From patchwork Sat Mar 29 09:21:28 2025 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Andreas Enge X-Patchwork-Id: 40952 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 0373827BBEA; Sat, 29 Mar 2025 09:32:23 +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 ABFBA27BBE2 for ; Sat, 29 Mar 2025 09:32:22 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1tySXM-0002hc-OA; Sat, 29 Mar 2025 05:31:38 -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 1tySW0-0002Sp-Em for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:17 -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 1tySVy-000703-DW for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:08 -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=/YsFNn7tuOEnYE+HPNJK0TID2WafC0IUUIHbyyWdQ2s=; b=gM+BUyTWwUc+4gyTJGBIlMZwwPzgW92lzpDhP8bbODKsJs4uhuP+0s33PZ0Df9xbHgO84YvxchJpPZs8gFOhP9FyIpZdTXrAWvEKbL/PO/u7FvSbkdI598WS4G3sbgeVeoyzVGkjH5MBzayhYggpenYCbWW/7TI6pHZywskynNjQP8JRVvN1ZTe8yZDxDPQ5qIXWWfk/k8JBQteY6Ooy/A5jjX9g25smdSh7Nq7GdZhOozmgYKLkSQxig3IH5J4xlwEAUamBQv+xwT5hz/o56FnYlOBG6TAidFytEwP9fD8jzf1ahw6z+LQXsxaS70ymV6Masr6jiA9NvK2A+duh/Q==; Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1tySVy-0004uU-4v for guix-patches@gnu.org; Sat, 29 Mar 2025 05:30:06 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#77287] [PATCH v2 4/8] gnu: Remove variant-tools. Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sat, 29 Mar 2025 09:30:06 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 77287 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77287@debbugs.gnu.org Cc: rekado@elephly.net, Andreas Enge Received: via spool by 77287-submit@debbugs.gnu.org id=B77287.174324057818740 (code B ref 77287); Sat, 29 Mar 2025 09:30:06 +0000 Received: (at 77287) by debbugs.gnu.org; 29 Mar 2025 09:29:38 +0000 Received: from localhost ([127.0.0.1]:56858 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1tySVW-0004sB-3y for submit@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:38 -0400 Received: from hera.aquilenet.fr ([185.233.100.1]:44914) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1tySV4-0004qJ-UI for 77287@debbugs.gnu.org; Sat, 29 Mar 2025 05:29:11 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 0AD942F8; Sat, 29 Mar 2025 10:29:05 +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 r5Fe8NUORS7X; Sat, 29 Mar 2025 10:29:04 +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 E4A79172; Sat, 29 Mar 2025 10:29:02 +0100 (CET) From: Andreas Enge Date: Sat, 29 Mar 2025 10:21:28 +0100 Message-ID: <7e352f0d38c546703ababed978329d754df2eeaf.1743240092.git.andreas@enge.fr> X-Mailer: git-send-email 2.49.0 In-Reply-To: References: MIME-Version: 1.0 X-Rspamd-Queue-Id: 0AD942F8 X-Spamd-Result: default: False [-6.43 / 15.00]; REPLY(-4.00)[]; BAYES_HAM(-3.00)[100.00%]; NEURAL_HAM(-2.83)[-0.943]; 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)[]; RCPT_COUNT_THREE(0.00)[3]; TO_DN_SOME(0.00)[]; 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-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 * gnu/packages/bioinformatics.scm (variant-tools): Delete variable. The package does not compile any more and has no dependent packages. The last release dates from 2020; there is an additional commit in 2022; the git repository has been archived in 2023. Change-Id: Idb5df024121c5085f764f179d31ac67cff3fc5c7 --- gnu/packages/bioinformatics.scm | 37 --------------------------------- 1 file changed, 37 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0825fbb6ef..e8b585e495 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15248,43 +15248,6 @@ (define-public multiqc common bioinformatics tools.") (license license:gpl3+))) -(define-public variant-tools - (package - (name "variant-tools") - (version "3.1.2") - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/vatlab/varianttools") - ;; There is no tag corresponding to version 3.1.2 - (commit "813ae4a90d25b69abc8a40f4f70441fe09015249"))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "12ibdmksj7icyqhks4xyvd61bygk4pjmxn618kp6vgk1af01y34g")))) - (build-system python-build-system) - (inputs - (list boost - c-blosc - gsl - hdf5 - hdf5-blosc - python-cython - zlib)) - (propagated-inputs - (list python-numpy python-pycurl python-pyzmq python-scipy - python-tables)) - (home-page "https://vatlab.github.io/vat-docs/") - (synopsis "Analyze genetic variants from Next-Gen sequencing studies") - (description - "Variant tools is a tool for the manipulation, annotation, -selection, simulation, and analysis of variants in the context of next-gen -sequencing analysis. Unlike some other tools used for next-gen sequencing -analysis, variant tools is project based and provides a whole set of tools to -manipulate and analyze genetic variants.") - (license license:gpl3+))) - (define-public r-chromvarmotifs (let ((commit "38bed559c1f4770b6c91c80bf3f8ea965da26076") (revision "1"))