import: cran: Use Bioconductor 3.6 helpers.
* guix/import/cran.scm (bioconductor-mirror-url): Remove procedure. (fetch-description): Extract DESCRIPTION file from tarball for Bioconductor packages. (latest-bioconductor-release): Use latest-bioconductor-package-version.
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@ -130,9 +130,6 @@ package definition."
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;; The latest Bioconductor release is 3.6. 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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;; 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-version "3.6")
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(define %bioconductor-packages-list-url
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(define %bioconductor-packages-list-url
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@ -168,20 +165,35 @@ bioconductor package NAME, or #F if the package is unknown."
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"Return an alist of the contents of the DESCRIPTION file for the R package
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"Return an alist of the contents of the DESCRIPTION file for the R package
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NAME in the given REPOSITORY, or #f in case of failure. NAME is
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NAME in the given REPOSITORY, or #f in case of failure. NAME is
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case-sensitive."
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case-sensitive."
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;; This API always returns the latest release of the module.
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(case repository
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(let ((url (string-append (case repository
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((cran)
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((cran) (string-append %cran-url name))
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(let ((url (string-append %cran-url name "/DESCRIPTION")))
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((bioconductor) (bioconductor-mirror-url name)))
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(guard (c ((http-get-error? c)
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"/DESCRIPTION")))
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(format (current-error-port)
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(guard (c ((http-get-error? c)
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"error: failed to retrieve package information \
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(format (current-error-port)
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"error: failed to retrieve package information \
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from ~s: ~a (~s)~%"
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from ~s: ~a (~s)~%"
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(uri->string (http-get-error-uri c))
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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-code c)
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(http-get-error-reason c))
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(http-get-error-reason c))
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#f))
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#f))
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(description->alist (read-string (http-fetch url))))))
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(description->alist (read-string (http-fetch url))))))
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((bioconductor)
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;; Currently, the bioconductor project does not offer a way to access a
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;; package's DESCRIPTION file over HTTP, so we determine the version,
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;; download the source tarball, and then extract the DESCRIPTION file.
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(let* ((version (latest-bioconductor-package-version name))
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(url (bioconductor-uri name version))
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(tarball (with-store store (download-to-store store url))))
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(call-with-temporary-directory
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(lambda (dir)
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(parameterize ((current-error-port (%make-void-port "rw+"))
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(current-output-port (%make-void-port "rw+")))
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(and (zero? (system* "tar" "--wildcards" "-x"
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"--strip-components=1"
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"-C" dir
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"-f" tarball "*/DESCRIPTION"))
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(description->alist (with-input-from-file
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(string-append dir "/DESCRIPTION") read-string))))))))))
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(define (listify meta field)
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(define (listify meta field)
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"Look up FIELD in the alist META. If FIELD contains a comma-separated
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"Look up FIELD in the alist META. If FIELD contains a comma-separated
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@ -449,16 +461,15 @@ dependencies."
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(define upstream-name
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(define upstream-name
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(package->upstream-name package))
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(package->upstream-name package))
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(define meta
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(define version
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(fetch-description 'bioconductor upstream-name))
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(latest-bioconductor-package-version upstream-name))
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(and meta
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(and version
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(let ((version (assoc-ref meta "Version")))
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;; Bioconductor does not provide signatures.
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;; Bioconductor does not provide signatures.
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(upstream-source
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(upstream-source
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(package (package-name package))
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(package (package-name package))
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(version version)
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(version version)
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(urls (list (bioconductor-uri upstream-name version))))))
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(urls (list (bioconductor-uri upstream-name version)))))))
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(define (cran-package? package)
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(define (cran-package? package)
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"Return true if PACKAGE is an R package from CRAN."
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"Return true if PACKAGE is an R package from CRAN."
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