From unknown Sun Aug 17 22:03:32 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 0/2] Remove a deprecated R package and a depending package Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: laurent.gatto@gmail.com, rekado@elephly.net, zimon.toutoune@gmail.com, guix-patches@gnu.org Resent-Date: Tue, 01 Apr 2025 22:50:04 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 77442 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77442@debbugs.gnu.org Cc: Andreas Enge , Laurent Gatto , Ricardo Wurmus , Simon Tournier X-Debbugs-Original-To: guix-patches@gnu.org X-Debbugs-Original-Xcc: Laurent Gatto , Ricardo Wurmus , Simon Tournier Received: via spool by submit@debbugs.gnu.org id=B.174354780029705 (code B ref -1); Tue, 01 Apr 2025 22:50:04 +0000 Received: (at submit) by debbugs.gnu.org; 1 Apr 2025 22:50:00 +0000 Received: from localhost ([127.0.0.1]:52180 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzkQh-0007it-I9 for submit@debbugs.gnu.org; Tue, 01 Apr 2025 18:50:00 -0400 Received: from lists.gnu.org ([2001:470:142::17]:55706) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzkQd-0007hg-Db for submit@debbugs.gnu.org; Tue, 01 Apr 2025 18:49:57 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tzkQW-0007Ow-Oz for guix-patches@gnu.org; Tue, 01 Apr 2025 18:49:48 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tzkQU-0005oJ-M6 for guix-patches@gnu.org; Tue, 01 Apr 2025 18:49:48 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id ED91E2FF; Wed, 2 Apr 2025 00:49:43 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id uxO8h6ThAiib; Wed, 2 Apr 2025 00:49:42 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 976AB5BA; Wed, 2 Apr 2025 00:49:33 +0200 (CEST) From: Andreas Enge Date: Wed, 2 Apr 2025 00:48:42 +0200 Message-ID: X-Mailer: git-send-email 2.49.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: ED91E2FF X-Spamd-Result: default: False [0.40 / 15.00]; BAYES_HAM(-3.00)[99.99%]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_ALL(0.00)[]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; URIBL_BLOCKED(0.00)[localhost:helo,localhost:rdns]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: / X-Rspamd-Server: hera Received-SPF: pass client-ip=185.233.100.1; envelope-from=andreas@enge.fr; helo=hera.aquilenet.fr X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action 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 (-) Rationale in the two following packages. I suggest to remove them on or after May 2nd. Andreas Enge (2): gnu: Remove r-velocyto. gnu: Remove r-h5. gnu/packages/bioinformatics.scm | 44 --------------------------------- gnu/packages/cran.scm | 29 ---------------------- 2 files changed, 73 deletions(-) base-commit: 486caf5751543d760d94accd7ddc1789512438b0 -- 2.49.0 From unknown Sun Aug 17 22:03:32 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 1/2] gnu: Remove r-velocyto. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 01 Apr 2025 22:53:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77442 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77442@debbugs.gnu.org Cc: Andreas Enge Received: via spool by 77442-submit@debbugs.gnu.org id=B77442.174354793631129 (code B ref 77442); Tue, 01 Apr 2025 22:53:02 +0000 Received: (at 77442) by debbugs.gnu.org; 1 Apr 2025 22:52:16 +0000 Received: from localhost ([127.0.0.1]:52197 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzkSs-00085k-5Z for submit@debbugs.gnu.org; Tue, 01 Apr 2025 18:52:16 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:60748) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzkSp-00084g-7v for 77442@debbugs.gnu.org; Tue, 01 Apr 2025 18:52:12 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 252B22FF; Wed, 2 Apr 2025 00:52:05 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id 24pijB8CH4KB; Wed, 2 Apr 2025 00:52:04 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 8A492BF; Wed, 2 Apr 2025 00:51:57 +0200 (CEST) From: Andreas Enge Date: Wed, 2 Apr 2025 00:51:39 +0200 Message-ID: X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 252B22FF X-Spamd-Result: default: False [-3.60 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; TO_DN_SOME(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: --- X-Rspamd-Server: hera 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 (-) The package has not been updated since 2019 and depends on the deprecated r-h5. * gnu/packages/bioinformatics.scm (r-velocyto): Delete variable. Change-Id: I9783c67c92b5351647b964364c281a0d40319949 --- gnu/packages/bioinformatics.scm | 44 --------------------------------- 1 file changed, 44 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 8fd7789028..226594d8ed 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -22632,50 +22632,6 @@ (define-public r-imagearray (description "@code{DelayedArray} based image operations.") (license license:expat)))) -(define-public r-velocyto - (let ((commit "d7790346cb99f49ab9c2b23ba70dcf9d2c9fc350") - (revision "1")) - (package - (name "r-velocyto") - (version (git-version "0.6" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/velocyto-team/velocyto.R") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "16wqf70j7rd7pay2q513iyz12i8n9vrpg1bisah4lddbcpx5dz1n")))) - (build-system r-build-system) - (inputs - (list boost)) - (propagated-inputs - (list r-hdf5r - r-mass - r-mgcv - r-pcamethods - r-rcpp - r-rcpparmadillo - ;; Suggested packages - r-rtsne - r-cluster - r-abind - r-h5 - r-biocgenerics - r-genomicalignments - r-rsamtools - r-edger - r-igraph)) - (home-page "https://velocyto.org") - (synopsis "RNA velocity estimation in R") - (description - "This package provides basic routines for estimation of gene-specific -transcriptional derivatives and visualization of the resulting velocity -patterns.") - (license license:gpl3)))) - (define-public r-voltron (let ((commit "21886d82292dc46521da2a03d978d78f3bd7210b") (revision "5")) -- 2.49.0 From unknown Sun Aug 17 22:03:32 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 2/2] gnu: Remove r-h5. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: laurent.gatto@gmail.com, rekado@elephly.net, zimon.toutoune@gmail.com, guix-patches@gnu.org Resent-Date: Tue, 01 Apr 2025 22:53:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77442 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77442@debbugs.gnu.org Cc: Andreas Enge , Laurent Gatto , Ricardo Wurmus , Simon Tournier X-Debbugs-Original-Xcc: Laurent Gatto , Ricardo Wurmus , Simon Tournier Received: via spool by 77442-submit@debbugs.gnu.org id=B77442.174354794131174 (code B ref 77442); Tue, 01 Apr 2025 22:53:03 +0000 Received: (at 77442) by debbugs.gnu.org; 1 Apr 2025 22:52:21 +0000 Received: from localhost ([127.0.0.1]:52199 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzkSx-00086W-9o for submit@debbugs.gnu.org; Tue, 01 Apr 2025 18:52:20 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:60756) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzkSr-00084y-FM for 77442@debbugs.gnu.org; Tue, 01 Apr 2025 18:52:14 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 6101E303; Wed, 2 Apr 2025 00:52:07 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id u418urDW0AjM; Wed, 2 Apr 2025 00:52:06 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 62CACBF; Wed, 2 Apr 2025 00:52:05 +0200 (CEST) From: Andreas Enge Date: Wed, 2 Apr 2025 00:51:40 +0200 Message-ID: <69744c9f90b8c87efd63c107654ac7818682fee9.1743547708.git.andreas@enge.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 6101E303 X-Spamd-Result: default: False [-3.60 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; TO_DN_SOME(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; RCVD_VIA_SMTP_AUTH(0.00)[]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: --- X-Rspamd-Server: hera 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 (-) The package has been deprecated by its author in 2017 in favor of r-hdf5r. It does not build with current hdf5@1.14. * gnu/packages/cran.scm (r-h5): Delete variable. Change-Id: Iaceb59b31af870a1aea1630d74bb5c03932808b0 --- gnu/packages/cran.scm | 29 ----------------------------- 1 file changed, 29 deletions(-) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4e96d70849..8d80bc2091 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -14921,35 +14921,6 @@ (define-public r-heatmaply ;; Either version of the license. (license (list license:gpl2 license:gpl3)))) -(define-public r-h5 - (package - (name "r-h5") - (version "0.9.9") - (source - (origin - (method