diff options
Diffstat (limited to 'guix/import/cran.scm')
| -rw-r--r-- | guix/import/cran.scm | 64 |
1 files changed, 53 insertions, 11 deletions
diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 59c65f9fa5..d7497e6fb9 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -1,5 +1,5 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2015-2023 Ricardo Wurmus <rekado@elephly.net> +;;; 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> @@ -55,6 +55,10 @@ #:use-module (guix sets) #:export (%input-style + %bioconductor-version + download + fetch-description + cran->guix-package bioconductor->guix-package cran-recursive-import @@ -81,6 +85,21 @@ (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-ci<? (upstream-input-name a) + (upstream-input-name b)))))) + (define (string->licenses license-string license-prefix) (let ((licenses (map string-trim-both @@ -173,17 +192,15 @@ package definition." (() '()) ((package-inputs ...) - `((,input-type (list ,@(map (compose string->symbol - upstream-input-downstream-name) - 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 3.17. Bioconductor packages should be +;; The latest Bioconductor release is 3.18. Bioconductor packages should be ;; updated together. -(define %bioconductor-version "3.17") +(define %bioconductor-version "3.18") (define* (bioconductor-packages-list-url #:optional type) (string-append "https://bioconductor.org/packages/" @@ -253,7 +270,7 @@ bioconductor package NAME, or #F if the package is unknown." ;; of the URLs is the /Archive CRAN URL. (any (cut download-to-store store <>) urls))))))))) -(define (fetch-description-from-tarball url) +(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) @@ -271,7 +288,7 @@ return the resulting alist." (call-with-input-file (string-append dir "/DESCRIPTION") read-string))))))))) -(define* (fetch-description repository name #:optional version) +(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." @@ -293,7 +310,9 @@ from ~a: ~a (~a)~%") (string-append "mirror://cran/src/contrib/Archive/" name "/" name "_" version ".tar.gz")))) - (fetch-description-from-tarball urls)) + (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)))) @@ -310,7 +329,9 @@ from ~a: ~a (~a)~%") ;; TODO: Honor VERSION. (version (latest-bioconductor-package-version name type)) (url (car (bioconductor-uri name version type))) - (meta (fetch-description-from-tarball url))) + (meta (fetch-description-from-tarball + url #:download (or replacement-download + download)))) (if (boolean? type) meta (cons `(bioconductor-type . ,type) meta)))) @@ -383,7 +404,8 @@ empty list when the FIELD cannot be found." ;; 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 "c++" + (list "build-essential" + "c++" "c++11" "c++14" "c++17" @@ -392,7 +414,9 @@ empty list when the FIELD cannot be found." "gnu" "posix.1-2001" "linux" + "libR" "none" + "rtools" "unix" "windows" "xcode" @@ -410,6 +434,9 @@ empty list when the FIELD cannot be found." ("freetype2" "freetype") ("gettext" "gnu-gettext") ("gmake" "gnu-make") + ("h5py" "python-h5py") + ("hmmer3" "hmmer") + ("leidenalg" "python-leidenalg") ("libarchive-devel" "libarchive") ("libarchive_dev" "libarchive") ("libbz2" "bzip2") @@ -417,13 +444,27 @@ empty list when the FIELD cannot be found." ("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") @@ -432,6 +473,7 @@ empty list when the FIELD cannot be found." ("x11" "libx11") ("xml2" "libxml2") ("zlib-devel" "zlib") + ("zlib1g-dev" "zlib") (_ sysname))) (define cran-guix-name (cut guix-name "r-" <>)) |