--- Begin Message ---
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Subject: |
[PATCH] import cran: Fetch DESCRIPTION files from Github mirror. |
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Date: |
Wed, 5 Apr 2017 15:37:03 +0200 |
* 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.
---
guix/import/cran.scm | 34 ++++++++++++++++++----------------
1 file changed, 18 insertions(+), 16 deletions(-)
diff --git a/guix/import/cran.scm b/guix/import/cran.scm
index 4d36882cf..8e24f6e17 100644
--- a/guix/import/cran.scm
+++ b/guix/import/cran.scm
@@ -124,17 +124,19 @@ package definition."
;; The latest Bioconductor release is 3.4. Bioconductor packages should be
;; updated together.
-(define %bioconductor-svn-url
- (string-append "https://readonly:readonly@";
- "hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/"
- "madman/Rpacks/"))
+(define (bioconductor-mirror-url name)
+ (string-append "https://raw.githubusercontent.com/Bioconductor-mirror/";
+ name "/release-3.4"))
-
-(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 \
@@ -290,11 +292,8 @@ 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
@@ -385,7 +384,7 @@ 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")))
@@ -402,7 +401,7 @@ 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")))
@@ -426,7 +425,10 @@ 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)
--
2.12.2
--- End Message ---
--- Begin Message ---
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Subject: |
Re: bug#26369: [PATCH] import cran: Fetch DESCRIPTION files from Github mirror. |
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Date: |
Tue, 16 May 2017 21:39:41 +0200 |
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User-agent: |
mu4e 0.9.18; emacs 25.2.1 |
Ricardo Wurmus <address@hidden> writes:
> Ludovic Courtès <address@hidden> writes:
>
>> Ricardo Wurmus <address@hidden> skribis:
>>
>>> * 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.
>>
>> LGTM.
>>
>> Out of curiosity, what’s the rationale for using the GitHub mirror
>> instead of the SVN repo?
>
> The Bioconductor people have been planning for a while to retire their
> SVN repository and use the Github mirror exclusively. I heard from
> Bioconductor users that this move is going to happen soon.
Pushed to master.
--
Ricardo
--- End Message ---