url-fetch) - (uri (cran-uri "h5" version)) - (sha256 - (base32 - "14p7i1sj24ky87kd7qr3n9fc9l64s0bp0rwbyl6i2x69xn75gpsx")))) - (build-system r-build-system) - (inputs - (list zlib hdf5-1.10)) - (native-inputs - (list r-knitr r-testthat which)) - (propagated-inputs - (list r-rcpp)) - (home-page "https://github.com/mannau/h5") - (synopsis "Interface to the HDF5 Library") - (description - "This package provides an S4 interface to the HDF5 library supporting -fast storage and retrieval of R-objects like vectors, matrices and arrays to -binary files in a language independent format. The HDF5 format can therefore -be used as an alternative to R's save/load mechanism. Since h5 is able to -access only subsets of stored data it can also handle data sets which do not -fit into memory.") - (license license:bsd-2))) - (define-public r-cgdsr (package (name "r-cgdsr") -- 2.49.0 From unknown Sun Aug 17 22:03:32 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 2/2] gnu: Remove r-h5. 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[194.254.61.42]) by smtp.gmail.com with ESMTPSA id ffacd0b85a97d-39eaf4456fdsm17246246f8f.86.2025.04.16.09.33.02 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 16 Apr 2025 09:33:03 -0700 (PDT) From: Simon Tournier In-Reply-To: <69744c9f90b8c87efd63c107654ac7818682fee9.1743547708.git.andreas@enge.fr> References: <69744c9f90b8c87efd63c107654ac7818682fee9.1743547708.git.andreas@enge.fr> Date: Wed, 16 Apr 2025 18:31:19 +0200 Message-ID: <87bjsw3w6g.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain 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 Andreas, On Wed, 02 Apr 2025 at 00:51, Andreas Enge wrote: > The package has been deprecated by its author in 2017 in favor of r-hdf5r. > It does not build with current hdf5@1.14. [...] > - (inputs > - (list zlib hdf5-1.10)) Well, I have nothing against the removal of this package. But please note that we still have hdf5-1.8 and will keep hdf5-1.10 for some time. Somehow, r-h5 does not need to upgrade its hdf5 input. Somehow, I would be in favor to delay this removal. Cheers, simon From unknown Sun Aug 17 22:03:32 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 1/2] gnu: Remove r-velocyto. 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[194.254.61.46]) by smtp.gmail.com with ESMTPSA id 5b1f17b1804b1-4405b4f2b72sm25420675e9.19.2025.04.16.09.33.06 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 16 Apr 2025 09:33:06 -0700 (PDT) From: Simon Tournier In-Reply-To: References: Date: Wed, 16 Apr 2025 18:32:37 +0200 Message-ID: <877c3k3w4a.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain 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 Andreas, On Wed, 02 Apr 2025 at 00:51, Andreas Enge wrote: > The package has not been updated since 2019 and depends on the > deprecated r-h5. This package builds with r-hdf5r, based on my small test. Therefore, I would be in favor to replace r-h5 by r-hdf5r. WDYT? Cheers, simon From unknown Sun Aug 17 22:03:32 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 1/2] gnu: Remove r-velocyto. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 16 Apr 2025 16:57:08 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77442 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Simon Tournier Cc: 77442@debbugs.gnu.org Received: via spool by 77442-submit@debbugs.gnu.org id=B77442.174482257823454 (code B ref 77442); Wed, 16 Apr 2025 16:57:08 +0000 Received: (at 77442) by debbugs.gnu.org; 16 Apr 2025 16:56:18 +0000 Received: from localhost ([127.0.0.1]:41168 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u563b-000665-MP for submit@debbugs.gnu.org; Wed, 16 Apr 2025 12:56:17 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:34566) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u563U-00064W-Qw for 77442@debbugs.gnu.org; Wed, 16 Apr 2025 12:56:12 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id B06F7412; Wed, 16 Apr 2025 18:56:01 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id QeEOueXd0Xfu; Wed, 16 Apr 2025 18:56:01 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 4D253A4; Wed, 16 Apr 2025 18:55:58 +0200 (CEST) Date: Wed, 16 Apr 2025 18:55:54 +0200 From: Andreas Enge Message-ID: References: <877c3k3w4a.