@@ 128,11 128,41 @@ package definition."
(define %cran-url "http://cran.r-project.org/web/packages/")
(define %bioconductor-url "https://bioconductor.org/packages/")
-;; The latest Bioconductor release is 3.5. Bioconductor packages should be
+;; The latest Bioconductor release is 3.6. Bioconductor packages should be
;; updated together.
(define (bioconductor-mirror-url name)
(string-append "https://raw.githubusercontent.com/Bioconductor-mirror/"
name "/release-3.5"))
+(define %bioconductor-version "3.6")
+
+(define %bioconductor-packages-list-url
+ (string-append "https://bioconductor.org/packages/"
+ %bioconductor-version "/bioc/src/contrib/PACKAGES"))
+
+(define (bioconductor-packages-list)
+ "Return the latest version of package NAME for the current bioconductor
+release."
+ (let ((url (string->uri %bioconductor-packages-list-url)))
+ (guard (c ((http-get-error? c)
+ (format (current-error-port)
+ "error: failed to retrieve list of packages from ~s: ~a (~s)~%"
+ (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")))
+ (chunk-lines (read-lines (http-fetch/cached url)))))))
+
+(define (latest-bioconductor-package-version name)
+ "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))
+ (cut assoc-ref <> "Version")))
(define (fetch-description repository name)
"Return an alist of the contents of the DESCRIPTION file for the R package