From debbugs-submit-bounces@debbugs.gnu.org Sat Mar 29 05:57:48 2025 Received: (at submit) by debbugs.gnu.org; 29 Mar 2025 09:57:48 +0000 Received: from localhost ([127.0.0.1]:56953 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySwm-0006Jf-6K for submit@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 ) id 1tySwj-0006JD-49 for submit@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 ) id 1tySwW-0006i0-EC for guix-patches@gnu.org; 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 ) id 1tySwU-0001f8-9V for guix-patches@gnu.org; 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 To: guix-patches@gnu.org Subject: [PATCH 0/1] Remove freebayes Date: Sat, 29 Mar 2025 10:52:45 +0100 Message-ID: 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@enge.fr,s:andreas.enge@aquilenet.fr]; 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@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: rekado@elephly.net, 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 (-) 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 From debbugs-submit-bounces@debbugs.gnu.org Sat Mar 29 06:02:05 2025 Received: (at 77357) by debbugs.gnu.org; 29 Mar 2025 10:02:05 +0000 Received: from localhost ([127.0.0.1]:56978 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tyT0v-0006b0-13 for submit@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 ) id 1tyT0m-0006aC-Bw for 77357@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 To: 77357@debbugs.gnu.org Subject: Re: [PATCH 0/1] Remove freebayes Message-ID: References: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: 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@elephly.net 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 (-) 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 From debbugs-submit-bounces@debbugs.gnu.org Sun Mar 30 12:56:36 2025 Received: (at 77357) by debbugs.gnu.org; 30 Mar 2025 16:56:36 +0000 Received: from localhost ([127.0.0.1]:37955 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tyvxb-0002Da-MN for submit@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 ) id 1tyvRV-0000V4-S3 for 77357@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@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@debbugs.gnu.org>; Sun, 30 Mar 2025 18:12:01 +0200 (CEST) Message-ID: <8ba60fd9-d853-0414-dec5-b8e410caaf78@sam-d.com> 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@debbugs.gnu.org From: =?UTF-8?Q?Sebastian_D=c3=bcmcke?= 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@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 (-) 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 From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 02 03:54:12 2025 Received: (at 77357) by debbugs.gnu.org; 2 Apr 2025 07:54:12 +0000 Received: from localhost ([127.0.0.1]:54362 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzsvL-0000By-Rq for submit@debbugs.gnu.org; Wed, 02 Apr 2025 03:54:12 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21138) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzsvJ-0000BM-3S for 77357@debbugs.gnu.org; Wed, 02 Apr 2025 03:54:09 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1743580447; cv=none; d=zohomail.com; s=zohoarc; b=np8P8+X8UjmE5GWYyXs5vLn4qHPDTQzTyRNtz6+PIiamqzpAQ0bko4OKfo4ZC7kKJRFknfItAJvUJ6w60f1TeeR5JNcnjsTOCbYedWGLD+E6D2VOORdeuw7vY0rd2yB9aSAn2G11IPDBYsWQgaVNgEFLOIZQRpkqh1t3Et64B3k= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; 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Wed, 2 Apr 2025 00:54:04 -0700 (PDT) From: Ricardo Wurmus To: Andreas Enge Subject: Re: [PATCH 0/1] Remove freebayes In-Reply-To: (Andreas Enge's message of "Sat, 29 Mar 2025 11:01:43 +0100") References: User-Agent: mu4e 1.12.9; emacs 29.4 Date: Wed, 02 Apr 2025 09:54:01 +0200 Message-ID: <877c43dmna.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; format=flowed X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77357 Cc: 77357@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 (-) I have previously brought this up with upstream in an attempt to fix this, but I haven't yet been successful in fixing it. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 02 04:45:24 2025 Received: (at 77357) by debbugs.gnu.org; 2 Apr 2025 08:45:24 +0000 Received: from localhost ([127.0.0.1]:54642 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tztit-0007JI-Sf for submit@debbugs.gnu.org; Wed, 02 Apr 2025 04:45:24 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:36714) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tztir-0007IO-LW for 77357@debbugs.gnu.org; Wed, 02 Apr 2025 04:45:22 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 55F0313C; Wed, 2 Apr 2025 10:45:15 +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 oNsSBR6r_2cr; Wed, 2 Apr 2025 10:45:15 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 6E47F113; Wed, 2 Apr 2025 10:45:13 +0200 (CEST) Date: Wed, 2 Apr 2025 10:45:11 +0200 From: Andreas Enge To: Ricardo Wurmus Subject: Re: [PATCH 0/1] Remove freebayes Message-ID: References: <877c43dmna.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <877c43dmna.fsf@elephly.net> X-Rspamd-Queue-Id: 55F0313C X-Spamd-Result: default: False [5.40 / 15.00]; SPAM_FLAG(5.00)[]; BAYES_HAM(-3.00)[99.99%]; NEURAL_SPAM(3.00)[0.999]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; TO_DN_SOME(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; RCPT_COUNT_THREE(0.00)[3]; FROM_EQ_ENVFROM(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_MATCH_ENVRCPT_ALL(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: Sebastian =?iso-8859-15?Q?D=FCmcke?= , 77357@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 (-) Hello, cc-ing all discussion participants, as unfortunately debbugs does not do so. If I understand Sebastian correctly, then freebayes works, just the test suite does not? In that case, we could also just disable the tests with a pointer to the upstream issue. But then it would be nice if someone could first confirm that the package itself works :) Concerning guix-science, its description on codeberg says This GNU Guix channel provides recent versions of scientific software, which cannot be included upstream. This clearly is not the case of freebayes, which already is included :) Andreas From debbugs-submit-bounces@debbugs.gnu.org Wed Apr 02 05:05:21 2025 Received: (at 77357) by debbugs.gnu.org; 2 Apr 2025 09:05:21 +0000 Received: from localhost ([127.0.0.1]:54745 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tzu2D-0001d3-BM for submit@debbugs.gnu.org; Wed, 02 Apr 2025 05:05:21 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:45864) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tzu2A-0001bB-BK for 77357@debbugs.gnu.org; Wed, 02 Apr 2025 05:05:19 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 9FDAF181; Wed, 2 Apr 2025 11:05:11 +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 GbNmKUZvDAi6; Wed, 2 Apr 2025 11:05:11 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 8512AF6; Wed, 2 Apr 2025 11:05:10 +0200 (CEST) Date: Wed, 2 Apr 2025 11:05:08 +0200 From: Andreas Enge To: Ricardo Wurmus Subject: Re: [PATCH 0/1] Remove freebayes Message-ID: References: <877c43dmna.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: X-Rspamd-Queue-Id: 9FDAF181 X-Spamd-Result: default: False [5.39 / 15.00]; SPAM_FLAG(5.00)[]; BAYES_HAM(-3.00)[99.99%]; NEURAL_SPAM(2.99)[0.997]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; TO_DN_SOME(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; RCPT_COUNT_THREE(0.00)[3]; FROM_EQ_ENVFROM(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_MATCH_ENVRCPT_ALL(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: Sebastian =?iso-8859-15?Q?D=FCmcke?= , 77357@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 (-) Ricardo sent a bug upstream about a year ago: https://github.com/freebayes/freebayes/issues/825 Pjotrp mentions vcflib, which is a package with only freebayes as dependency in Guix. We are at version 1.0.9 of February 2023, and there is a 1.0.12 from November 2024. But the package recipe is quite the nightmare... Andreas From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 03 11:09:27 2025 Received: (at 77357) by debbugs.gnu.org; 3 Apr 2025 15:09:27 +0000 Received: from localhost ([127.0.0.1]:35184 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u0MC7-0004Sq-G1 for submit@debbugs.gnu.org; Thu, 03 Apr 2025 11:09:27 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21148) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u0MC4-0004Sd-Vm for 77357@debbugs.gnu.org; Thu, 03 Apr 2025 11:09:26 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1743692960; cv=none; d=zohomail.com; s=zohoarc; b=kWq/xyD//L5k8e/fBf0hn7eAt4kb28kNJ+8dUOkQjMJP3Y2EjBPadxMniqW+E4sfHSj3oz34PH0w/9yxTWKMPZjZ1anq6q0GI+waPlUCVrfuGJtHvSWhtn1pHoY8KP0dmp/J8RYrVpk/+WE9d1Pi58x+a9auhTq9DG8TDXnOGgo= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1743692960; h=Content-Type:Cc:Cc:Date:Date:From:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:Subject:To:To:Message-Id:Reply-To; bh=rA1i8ozoxqAnyo+fibTBXA9eUNT1eYi8kHEw23ZpWKo=; b=T2RrlMlZU1OhlYz6TFyteyVG/k1ZzP5ArE568Z0RyNTfoaM9/plRT6p417O5y1kLjbbneTDsIHQaEAnx59uWODTFIl8TQJG/Y5fV5aj500gQzonWgYJiy5fQa8iJZHQzIoa3/Q1CTT8TVI96peLjCnSTA1vH0imTgn9neeZWBDk= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1743692960; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:In-Reply-To:References:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=rA1i8ozoxqAnyo+fibTBXA9eUNT1eYi8kHEw23ZpWKo=; b=PFZ03Rpzu7Tqg7JV3QD5v7awTIfgCKXku7nW3Nm+X1SuYujvAldfLRDedC7F7rUp gLn7S9Je3CHu3ZbMQlPR07zq9AcfS6xBl1UYUXDigTjMHThhy/mofPlZkIsP9Cwq5+u bSUY9rkrnwKJvhM22seOaP28HV516nrf5sebaWt0= Received: by mx.zohomail.com with SMTPS id 1743692957386336.5680289794327; Thu, 3 Apr 2025 08:09:17 -0700 (PDT) From: Ricardo Wurmus To: Andreas Enge Subject: Re: [PATCH 0/1] Remove freebayes In-Reply-To: (Andreas Enge's message of "Wed, 2 Apr 2025 11:05:08 +0200") References: <877c43dmna.fsf@elephly.net> User-Agent: mu4e 1.12.9; emacs 29.4 Date: Thu, 03 Apr 2025 17:09:13 +0200 Message-ID: <87cydts2na.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; format=flowed X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77357 Cc: Sebastian =?utf-8?Q?D=C3=BCmcke?= , 77357@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 (-) Andreas Enge writes: > Ricardo sent a bug upstream about a year ago: > https://github.com/freebayes/freebayes/issues/825 > > Pjotrp mentions vcflib, which is a package with only freebayes > as > dependency in Guix. We are at version 1.0.9 of February 2023, > and there > is a 1.0.12 from November 2024. But the package recipe is quite > the > nightmare... I have locally updated vcflib to 1.0.12 and managed to build the latest version of freebayes. It was not fun. I'll push this once I've cleaned up my unrelated WIP for ITK. -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 03 11:15:32 2025 Received: (at 77357) by debbugs.gnu.org; 3 Apr 2025 15:15:32 +0000 Received: from localhost ([127.0.0.1]:35207 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u0MI0-0004or-G4 for submit@debbugs.gnu.org; Thu, 03 Apr 2025 11:15:32 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:41176) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u0MHy-0004oY-5R for 77357@debbugs.gnu.org; Thu, 03 Apr 2025 11:15:30 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 499342FE; Thu, 3 Apr 2025 17:15:23 +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 RZFye9W8-8QN; Thu, 3 Apr 2025 17:15:22 +0200 (CEST) Received: from jurong (176-179-191-150.abo.bbox.fr [176.179.191.150]) by hera.aquilenet.fr (Postfix) with ESMTPSA id 26AC4156; Thu, 3 Apr 2025 17:15:21 +0200 (CEST) Date: Thu, 3 Apr 2025 17:15:19 +0200 From: Andreas Enge To: Ricardo Wurmus Subject: Re: [PATCH 0/1] Remove freebayes Message-ID: References: <877c43dmna.fsf@elephly.net> <87cydts2na.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline In-Reply-To: <87cydts2na.fsf@elephly.net> X-Rspamd-Queue-Id: 499342FE X-Spamd-Result: default: False [5.40 / 15.00]; SPAM_FLAG(5.00)[]; NEURAL_SPAM(3.00)[1.000]; BAYES_HAM(-3.00)[99.98%]; MID_RHS_NOT_FQDN(0.50)[]; MIME_GOOD(-0.10)[text/plain]; TO_DN_SOME(0.00)[]; MIME_TRACE(0.00)[0:+]; RCVD_VIA_SMTP_AUTH(0.00)[]; RCVD_COUNT_TWO(0.00)[2]; RCPT_COUNT_THREE(0.00)[3]; FROM_EQ_ENVFROM(0.00)[]; RCVD_TLS_ALL(0.00)[]; FROM_HAS_DN(0.00)[]; TO_MATCH_ENVRCPT_ALL(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: Sebastian =?iso-8859-15?Q?D=FCmcke?= , 77357@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 (-) Am Thu, Apr 03, 2025 at 05:09:13PM +0200 schrieb Ricardo Wurmus: > I have locally updated vcflib to 1.0.12 and managed to build the latest > version of freebayes. > It was not fun. I imagine, congratulations! Andreas From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 03 17:25:31 2025 Received: (at 77357) by debbugs.gnu.org; 3 Apr 2025 21:25:31 +0000 Received: from localhost ([127.0.0.1]:35982 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u0S43-0005b4-Fd for submit@debbugs.gnu.org; Thu, 03 Apr 2025 17:25:31 -0400 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21113) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u0S3z-0005aq-E0 for 77357@debbugs.gnu.org; Thu, 03 Apr 2025 17:25:29 -0400 ARC-Seal: i=1; a=rsa-sha256; t=1743715522; cv=none; d=zohomail.com; s=zohoarc; b=eAvalf0Rkk0uT7elGL0pe4OlYNxo74q4osDL6wNO9TevUv9InWVPGVHEkkPQQXSYbTi0o7xabtYcOWPJhUwmOcCc4mOazxld8gExxvQnACj9u4kp4pwiRR7oge5Zt4BlJsVqex/NNwsP2xJ7nG6vz/aiFst+xxzNPo5TWuf3eoo= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1743715522; h=Content-Type:Cc:Cc:Date:Date:From:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:Subject:To:To:Message-Id:Reply-To; bh=932SlDF7P+6Uv38E8imLNDlt73VLtRnE1JyCixoEnpY=; b=c9OQIp05ZyCD2ClzIzqbbGuzwf849AHczGxMwmeByl7RP8p/LgxMxxOGfdmZbNixv1HBDT4eNQtMfL+Dyxt0bfeidMsoNmXt+cJBg96Cwn8ZOYLpDtHb7soWUUiPGmFsJpEKOSHjsVygCHcmJ03eQlNJRvpu4uj7jVxp2cy+2m0= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1743715522; s=zoho; d=elephly.net; i=rekado@elephly.net; h=From:From:To:To:Cc:Cc:Subject:Subject:In-Reply-To:References:Date:Date:Message-ID:MIME-Version:Content-Type:Message-Id:Reply-To; bh=932SlDF7P+6Uv38E8imLNDlt73VLtRnE1JyCixoEnpY=; b=CmH9em23mJnKHis7n+TaUwplwkrz6nk8jGBPyBH/jatRlpilouorzV7SDd/yffip vupMdYmb9KlTRMnt9s8Ll9Ll9GaCl5p6d2x7YoqxY3ARALCiLzmGVbsx1byDSwrK2Li ddZU09pC5w6ZoSyHHaTLOiwkaCexbs5FwN4TR+p0= Received: by mx.zohomail.com with SMTPS id 1743715519022211.50586728907513; Thu, 3 Apr 2025 14:25:19 -0700 (PDT) From: Ricardo Wurmus To: Andreas Enge Subject: Re: [PATCH 0/1] Remove freebayes In-Reply-To: (Andreas Enge's message of "Thu, 3 Apr 2025 17:15:19 +0200") References: <877c43dmna.fsf@elephly.net> <87cydts2na.fsf@elephly.net> User-Agent: mu4e 1.12.9; emacs 29.4 Date: Thu, 03 Apr 2025 23:25:16 +0200 Message-ID: <877c41rl8j.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; format=flowed X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77357 Cc: Sebastian =?utf-8?Q?D=C3=BCmcke?= , 77357@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 (-) Andreas Enge writes: > Am Thu, Apr 03, 2025 at 05:09:13PM +0200 schrieb Ricardo Wurmus: >> I have locally updated vcflib to 1.0.12 and managed to build >> the latest >> version of freebayes. >> It was not fun. Pushed with commit efaa20d2d86bc4f10dfc45a25fca50a0dad6e917. Can we close this issue? -- Ricardo From debbugs-submit-bounces@debbugs.gnu.org Thu Apr 03 20:42:11 2025 Received: (at 77357-done) by debbugs.gnu.org; 4 Apr 2025 00:42:11 +0000 Received: from localhost ([127.0.0.1]:36288 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1u0V8N-0003eg-G7 for submit@debbugs.gnu.org; Thu, 03 Apr 2025 20:42:11 -0400 Received: from mugam.systemreboot.net ([139.59.75.54]:51348) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1u0V8I-0003eB-IN for 77357-done@debbugs.gnu.org; Thu, 03 Apr 2025 20:42:09 -0400 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=systemreboot.net; s=default; t=1743727301; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: in-reply-to:in-reply-to; bh=5TbJ4nPcVjLAaID38eoP1jzLf4MQAFolCC8ZLupcmzQ=; b=WX/8zYxCevTXO6ZrBExfsfRAxYDhiYnZKR32T2rrHf+rlKVx82YR7RMniNLzFq/YStvBXB H4N/lgDFUeVbYEGqa3zGr4J10B0wqKTdeD4kYbXiZ47J+L18jkdtR6xsAOBS7Q5oU7PJYb 1GaOVktVjRFLnEBwrxDMLHx4bwB+jm1VGKDEArNb+pesc0lI6YEdHayqD9Dnu8zHfhBfj6 gARtOrLaydKPKJF2ZMnBnYu8zsXqexl3KIqw1uMJ9cnlrRnGWEvNgNTLky/xp1xL4EwQVd 4AjDgqBHxF/4Et0XrHCMtaH+mGsUM/ClDF2PtEwS5HEwkF6MRf63sPpUmLSj+w== Received: from localhost ( [192.168.2.1]) by mugam.systemreboot.net (OpenSMTPD) with ESMTPSA id c751ac54 (TLSv1.3:TLS_AES_256_GCM_SHA384:256:NO); Fri, 4 Apr 2025 00:41:40 +0000 (UTC) From: Arun Isaac To: 77357-done@debbugs.gnu.org Subject: Re: [PATCH 0/1] Remove freebayes In-Reply-To: <877c41rl8j.fsf@elephly.net> Date: Fri, 04 Apr 2025 01:41:34 +0100 Message-ID: <87y0wgkbb5.fsf@systemreboot.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 77357-done Cc: Ricardo Wurmus , Andreas Enge , Sebastian =?utf-8?Q?D=C3=BCmcke?= 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 all, Thank you all for your hard work. I use freebayes in my research, and I can confirm that it actually works and produces scientifically meaningful results. Regards, Arun From unknown Mon Aug 18 19:31:29 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 02 May 2025 11:24:13 +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