From patchwork Sat Mar 29 09:52:46 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40958 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 35D3227BBEA; Sat, 29 Mar 2025 09:58:29 +0000 (GMT) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-7.6 required=5.0 tests=BAYES_00,DKIMWL_WL_HIGH, DKIM_SIGNED,DKIM_VALID,MAILING_LIST_MULTI,RCVD_IN_DNSWL_BLOCKED, RCVD_IN_VALIDITY_CERTIFIED,RCVD_IN_VALIDITY_RPBL,RCVD_IN_VALIDITY_SAFE, SPF_HELO_PASS,URIBL_BLOCKED autolearn=ham autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 9AAA027BBE2 for ; Sat, 29 Mar 2025 09:58:28 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tySxB-0006ki-Tm; Sat, 29 Mar 2025 05:58:13 -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 1tySx1-0006jl-Sl for guix-patches@gnu.org; Sat, 29 Mar 2025 05:58:05 -0400 Received: from debbugs.gnu.org ([2001:470:142:5::43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1tySx1-0001gf-JO for guix-patches@gnu.org; Sat, 29 Mar 2025 05:58:03 -0400 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debbugs.gnu.org; s=debbugs-gnu-org; h=MIME-Version:References:In-Reply-To:Date:From:To:Subject; bh=owzSdwNsaFImqyFrEsZsJUQ9eC2Dk+l9Jv/hhcjCBAQ=; b=UqXfaT47piAxVFaEgKlVBI85MYQb89sv0eryDy/MWOds1GRvrOHjHOS2dbWorxe8OA8nqsIy3Rsu195xWX7aTJvWS29gyvV5XsrGmZmRjGjjXEabV8qORjSNYDQSYoWswWpFfSLMDrxzba9Bx1xXS9Oz9vYvhBB3RuNZFAL2VmGTIgDEi4hNRulJ0BccvCdiJuMB0tRWSJxC+ae9IDLo1H1LWWxzEjrs+jdUObD1/1GGr/T5HkyQRCWshDeCeWzN9nsVXHJVKNQZ3C72Sj4W7f0L/bQFR6Rg5TGmyzcBE8vjJlBJQfHFgj7K894psU35lkO7h3ci5LQmOASxo52dWg==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tySx1-0006Kj-Cq for guix-patches@gnu.org; Sat, 29 Mar 2025 05:58:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77358] [PATCH 1/1] gnu: Remove freebayes. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:58:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 77358 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77358@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.174324228224331 (code B ref -1); Sat, 29 Mar 2025 09:58:03 +0000 Received: (at submit) by debbugs.gnu.org; 29 Mar 2025 09:58:02 +0000 Received: from localhost ([127.0.0.1]:56956 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySwz-0006KD-Kp for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:58:02 -0400 Received: from lists.gnu.org ([2001:470:142::17]:48852) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySwx-0006JW-HN for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:58:00 -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 1tySwc-0006iL-3W for guix-patches@gnu.org; Sat, 29 Mar 2025 05:57:41 -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 1tySwX-0001fP-Or for guix-patches@gnu.org; Sat, 29 Mar 2025 05:57:37 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 909B72E6; Sat, 29 Mar 2025 10:57:31 +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 UPk6WHlmu78j; Sat, 29 Mar 2025 10:57:30 +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 46B5C297; Sat, 29 Mar 2025 10:57:28 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:52:46 +0100 Message-ID: <80c60a86e364b1d634cb330abc19a40c1ca680e6.1743241966.git.andreas@enge.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: 909B72E6 X-Spamd-Result: default: False [8.40 / 15.00]; SPAM_FLAG(5.00)[]; BAYES_HAM(-3.00)[100.00%]; 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-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-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org X-getmail-retrieved-from-mailbox: Patches The package does not build since 2023, it fails most of its tests. Updating to the latest version does not solve the problem. * gnu/packages/bioinformatics.scm (freebayes): Delete variable. Change-Id: Ib61e298d639f7c5a86a2fc33cbedf0c764045441 --- gnu/packages/bioinformatics.scm | 82 --------------------------------- 1 file changed, 82 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0825fbb6ef..96a4c6a2d6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -22501,88 +22501,6 @@ (define-public vcflib manipulations on VCF files.") (license license:expat))) -(define-public freebayes - (package - (name "freebayes") - (version "1.3.7") - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/freebayes/freebayes") - (commit (string-append "v" version)))) - (file-name (git-file-name name version)) - (sha256 - (base32 "163nd1xkq547za80khlys4qkgal64f3sgl6ap3yvik68r0rgyisv")))) - (build-system meson-build-system) - (inputs - (list fastahack htslib smithwaterman tabixpp vcflib)) - (native-inputs - `(("bash-tap" ,bash-tap) - ("bc" ,bc) - ("grep" ,grep) ; Built with perl support. - ("parallel" ,parallel) - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("python" ,python) - ("samtools" ,samtools) - ("simde" ,simde) - ;; This submodule is needed to run the tests. - ("test-simple-bash-src" - ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ingydotnet/test-simple-bash/") - (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc"))) - (file-name "test-simple-bash-src-checkout") - (sha256 - (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) - (arguments - `(#:phases - (modify-phases %standard-phases - (add-after 'unpack 'patch-source - (lambda* (#:key inputs #:allow-other-keys) - (let ((bash-tap (assoc-ref inputs "bash-tap"))) - (substitute* (find-files "test/t") - (("BASH_TAP_ROOT=bash-tap") - (string-append "BASH_TAP_ROOT=" bash-tap "/bin")) - (("bash-tap/bash-tap-bootstrap") - (string-append bash-tap "/bin/bash-tap-bootstrap")) - (("source.*bash-tap-bootstrap") - (string-append "source " bash-tap "/bin/bash-tap-bootstrap"))) - (substitute* '("src/BedReader.cpp" - "src/BedReader.h") - (("../intervaltree/IntervalTree.h") "IntervalTree.h")) - ;; We don't have Perl support in grep -E. - (substitute* '("test/t/01_call_variants.t" - "test/t/01b_call_variants.t") - (("grep -P") "grep -E") - (("\\\\t") " ")) - (substitute* "meson.build" - ;; Our pkg-config file is vcflib.pc - (("libvcflib") "vcflib") - (("vcflib_inc,") ""))))) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (mkdir-p "test/test-simple-bash") - (copy-recursively (assoc-ref inputs "test-simple-bash-src") - "test/test-simple-bash"))) - ;; The slow tests take longer than the specified timeout. - ,@(if (any (cute string=? <> (%current-system)) - '("armhf-linux" "aarch64-linux")) - '((replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "meson" "test" "--timeout-multiplier" "5"))))) - '())))) - (home-page "https://github.com/freebayes/freebayes") - (synopsis "Haplotype-based variant detector") - (description "FreeBayes is a Bayesian genetic variant detector designed to -find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), -indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and -complex events (composite insertion and substitution events) smaller than the -length of a short-read sequencing alignment.") - (license license:expat))) - (define-public samblaster (package (name "samblaster")