From unknown Sat Jun 14 19:09:26 2025 X-Loop: help-debbugs@gnu.org Subject: bug#48792: CRAN/bioconductor updater downloads tarballs twice Resent-From: Ricardo Wurmus Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Wed, 02 Jun 2021 15:55:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 48792 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 48792@debbugs.gnu.org X-Debbugs-Original-To: bug-guix@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.162264928228819 (code B ref -1); Wed, 02 Jun 2021 15:55:02 +0000 Received: (at submit) by debbugs.gnu.org; 2 Jun 2021 15:54:42 +0000 Received: from localhost ([127.0.0.1]:41218 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1loTCc-0007Ul-3E for submit@debbugs.gnu.org; Wed, 02 Jun 2021 11:54:42 -0400 Received: from lists.gnu.org ([209.51.188.17]:49042) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1loTCa-0007Ub-G1 for submit@debbugs.gnu.org; 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charset=utf-8; format=flowed Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External Received-SPF: pass client-ip=136.143.188.51; envelope-from=rekado@elephly.net; helo=sender4-of-o51.zoho.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_NONE=-0.0001, RCVD_IN_MSPIKE_H2=-0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -0.1 (/) 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: -1.1 (-) When upgrading packages with =E2=80=9Cguix refresh -t bioconductor -u=E2=80= =9D=20 Guix downloads tarballs for every package twice. --=20 Ricardo From unknown Sat Jun 14 19:09:26 2025 X-Loop: help-debbugs@gnu.org Subject: bug#48792: CRAN/bioconductor updater downloads tarballs twice Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Thu, 10 Jun 2021 16:10:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48792 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 48792@debbugs.gnu.org Received: via spool by 48792-submit@debbugs.gnu.org id=B48792.162334135818320 (code B ref 48792); 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Thu, 10 Jun 2021 09:09:08 -0700 (PDT) From: zimoun References: <87pmx4uury.fsf@elephly.net> Date: Wed, 09 Jun 2021 16:21:08 +0200 In-Reply-To: <87pmx4uury.fsf@elephly.net> (Ricardo Wurmus's message of "Wed, 02 Jun 2021 17:54:25 +0200") Message-ID: <87bl8fjezv.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.5 (/) 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: -0.5 (/) Hi Ricardo, On Wed, 02 Jun 2021 at 17:54, Ricardo Wurmus wrote: > When upgrading packages with =E2=80=9Cguix refresh -t bioconductor -u=E2= =80=9D Guix downloads > tarballs for every package twice. It is duplicated with bug#44256, IMHO. Merge? 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Fri, 02 Jul 2021 09:33:28 -0700 (PDT) Date: Fri, 02 Jul 2021 18:32:17 +0200 Message-Id: <87h7hcn0by.fsf@gmail.com> To: control@debbugs.gnu.org From: zimoun Subject: control message for bug #48792 X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: control 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: -1.0 (-) merge 48792 44256 quit From unknown Sat Jun 14 19:09:26 2025 X-Loop: help-debbugs@gnu.org Subject: bug#48792: CRAN/bioconductor updater downloads tarballs twice Resent-From: zimoun Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Fri, 04 Nov 2022 12:29:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 48792 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Ricardo Wurmus Cc: 48792@debbugs.gnu.org Received: via spool by 48792-submit@debbugs.gnu.org id=B48792.166756493627218 (code B ref 48792); 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Fri, 04 Nov 2022 05:28:46 -0700 (PDT) From: zimoun References: <87pmx4uury.fsf@elephly.net> Date: Fri, 04 Nov 2022 13:27:39 +0100 In-Reply-To: <87pmx4uury.fsf@elephly.net> (Ricardo Wurmus's message of "Wed, 02 Jun 2021 17:54:25 +0200") Message-ID: <87mt96aoqs.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Spam-Score: 0.0 (/) 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: -1.0 (-) Hi, On mer., 02 juin 2021 at 17:54, Ricardo Wurmus wrote: > When upgrading packages with =E2=80=9Cguix refresh -t bioconductor -u=E2= =80=9D Guix downloads > tarballs for every package twice. It can be worse with 3 downloads. --8<---------------cut here---------------start------------->8--- $ ./pre-inst-env guix refresh -u r-rhdf5lib Starting download of /tmp/guix-file.IjNx2z >From https://bioconductor.org/packages/release/bioc/src/contrib/Rhdf5lib_1.= 20.0.tar.gz... =E2=80=A620.0.tar.gz 14.0MiB 96.9MiB/s 00:00 [#############= #####] 100.0% gnu/packages/bioconductor.scm:14362:13: r-rhdf5lib: updating from version 1= .18.2 to version 1.20.0... Starting download of /tmp/guix-file.NmqLjM >From https://bioconductor.org/packages/release/bioc/src/contrib/Rhdf5lib_1.= 20.0.tar.gz... =E2=80=A620.0.tar.gz 14.0MiB 97.3MiB/s 00:00 [#############= #####] 100.0% Starting download of /tmp/guix-file.ytAuK3 >From https://bioconductor.org/packages/release/bioc/src/contrib/Rhdf5lib_1.= 20.0.tar.gz... =E2=80=A620.0.tar.gz 14.0MiB 103.3MiB/s 00:00 [#############= #####] 100.0% guix refresh: r-rhdf5lib: consider adding this input: zlib gnu/packages/bioconductor.scm:14431:5: r-rhdf5lib: consider removing this n= ative input: hdf5-source gnu/packages/bioconductor.scm:14429:5: r-rhdf5lib: consider removing this p= ropagated input: hdf5 gnu/packages/bioconductor.scm:14429:5: r-rhdf5lib: consider removing this p= ropagated input: zlib --8<---------------cut here---------------end--------------->8--- Cheers, simon PS: Noted when upgrading from 3.15 to 3.16 with this change. --8<---------------cut here---------------start------------->8--- diff --git a/guix/build-system/r.scm b/guix/build-system/r.scm index 620822b870..9b360ae581 100644 --- a/guix/build-system/r.scm +++ b/guix/build-system/r.scm @@ -61,7 +61,7 @@ (define* (bioconductor-uri name version #:optional type) "/src/contrib/" name "_" version ".tar.gz") ;; TODO: use %bioconductor-version from (guix import cran) - (string-append "https://bioconductor.org/packages/3.15" + (string-append "https://bioconductor.org/packages/3.16" type-url-part "/src/contrib/" name "_" version ".tar.gz")))) diff --git a/guix/import/cran.scm b/guix/import/cran.scm index 4e1ce7c010..cdc6b806b2 100644 --- a/guix/import/cran.scm +++ b/guix/import/cran.scm @@ -156,9 +156,9 @@ (define %cran-url "https://cran.r-project.org/web/packa= ges/") (define %cran-canonical-url "https://cran.r-project.org/package=3D") (define %bioconductor-url "https://bioconductor.org/packages/") -;; The latest Bioconductor release is 3.15. Bioconductor packages should = be +;; The latest Bioconductor release is 3.16. Bioconductor packages should = be ;; updated together. -(define %bioconductor-version "3.15") +(define %bioconductor-version "3.16") (define* (bioconductor-packages-list-url #:optional type) (string-append "https://bioconductor.org/packages/" --8<---------------cut here---------------end--------------->8---