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.
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@ -128,11 +128,41 @@ (define* (maybe-inputs package-inputs #:optional (type 'inputs))
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(define %cran-url "http://cran.r-project.org/web/packages/")
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(define %bioconductor-url "https://bioconductor.org/packages/")
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;; The latest Bioconductor release is 3.5. Bioconductor packages should be
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;; The latest Bioconductor release is 3.6. Bioconductor packages should be
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;; updated together.
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(define (bioconductor-mirror-url name)
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(string-append "https://raw.githubusercontent.com/Bioconductor-mirror/"
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name "/release-3.5"))
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(define %bioconductor-version "3.6")
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(define %bioconductor-packages-list-url
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(string-append "https://bioconductor.org/packages/"
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%bioconductor-version "/bioc/src/contrib/PACKAGES"))
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(define (bioconductor-packages-list)
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"Return the latest version of package NAME for the current bioconductor
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release."
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(let ((url (string->uri %bioconductor-packages-list-url)))
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(guard (c ((http-get-error? c)
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(format (current-error-port)
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"error: failed to retrieve list of packages from ~s: ~a (~s)~%"
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(uri->string (http-get-error-uri c))
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(http-get-error-code c)
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(http-get-error-reason c))
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#f))
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;; Split the big list on empty lines, then turn each chunk into an
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;; alist of attributes.
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(map (lambda (chunk)
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(description->alist (string-join chunk "\n")))
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(chunk-lines (read-lines (http-fetch/cached url)))))))
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(define (latest-bioconductor-package-version name)
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"Return the version string corresponding to the latest release of the
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bioconductor package NAME, or #F if the package is unknown."
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(and=> (find (lambda (meta)
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(string=? (assoc-ref meta "Package") name))
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(bioconductor-packages-list))
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(cut assoc-ref <> "Version")))
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(define (fetch-description repository name)
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"Return an alist of the contents of the DESCRIPTION file for the R package
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