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Resent-From: Andreas Enge Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Fri, 28 Mar 2025 09:55:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 77331 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 77331@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.17431556812136 (code B ref -1); Fri, 28 Mar 2025 09:55:01 +0000 Received: (at submit) by debbugs.gnu.org; 28 Mar 2025 09:54:41 +0000 Received: from localhost ([127.0.0.1]:52925 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ty6QC-0000YO-KW for submit@debbugs.gnu.org; Fri, 28 Mar 2025 05:54:41 -0400 Received: from lists.gnu.org ([2001:470:142::17]:37016) by debbugs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.84_2) (envelope-from ) id 1ty6Q8-0000Y2-6K for submit@debbugs.gnu.org; Fri, 28 Mar 2025 05:54:38 -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 1ty6Q1-0002Vj-Dz for guix-patches@gnu.org; Fri, 28 Mar 2025 05:54:29 -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 1ty6Py-0003jH-Bt for guix-patches@gnu.org; Fri, 28 Mar 2025 05:54:29 -0400 Received: from localhost (localhost [127.0.0.1]) by hera.aquilenet.fr (Postfix) with ESMTP id 31F7130D; Fri, 28 Mar 2025 10:54:22 +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 DVP-Id3gCQaH; Fri, 28 Mar 2025 10:54:21 +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 1B7B5126; Fri, 28 Mar 2025 10:54:20 +0100 (CET) From: Andreas Enge Date: Fri, 28 Mar 2025 10:52:48 +0100 Message-ID: X-Mailer: git-send-email 2.49.0 MIME-Version: 1.0 X-Rspamd-Queue-Id: 31F7130D 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_RPBL_BLOCKED=0.001, RCVD_IN_VALIDITY_SAFE_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 * 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 --- Yet another package depending on hdf5, which I noticed does not compile when I tried to update hdf5, but it already does not compile now. There is a package r-varianttools in bioconductor, but I think they are not related. gnu/packages/bioinformatics.scm | 37 --------------------------------- 1 file changed, 37 deletions(-) base-commit: decc863d46274ef53e5ef6b33e00070fd920a6a7 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 473e91bda9..8fd7789028 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"))