From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 05 09:37:32 2017 Received: (at submit) by debbugs.gnu.org; 5 Apr 2017 13:37:32 +0000 Received: from localhost ([127.0.0.1]:33315 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvl7m-0005UL-7x for submit@debbugs.gnu.org; Wed, 05 Apr 2017 09:37:31 -0400 Received: from eggs.gnu.org ([208.118.235.92]:39907) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cvl7j-0005U5-To for submit@debbugs.gnu.org; Wed, 05 Apr 2017 09:37:24 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cvl7d-0006tC-Em for submit@debbugs.gnu.org; Wed, 05 Apr 2017 09:37:18 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50 autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:44505) by eggs.gnu.org with esmtps (TLS1.0:RSA_AES_256_CBC_SHA1:32) (Exim 4.71) (envelope-from ) id 1cvl7d-0006t7-BZ for submit@debbugs.gnu.org; Wed, 05 Apr 2017 09:37:17 -0400 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 Received: from localhost (141.80.148.231 [141.80.148.231]) by mx.zohomail.com with SMTPS id 1491399426942161.06634264381273; Wed, 5 Apr 2017 06:37:06 -0700 (PDT) From: Ricardo Wurmus To: guix-patches@gnu.org Subject: [PATCH] import cran: Fetch DESCRIPTION files from Github mirror. Date: Wed, 5 Apr 2017 15:37:03 +0200 Message-Id: <20170405133703.4302-1-rekado@elephly.net> X-Mailer: git-send-email 2.12.2 X-ZohoMailClient: External X-ZohoMail: Z_26063301 SPT_1 Z_26062608 SPT_0 X-detected-operating-system: by eggs.gnu.org: GNU/Linux 3.x [fuzzy] X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.6.x X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -4.0 (----) X-Debbugs-Envelope-To: submit Cc: Ricardo Wurmus X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -4.0 (----) * 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 From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 10 05:57:49 2017 Received: (at 26369) by debbugs.gnu.org; 10 Apr 2017 09:57:49 +0000 Received: from localhost ([127.0.0.1]:40613 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxW4z-0001Cc-1O for submit@debbugs.gnu.org; Mon, 10 Apr 2017 05:57:49 -0400 Received: from eggs.gnu.org ([208.118.235.92]:52787) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxW4x-0001CK-Ca for 26369@debbugs.gnu.org; Mon, 10 Apr 2017 05:57:47 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1cxW4o-00011D-DF for 26369@debbugs.gnu.org; Mon, 10 Apr 2017 05:57:42 -0400 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:36412) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1cxW4o-000117-AC; Mon, 10 Apr 2017 05:57:38 -0400 Received: from [193.50.110.120] (port=50220 helo=ribbon) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_256_CBC_SHA1:256) (Exim 4.82) (envelope-from ) id 1cxW4n-0006qQ-N4; Mon, 10 Apr 2017 05:57:38 -0400 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: bug#26369: [PATCH] import cran: Fetch DESCRIPTION files from Github mirror. References: <20170405133703.4302-1-rekado@elephly.net> Date: Mon, 10 Apr 2017 11:57:35 +0200 In-Reply-To: <20170405133703.4302-1-rekado@elephly.net> (Ricardo Wurmus's message of "Wed, 5 Apr 2017 15:37:03 +0200") Message-ID: <87a87oega8.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 26369 Cc: 26369@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -5.0 (-----) Ricardo Wurmus 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 strin= g. > (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=E2=80=99s the rationale for using the GitHub mirror instead of the SVN repo? Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Mon Apr 10 07:14:31 2017 Received: (at 26369) by debbugs.gnu.org; 10 Apr 2017 11:14:31 +0000 Received: from localhost ([127.0.0.1]:40634 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxXHD-0003Ac-AC for submit@debbugs.gnu.org; Mon, 10 Apr 2017 07:14:31 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21147) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1cxXHB-0003AT-6o for 26369@debbugs.gnu.org; Mon, 10 Apr 2017 07:14:29 -0400 Received: from localhost (x4d0cdd2a.dyn.telefonica.de [77.12.221.42]) by mx.zohomail.com with SMTPS id 149182286558458.93353251843928; Mon, 10 Apr 2017 04:14:25 -0700 (PDT) References: <20170405133703.4302-1-rekado@elephly.net> <87a87oega8.fsf@gnu.org> User-agent: mu4e 0.9.18; emacs 25.1.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#26369: [PATCH] import cran: Fetch DESCRIPTION files from Github mirror. In-reply-to: <87a87oega8.fsf@gnu.org> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Mon, 10 Apr 2017 13:14:22 +0200 Message-ID: <87r3101pm9.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: -1.8 (-) X-Debbugs-Envelope-To: 26369 Cc: 26369@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) Ludovic Courtès writes: > Ricardo Wurmus 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. -- Ricardo GPG: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC https://elephly.net From debbugs-submit-bounces@debbugs.gnu.org Tue May 16 15:39:50 2017 Received: (at 26369-done) by debbugs.gnu.org; 16 May 2017 19:39:50 +0000 Received: from localhost ([127.0.0.1]:49093 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dAiJy-0000Hy-8Z for submit@debbugs.gnu.org; Tue, 16 May 2017 15:39:50 -0400 Received: from sender-of-o51.zoho.com ([135.84.80.216]:21009) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1dAiJw-0000Hq-EB for 26369-done@debbugs.gnu.org; Tue, 16 May 2017 15:39:48 -0400 Received: from localhost (port-92-200-229-218.dynamic.qsc.de [92.200.229.218]) by mx.zohomail.com with SMTPS id 1494963584401646.3029641267495; Tue, 16 May 2017 12:39:44 -0700 (PDT) References: <20170405133703.4302-1-rekado@elephly.net> <87a87oega8.fsf@gnu.org> <87r3101pm9.fsf@elephly.net> User-agent: mu4e 0.9.18; emacs 25.2.1 From: Ricardo Wurmus To: 26369-done@debbugs.gnu.org Subject: Re: bug#26369: [PATCH] import cran: Fetch DESCRIPTION files from Github mirror. In-reply-to: <87r3101pm9.fsf@elephly.net> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Tue, 16 May 2017 21:39:41 +0200 Message-ID: <87tw4ka8w2.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-ZohoMailClient: External X-Spam-Score: -1.8 (-) X-Debbugs-Envelope-To: 26369-done X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.8 (-) Ricardo Wurmus writes: > Ludovic Courtès writes: > >> Ricardo Wurmus 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 From unknown Sat Sep 06 02:03:21 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 14 Jun 2017 11:24:03 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator