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import cran: Fetch DESCRIPTION files from Github mirror.

* guix/import/cran.scm (%bioconductor-svn-url): Remove variable.
(bioconductor-mirror-url): New procedure.
(fetch-description): Take a REPOSITORY symbol instead of a BASE-URL string.
(cran->guix-package): Pass REPOSITORY symbol to "fetch-description".
(latest-cran-release, latest-bioconductor-release): Adjust accordingly.
(bioconductor-package?): Update comment about SVN.
wip-gexp-hygiene
Ricardo Wurmus 5 years ago
parent
commit
7c9fcb0825
No known key found for this signature in database GPG Key ID: 197A5888235FACAC
  1. 34
      guix/import/cran.scm

34
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)

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