Received: (at 77357) by debbugs.gnu.org; 30 Mar 2025 16:56:36 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sun Mar 30 12:56:36 2025 Received: from localhost ([127.0.0.1]:37955 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tyvxb-0002Da-MN for submit <at> debbugs.gnu.org; Sun, 30 Mar 2025 12:56:36 -0400 Received: from relay07.alfahosting-server.de ([109.237.142.243]:47215) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <code@HIDDEN>) id 1tyvRV-0000V4-S3 for 77357 <at> debbugs.gnu.org; Sun, 30 Mar 2025 12:23:27 -0400 Received: by relay01.alfahosting-server.de (Postfix, from userid 1001) id 63C3A3366349; Sun, 30 Mar 2025 18:12:05 +0200 (CEST) X-Spam-DCC: : X-Spam-Level: * X-Spam-Status: No, score=1.5 required=7.0 tests=BAYES_50,URIBL_SBL autolearn=disabled version=3.2.5 Received: from alfa3058.alfahosting-server.de (alfa3058.alfahosting-server.de [109.237.138.26]) by relay01.alfahosting-server.de (Postfix) with ESMTPS id 407313366332 for <77357 <at> debbugs.gnu.org>; Sun, 30 Mar 2025 18:12:03 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=sam-d.com; s=cloudpit; t=1743351123; bh=yYK0Qz3q6f3+pIaq3fsmvgg7n/1/FmNHtuM3Ilc23vA=; h=Date:To:From:Subject:From; b=CcRJ6NaYMssSvNRFdq9CkEzHdqxekMAvLpb6Vv/xb+egNNnvx1jP1VSrQt6DA1Wc3 hY4e1Hx2hPJ3IS2YZIaih8JzKk0W5ncGD0RdORVVvL/TiF2yP9u6xeJcsgfHOsPZiz UGFPCPUv1qXM0EjH6FEuUW4LY+sjAAEzZlnVtjAw= Received: from [192.168.178.36] (dslc-082-083-151-023.pools.arcor-ip.net [82.83.151.23]) by alfa3058.alfahosting-server.de (Postfix) with ESMTPSA id ADD63585D8CA for <77357 <at> debbugs.gnu.org>; Sun, 30 Mar 2025 18:12:01 +0200 (CEST) Message-ID: <8ba60fd9-d853-0414-dec5-b8e410caaf78@HIDDEN> Date: Sun, 30 Mar 2025 18:12:01 +0200 MIME-Version: 1.0 User-Agent: Mozilla/5.0 (X11; Linux x86_64; rv:91.0) Gecko/20100101 Thunderbird/91.8.1 Content-Language: en-US To: 77357 <at> debbugs.gnu.org From: =?UTF-8?Q?Sebastian_D=c3=bcmcke?= <code@HIDDEN> Subject: Re: [PATCH 0/1] Remove freebayes Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77357 X-Mailman-Approved-At: Sun, 30 Mar 2025 12:56:34 -0400 X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) Dear Andreas, I know I have a manifest somewhere depending on freebayes. However, I am unsure when was the last time I ran it. And even then I could use time-machine to get a working version of freebayes running. So removing it is not a big deal. However, it seems that upstream is aware of the failing test suite [1]. Unfortubnately building --with-latest=freebayes did not immediately lead me to success. Perhaps what should be discussed is the potential overlap (at leat conceptually) between the guix channel bioinformatic tools (as found in bioinformatics.scm) and the many more tools in the guix-science channel. Would it make sense to move all these packages over to the guix-science channel? Best Sebastian [1]: https://github.com/freebayes/freebayes/issues/786
guix-patches@HIDDEN:bug#77357; Package guix-patches.
Full text available.Received: (at 77357) by debbugs.gnu.org; 29 Mar 2025 10:02:05 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sat Mar 29 06:02:05 2025 Received: from localhost ([127.0.0.1]:56978 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tyT0v-0006b0-13 for submit <at> debbugs.gnu.org; Sat, 29 Mar 2025 06:02:05 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:34134) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <andreas@HIDDEN>) id 1tyT0m-0006aC-Bw for 77357 <at> debbugs.gnu.org; Sat, 29 Mar 2025 06:01:56 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id ACA621C7; Sat, 29 Mar 2025 11:01:49 +0100 (CET) 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 M2oErri0NSZq; Sat, 29 Mar 2025 11:01:49 +0100 (CET) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id E33931AD; Sat, 29 Mar 2025 11:01:46 +0100 (CET) Date: Sat, 29 Mar 2025 11:01:43 +0100 From: Andreas Enge <andreas@HIDDEN> To: 77357 <at> debbugs.gnu.org Subject: Re: [PATCH 0/1] Remove freebayes Message-ID: <Z-fFBwyGvsIFqJwD@jurong> References: <cover.1743241966.git.andreas@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <cover.1743241966.git.andreas@HIDDEN> X-Rspamd-Queue-Id: ACA621C7 X-Spamd-Result: default: False [5.40 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[1.000]; BAYES_HAM(-3.00)[99.99%]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; MIME_TRACE(0.00)[0:+]; FROM_HAS_DN(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; RCPT_COUNT_TWO(0.00)[2]; RCVD_TLS_ALL(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; TO_MATCH_ENVRCPT_ALL(0.00)[]; TO_DN_NONE(0.00)[]; ARC_NA(0.00)[] X-Spam-Level: ***** X-Rspamd-Action: greylist X-Spamd-Bar: +++++ X-Rspamd-Server: hera X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77357 Cc: rekado@HIDDEN X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) I made a mistake in submitting the patch series; the (trivial) patch is in #77358, which I have closed; we can continue the discussion here. Andreas
guix-patches@HIDDEN:bug#77357; Package guix-patches.
Full text available.Received: (at submit) by debbugs.gnu.org; 29 Mar 2025 09:57:48 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Sat Mar 29 05:57:48 2025 Received: from localhost ([127.0.0.1]:56953 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1tySwm-0006Jf-6K for submit <at> debbugs.gnu.org; Sat, 29 Mar 2025 05:57:48 -0400 Received: from lists.gnu.org ([2001:470:142::17]:46170) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from <andreas@HIDDEN>) id 1tySwj-0006JD-49 for submit <at> debbugs.gnu.org; Sat, 29 Mar 2025 05:57:46 -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 <andreas@HIDDEN>) id 1tySwW-0006i0-EC for guix-patches@HIDDEN; Sat, 29 Mar 2025 05:57:32 -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 <andreas@HIDDEN>) id 1tySwU-0001f8-9V for guix-patches@HIDDEN; Sat, 29 Mar 2025 05:57:32 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 59045155; Sat, 29 Mar 2025 10:57:25 +0100 (CET) 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 7Z2LdBl_g_xG; Sat, 29 Mar 2025 10:57:24 +0100 (CET) Received: from jurong.lan (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 83AB2297; Sat, 29 Mar 2025 10:57:23 +0100 (CET) From: Andreas Enge <andreas@HIDDEN> To: guix-patches@HIDDEN Subject: [PATCH 0/1] Remove freebayes Date: Sat, 29 Mar 2025 10:52:45 +0100 Message-ID: <cover.1743241966.git.andreas@HIDDEN> X-Mailer: git-send-email 2.49.0 MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Rspamd-Queue-Id: 59045155 X-Spamd-Result: default: False [8.40 / 15.00]; SPAM_FLAG(5.00)[]; BAYES_HAM(-3.00)[99.99%]; NEURAL_SPAM(3.00)[1.000]; FORGED_RECIPIENTS(2.00)[m:andreas@HIDDEN,s:andreas.enge@HIDDEN]; MID_CONTAINS_FROM(1.00)[]; R_MISSING_CHARSET(0.50)[]; MIME_GOOD(-0.10)[text/plain]; MIME_TRACE(0.00)[0:+]; RCVD_TLS_ALL(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; FROM_EQ_ENVFROM(0.00)[]; RCPT_COUNT_THREE(0.00)[3]; TO_MATCH_ENVRCPT_SOME(0.00)[]; FROM_HAS_DN(0.00)[]; TO_DN_SOME(0.00)[]; RCVD_VIA_SMTP_AUTH(0.00)[]; ARC_NA(0.00)[] X-Spam-Level: ******** X-Rspamd-Action: add header X-Spamd-Bar: ++++++++ X-Rspamd-Server: hera X-Spam: Yes Received-SPF: pass client-ip=185.233.100.1; envelope-from=andreas@HIDDEN; 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: rekado@HIDDEN, Andreas Enge <andreas@HIDDEN> X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -1.0 (-) I noticed that the package does not build when updating parallel. It should be possible to somehow repair it, but apparently nobody has noticed that the package does not build any more for almost two years: https://ci.guix.gnu.org/build/9529724/details first failure: https://ci.guix.gnu.org/build/1171985/details So if there is no interest in it, there is maybe no point in spending time on it. I would suggest to remove it on or after April 29. Andreas Enge (1): gnu: Remove freebayes. gnu/packages/bioinformatics.scm | 82 --------------------------------- 1 file changed, 82 deletions(-) base-commit: 67f4a2feadbb6cc04a61b5a3bc7b8f4bace2a0bb -- 2.49.0
Andreas Enge <andreas@HIDDEN>:guix-patches@HIDDEN.
Full text available.guix-patches@HIDDEN:bug#77357; Package guix-patches.
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