From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:4830:134:3::10]:59508) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cvl8R-0006gg-AE for guix-patches@gnu.org; Wed, 05 Apr 2017 09:38:08 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cvl8M-0007IE-Hm for guix-patches@gnu.org; Wed, 05 Apr 2017 09:38:07 -0400 Received: from debbugs.gnu.org ([208.118.235.43]:35116) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_128_CBC_SHA1:16) (Exim 4.71) (envelope-from ) id 1cvl8M-0007I9-EF for guix-patches@gnu.org; Wed, 05 Apr 2017 09:38:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1cvl8M-0005VC-5Y for guix-patches@gnu.org; Wed, 05 Apr 2017 09:38:02 -0400 Subject: bug#26369: [PATCH] import cran: Fetch DESCRIPTION files from Github mirror. Resent-Message-ID: Received: from eggs.gnu.org ([2001:4830:134:3::10]:59066) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cvl7a-0005lt-Hb for guix-patches@gnu.org; Wed, 05 Apr 2017 09:37:17 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cvl7X-0006pa-DY for guix-patches@gnu.org; Wed, 05 Apr 2017 09:37:14 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21029) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cvl7X-0006nb-6j for guix-patches@gnu.org; Wed, 05 Apr 2017 09:37:11 -0400 From: Ricardo Wurmus Date: Wed, 5 Apr 2017 15:37:03 +0200 Message-Id: <20170405133703.4302-1-rekado@elephly.net> List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: 26369@debbugs.gnu.org Cc: Ricardo Wurmus * 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