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <877c3k3w4a.fsf@gmail.com> X-Rspamd-Queue-Id: B06F7412 X-Spamd-Result: default: False [-5.60 / 15.00]; BAYES_HAM(-3.00)[99.99%]; NEURAL_HAM(-3.00)[-1.000]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; FREEMAIL_TO(0.00)[gmail.com]; FROM_EQ_ENVFROM(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_ALL(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; TAGGED_RCPT(0.00)[]; FROM_HAS_DN(0.00)[]; FREEMAIL_ENVRCPT(0.00)[gmail.com]; TO_DN_SOME(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: ----- X-Rspamd-Server: hera 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 (-) Am Wed, Apr 16, 2025 at 06:32:37PM +0200 schrieb Simon Tournier: > This package builds with r-hdf5r, based on my small test. Therefore, I > would be in favor to replace r-h5 by r-hdf5r. WDYT? Sounds good! Andreas From unknown Sun Aug 17 22:03:32 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 2/2] gnu: Remove r-h5. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Wed, 16 Apr 2025 17:02:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77442 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Simon Tournier Cc: Ricardo Wurmus , 77442@debbugs.gnu.org, Laurent Gatto Received: via spool by 77442-submit@debbugs.gnu.org id=B77442.174482288725543 (code B ref 77442); Wed, 16 Apr 2025 17:02:06 +0000 Received: (at 77442) by debbugs.gnu.org; 16 Apr 2025 17:01:27 +0000 Received: from localhost ([127.0.0.1]:41193 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u568b-0006df-7a for submit@debbugs.gnu.org; Wed, 16 Apr 2025 13:01:26 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:56686) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u568W-0006cG-D1 for 77442@debbugs.gnu.org; Wed, 16 Apr 2025 13:01:22 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 4C97A3FA; Wed, 16 Apr 2025 19:01:14 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id KPQHrAWrUgN1; Wed, 16 Apr 2025 19:01:13 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 758BC124; Wed, 16 Apr 2025 19:01:07 +0200 (CEST) Date: Wed, 16 Apr 2025 19:01:02 +0200 From: Andreas Enge Message-ID: References: <69744c9f90b8c87efd63c107654ac7818682fee9.1743547708.git.andreas@enge.fr> <87bjsw3w6g.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <87bjsw3w6g.fsf@gmail.com> X-Rspamd-Queue-Id: 4C97A3FA X-Spamd-Result: default: False [6.90 / 15.00]; SPAM_FLAG(5.00)[]; BAYES_HAM(-3.00)[99.99%]; NEURAL_SPAM(3.00)[1.000]; SUSPICIOUS_RECIPS(1.50)[]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; FREEMAIL_TO(0.00)[gmail.com]; FROM_EQ_ENVFROM(0.00)[]; TO_DN_SOME(0.00)[]; ARC_NA(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; TAGGED_RCPT(0.00)[]; FROM_HAS_DN(0.00)[]; FREEMAIL_ENVRCPT(0.00)[gmail.com]; RCPT_COUNT_THREE(0.00)[4]; FREEMAIL_CC(0.00)[debbugs.gnu.org,gmail.com,elephly.net] X-Spamd-Bar: ++++++ X-Rspamd-Action: add header X-Rspamd-Server: hera X-Spam-Level: ****** X-Spam: Yes 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 (-) Am Wed, Apr 16, 2025 at 06:31:19PM +0200 schrieb Simon Tournier: > > - (inputs > > - (list zlib hdf5-1.10)) > Well, I have nothing against the removal of this package. But please > note that we still have hdf5-1.8 and will keep hdf5-1.10 for some time. > Somehow, r-h5 does not need to upgrade its hdf5 input. > Somehow, I would be in favor to delay this removal. Well, we would like to get rid of hfd5-1.10, which is EOL and superseded by 1.14 upstream. (This may not be possible immediately if some other useful package depends on it, but we should not artificially delay the transition.) This package itself has been deprecated upstream for more than 7 years, with a suggested replacement, so I see no point in keeping it. I think we have a tendency to accumulate cruft in Guix and am trying to get rid of it... Andreas From unknown Sun Aug 17 22:03:32 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 2/2] gnu: Remove r-h5. 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[194.254.61.47]) by smtp.gmail.com with ESMTPSA id ffacd0b85a97d-39eae97b249sm19967988f8f.58.2025.04.17.04.11.13 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 17 Apr 2025 04:11:13 -0700 (PDT) From: Simon Tournier In-Reply-To: References: <69744c9f90b8c87efd63c107654ac7818682fee9.1743547708.git.andreas@enge.fr> <87bjsw3w6g.fsf@gmail.com> Date: Thu, 17 Apr 2025 12:40:15 +0200 Message-ID: <87r01rnka8.