updater
(upstream-updater
(name 'cran)
(description "Updater for CRAN packages")
(pred cran-package?)
(import latest-cran-release)))
(define %bioconductor-updater
(upstream-updater
(name 'bioconductor)
(description "Updater for Bioconductor packages")
(pred (lambda (pkg)
(or (bioconductor-package? pkg)
(bioconductor-data-package? pkg)
(bioconductor-experiment-package? pkg))))
(import latest-bioconductor-release)))
;;; cran.scm ends here
