diff options
| -rw-r--r-- | guix/import/cran.scm | 34 |
1 files changed, 18 insertions, 16 deletions
diff --git a/guix/import/cran.scm b/guix/import/cran.scm index a94051655c..221b5420e2 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -125,17 +125,19 @@ package definition." ;; 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_5/" - "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 \ @@ -291,11 +293,8 @@ 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 @@ -386,7 +385,7 @@ 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"))) @@ -403,7 +402,7 @@ 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"))) @@ -430,7 +429,10 @@ dependencies." "Return true if PACKAGE is an R package from Bioconductor." (let ((predicate (lambda (uri) (and (string-prefix? "http://bioconductor.org" uri) - ;; Data packages are not listed in SVN + ;; 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/")))))) (and (string-prefix? "r-" (package-name package)) (match (and=> (package-source package) origin-uri) |