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain 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 Andreas, On Wed, 16 Apr 2025 at 19:01, Andreas Enge wrote: > we should not artificially delay the > transition.) This package itself has been deprecated upstream for more > than 7 years, with a suggested replacement, so I see no point in keeping it. OK, I agree. Let remove r-h5 and replace r-h5 by r-hdf5r in r-velocyto. Thanks for all this janitor work. Cheers, simon From unknown Sun Aug 17 22:03:32 2025 X-Loop: help-debbugs@gnu.org Subject: [bug#77442] [PATCH 1/2] gnu: Remove r-velocyto. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Tue, 29 Apr 2025 09:52:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77442 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: Simon Tournier Cc: 77442@debbugs.gnu.org Received: via spool by 77442-submit@debbugs.gnu.org id=B77442.17459202789942 (code B ref 77442); Tue, 29 Apr 2025 09:52:06 +0000 Received: (at 77442) by debbugs.gnu.org; 29 Apr 2025 09:51:18 +0000 Received: from localhost ([127.0.0.1]:49745 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u9hcS-0002aC-Da for submit@debbugs.gnu.org; Tue, 29 Apr 2025 05:51:17 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:40760) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u9hcN-0002Yd-BE for 77442@debbugs.gnu.org; Tue, 29 Apr 2025 05:51:13 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 8100D18D; Tue, 29 Apr 2025 11:51:03 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id fytW0OECVZVH; Tue, 29 Apr 2025 11:51:02 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 5C34B289; Tue, 29 Apr 2025 11:51:01 +0200 (CEST) Date: Tue, 29 Apr 2025 11:50:59 +0200 From: Andreas Enge Message-ID: References: <877c3k3w4a.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <877c3k3w4a.fsf@gmail.com> X-Rspamd-Queue-Id: 8100D18D X-Spamd-Result: default: False [-5.60 / 15.00]; BAYES_HAM(-3.00)[99.99%]; NEURAL_HAM(-3.00)[-1.000]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; FREEMAIL_TO(0.00)[gmail.com]; FROM_EQ_ENVFROM(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_ALL(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; TAGGED_RCPT(0.00)[]; FROM_HAS_DN(0.00)[]; FREEMAIL_ENVRCPT(0.00)[gmail.com]; TO_DN_SOME(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: ----- X-Rspamd-Server: hera 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 (-) Am Wed, Apr 16, 2025 at 06:32:37PM +0200 schrieb Simon Tournier: > This package builds with r-hdf5r, based on my small test. Therefore, I > would be in favor to replace r-h5 by r-hdf5r. WDYT? Interestingly enough, both inputs were already present. I have simply removed r-h5. The package still builds. But these inputs were propagated, I do not know if the package still works. Andreas From unknown Sun Aug 17 22:03:32 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Andreas Enge Subject: bug#77442: closed (Re: [bug#77442] [PATCH 1/2] gnu: Remove r-velocyto.) Message-ID: References: X-Gnu-PR-Message: they-closed 77442 X-Gnu-PR-Package: guix-patches X-Gnu-PR-Keywords: patch Reply-To: 77442@debbugs.gnu.org Date: Fri, 02 May 2025 15:52:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1746201122-11839-1" This is a multi-part message in MIME format... ------------=_1746201122-11839-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #77442: [PATCH 0/2] Remove a deprecated R package and a depending package which was filed against the guix-patches package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 77442@debbugs.gnu.org. --=20 77442: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D77442 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1746201122-11839-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at 77442-done) by debbugs.gnu.org; 2 May 2025 15:51:11 +0000 Received: from localhost ([127.0.0.1]:60660 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1uAsfO-00033O-Rp for submit@debbugs.gnu.org; Fri, 02 May 2025 11:51:11 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:49462) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1uAsfK-00032Z-9F for 77442-done@debbugs.gnu.org; Fri, 02 May 2025 11:51:08 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id E14996F7; Fri, 2 May 2025 17:50:57 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id n9EJ3_aWxowv; Fri, 2 May 2025 17:50:57 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 7608EE42; Fri, 2 May 2025 17:50:55 +0200 (CEST) Date: Fri, 2 May 2025 17:50:53 +0200 From: Andreas Enge To: Simon Tournier Subject: Re: [bug#77442] [PATCH 1/2] gnu: Remove r-velocyto. Message-ID: References: <877c3k3w4a.