From patchwork Sun Jan 29 13:09:24 2023 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: Efraim Flashner X-Patchwork-Id: 1233 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 5942527BBEB; Sun, 29 Jan 2023 13:10:27 +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=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS autolearn=unavailable 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 59D4227BBE9 for ; Sun, 29 Jan 2023 13:10:25 +0000 (GMT) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1pM7Ri-0002ew-Gi; Sun, 29 Jan 2023 08:10:10 -0500 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 1pM7Rf-0002ei-C7 for guix-patches@gnu.org; Sun, 29 Jan 2023 08:10:07 -0500 Received: from debbugs.gnu.org ([209.51.188.43]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1pM7Ra-0006wH-6T for guix-patches@gnu.org; Sun, 29 Jan 2023 08:10:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1pM7RZ-0003TM-S4 for guix-patches@gnu.org; Sun, 29 Jan 2023 08:10:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#61148] [PATCH 0/5] Update vcflib Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Sun, 29 Jan 2023 13:10:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 61148 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 61148@debbugs.gnu.org Cc: Pjotr Prins , Efraim Flashner X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.167499777713296 (code B ref -1); Sun, 29 Jan 2023 13:10:01 +0000 Received: (at submit) by debbugs.gnu.org; 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Sun, 29 Jan 2023 05:09:27 -0800 (PST) Received: from localhost ([141.226.15.115]) by smtp.gmail.com with ESMTPSA id bh13-20020a170906a0cd00b0084d14646fd9sm5230458ejb.165.2023.01.29.05.09.26 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Sun, 29 Jan 2023 05:09:26 -0800 (PST) From: Efraim Flashner Date: Sun, 29 Jan 2023 15:09:24 +0200 Message-Id: X-Mailer: git-send-email 2.39.1 MIME-Version: 1.0 Received-SPF: pass client-ip=2a00:1450:4864:20::634; envelope-from=efraim.flashner@gmail.com; helo=mail-ej1-x634.google.com X-Spam_score_int: -14 X-Spam_score: -1.5 X-Spam_bar: - X-Spam_report: (-1.5 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_EF=-0.1, FREEMAIL_FORGED_FROMDOMAIN=0.249, FREEMAIL_FROM=0.001, HEADER_FROM_DIFFERENT_DOMAINS=0.249, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=no 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 vcflib has a new update out so it's time to update it and the dependant packages. libvcfh doesn't seem to be used, perhaps Pjotr knows if it's needed? I don't love '-DTABIX_FOUND=ON' in vcflib but it seems to work. I'm also not sure that the simde headers are actually used. I'd like to use more of the unbundled sources since it seems like a waste to unbundle them and then just toss the sources back into the build but they don't natively produce libraries so I'd rather not. Perhaps it'd be better to just not unbundle them in the first place? Efraim Flashner (5): gnu: intervaltree: Update to 0.1-1.aa59377. gnu: tabixpp: Update to 1.1.2. gnu: Add wfa2-lib. gnu: Add libvcfh. gnu: vcflib: Update to 1.0.6. gnu/packages/bioinformatics.scm | 217 ++++++++++++++++++++++++-------- 1 file changed, 166 insertions(+), 51 deletions(-) base-commit: b9e6e31877cdb96cceba4d1ec6268f86b824dec4