diff options
Diffstat (limited to 'guix/import/cran.scm')
| -rw-r--r-- | guix/import/cran.scm | 136 |
1 files changed, 96 insertions, 40 deletions
diff --git a/guix/import/cran.scm b/guix/import/cran.scm index a5f91fe8d2..8d963a7475 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -1,6 +1,7 @@ ;;; 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. ;;; @@ -44,7 +45,12 @@ bioconductor->guix-package recursive-import %cran-updater - %bioconductor-updater)) + %bioconductor-updater + + cran-package? + bioconductor-package? + bioconductor-data-package? + bioconductor-experiment-package?)) ;;; Commentary: ;;; @@ -122,19 +128,21 @@ package definition." (define %cran-url "http://cran.r-project.org/web/packages/") (define %bioconductor-url "http://bioconductor.org/packages/") -;; The latest Bioconductor release is 3.4. Bioconductor packages should be +;; The latest Bioconductor release is 3.5. Bioconductor packages should be ;; updated together. -(define %bioconductor-svn-url - (string-append "https://readonly:readonly@" - "hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/" - "madman/Rpacks/")) - +(define (bioconductor-mirror-url name) + (string-append "https://raw.githubusercontent.com/Bioconductor-mirror/" + name "/release-3.5")) -(define (fetch-description base-url name) +(define (fetch-description repository name) "Return an alist of the contents of the DESCRIPTION file for the R package -NAME, or #f in case of failure. NAME is case-sensitive." +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 base-url name "/DESCRIPTION"))) + (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 \ @@ -199,17 +207,16 @@ empty list when the FIELD cannot be found." (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." +(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 "-lz"))) + (let ((pattern (make-regexp regexp))) (parameterize ((current-error-port (%make-void-port "rw+"))) - (system* "tar" - "xf" tarball "-C" dir - "--wildcards" - "*/src/Makevars*" "*/src/configure*" "*/configure*")) + (apply system* "tar" + "xf" tarball "-C" dir + `("--wildcards" ,@file-patterns))) (any (lambda (file) (call-with-input-file file (lambda (port) @@ -218,10 +225,23 @@ contain a zlib linker flag." (cond ((eof-object? line) #f) ((regexp-exec pattern line) #t) - (else (loop))))))) - #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." @@ -271,11 +291,12 @@ from the alist META, which was derived from the R package's DESCRIPTION file." (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))))) - '()) + ,@(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)) @@ -290,11 +311,8 @@ from the alist META, which was derived from the R package's DESCRIPTION file." (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* ((url (case repo - ((cran) %cran-url) - ((bioconductor) %bioconductor-svn-url))) - (module-meta (fetch-description url package-name))) - (and=> module-meta (cut description->package repo <>)))))) + (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 @@ -374,7 +392,7 @@ dependencies." (start (string-rindex url #\/))) ;; The URL ends on ;; (string-append "/" name "_" version ".tar.gz") - (substring url (+ start 1) end))) + (and start end (substring url (+ start 1) end)))) (_ #f))) (_ #f))))) @@ -385,7 +403,7 @@ dependencies." (package->upstream-name package)) (define meta - (fetch-description %cran-url upstream-name)) + (fetch-description 'cran upstream-name)) (and meta (let ((version (assoc-ref meta "Version"))) @@ -402,7 +420,7 @@ dependencies." (package->upstream-name package)) (define meta - (fetch-description %bioconductor-svn-url upstream-name)) + (fetch-description 'bioconductor upstream-name)) (and meta (let ((version (assoc-ref meta "Version"))) @@ -415,6 +433,9 @@ dependencies." (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)) @@ -424,13 +445,48 @@ dependencies." (define (bioconductor-package? package) "Return true if PACKAGE is an R package from Bioconductor." - (and (string-prefix? "r-" (package-name package)) - (match (and=> (package-source package) origin-uri) - ((? string? uri) - (string-prefix? "http://bioconductor.org" uri)) - ((? list? uris) - (any (cut string-prefix? "http://bioconductor.org" <>) uris)) - (_ #f)))) + (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 (bioconductor-experiment-package? package) + "Return true if PACKAGE is an R experiment package from Bioconductor." + (let ((predicate (lambda (uri) + (and (string-prefix? "http://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 |