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Rspamd-Queue-Id: E14996F7 X-Spamd-Result: default: False [5.48 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[1.000]; BAYES_HAM(-2.92)[99.67%]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; FREEMAIL_ENVRCPT(0.00)[gmail.com]; MIME_TRACE(0.00)[0:+]; FROM_EQ_ENVFROM(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; TO_DN_SOME(0.00)[]; FREEMAIL_TO(0.00)[gmail.com]; FROM_HAS_DN(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; TAGGED_RCPT(0.00)[]; RCVD_TLS_ALL(0.00)[]; ARC_NA(0.00)[] X-Spamd-Bar: +++++ X-Rspamd-Action: greylist X-Rspamd-Server: hera X-Spam-Level: ***** X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77442-done Cc: 77442-done@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: -1.0 (-) r-h5 removed, thanks for the comments! Andreas ------------=_1746201122-11839-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 1 Apr 2025 22:50:00 +0000 Received: from localhost ([127.0.0.1]:52180 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzkQh-0007it-I9 for submit@debbugs.gnu.org; Tue, 01 Apr 2025 18:50:00 -0400 Received: from lists.gnu.org ([2001:470:142::17]:55706) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzkQd-0007hg-Db for submit@debbugs.gnu.org; Tue, 01 Apr 2025 18:49:57 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tzkQW-0007Ow-Oz for guix-patches@gnu.org; Tue, 01 Apr 2025 18:49:48 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1tzkQU-0005oJ-M6 for guix-patches@gnu.org; Tue, 01 Apr 2025 18:49:48 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id ED91E2FF; Wed, 2 Apr 2025 00:49:43 +0200 (CEST) Authentication-Results: hera.aquilenet.fr; none X-Virus-Scanned: Debian amavis at hera.aquilenet.fr Received: from hera.aquilenet.fr ([127.0.0.1]) by localhost (hera.aquilenet.fr [127.0.0.1]) (amavis, port 10024) with ESMTP id uxO8h6ThAiib; Wed, 2 Apr 2025 00:49:42 +0200 (CEST) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 976AB5BA; Wed, 2 Apr 2025 00:49:33 +0200 (CEST) From: Andreas Enge To: guix-patches@gnu.org Subject: [PATCH 0/2] Remove a deprecated R package and a depending package Date: Wed, 2 Apr 2025 00:48:42 +0200 Message-ID: X-Mailer: git-send-email 2.49.0 MIME-Version: 1.0 X-Debbugs-Cc: Laurent Gatto , Ricardo Wurmus , Simon Tournier Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: ED91E2FF X-Spamd-Result: default: False [0.40 / 15.00]; BAYES_HAM(-3.00)[99.99%]; FORGED_RECIPIENTS(2.00)[m:andreas@enge.fr,s:andreas.enge@aquilenet.fr]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; RCVD_COUNT_TWO(0.00)[2]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_ALL(0.00)[]; FROM_EQ_ENVFROM(0.00)[]; TO_MATCH_ENVRCPT_SOME(0.00)[]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; URIBL_BLOCKED(0.00)[localhost:helo,localhost:rdns]; FROM_HAS_DN(0.00)[]; ARC_NA(0.00)[] X-Rspamd-Action: no action X-Spamd-Bar: / X-Rspamd-Server: hera Received-SPF: pass client-ip=185.233.100.1; envelope-from=andreas@enge.fr; helo=hera.aquilenet.fr X-Spam_score_int: -18 X-Spam_score: -1.9 X-Spam_bar: - X-Spam_report: (-1.9 / 5.0 requ) BAYES_00=-1.9, RCVD_IN_VALIDITY_CERTIFIED_BLOCKED=0.001, RCVD_IN_VALIDITY_RPBL_BLOCKED=0.001, SPF_HELO_PASS=-0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: submit Cc: Andreas Enge 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 (-) Rationale in the two following packages. I suggest to remove them on or after May 2nd. Andreas Enge (2): gnu: Remove r-velocyto. gnu: Remove r-h5. gnu/packages/bioinformatics.scm | 44 --------------------------------- gnu/packages/cran.scm | 29 ---------------------- 2 files changed, 73 deletions(-) base-commit: 486caf5751543d760d94accd7ddc1789512438b0 -- 2.49.0 ------------=_1746201122-11839-1--