;;; GNU Guix --- Functional package management for GNU ;;; Copyright © 2015-2024 Ricardo Wurmus ;;; Copyright © 2015-2017, 2019-2021, 2023 Ludovic Courtès ;;; Copyright © 2017 Mathieu Othacehe ;;; Copyright © 2020 Martin Becze ;;; Copyright © 2021 Sarah Morgensen ;;; Copyright © 2021 Simon Tournier ;;; Copyright © 2022 Hartmut Goebel ;;; ;;; 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 . (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-name input))) (else ((compose string->symbol upstream-input-downstream-name) input)))) (sort inputs (lambda (a b) (string-cilicenses 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://cran.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 3.18. Bioconductor packages should be ;; updated together. (define %bioconductor-version "3.18") (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) "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) "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)) (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))) (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" "unix" "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") ("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") ("openssl-devel" "openssl") ("openssl@1.1" "openssl-1.1") ("pandoc-citeproc" "pandoc") ("python3" "python-3") ("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 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 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 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) (stringpackage 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-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 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 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 latest-version (latest-bioconductor-package-version upstream-name)) (and latest-version ;; Bioconductor does not provide signatures. (upstream-source (package (package-name pkg)) (version latest-version) (urls (bioconductor-uri upstream-name latest-version)) (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 bioconductor-package?) (import latest-bioconductor-release))) ;;; cran.scm ends here