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import: cran: Add support for Bioconductor 3.6. 

* guix/import/cran.scm (%bioconductor-version,
%bioconductor-packages-list-url): New variables.
(bioconductor-packages-list, latest-bioconductor-package-version): New
procedures.
master
Ricardo Wurmus 2017-11-06 17:09:06 +01:00
parent 6b46b04f91
commit 84dfdc5759
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1 changed files with 31 additions and 1 deletions
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guix/import/cran.scm
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@ -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