[From nobody Mon Sep 21 13:19:06 2026 Received: (at 1114084-close) by bugs.debian.org; 21 Sep 2026 12:17:05 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-111.0 required=4.0 tests=BAYES_00,DKIM_SIGNED, DKIM_VALID,DKIM_VALID_AU,DKIM_VALID_EF,FOURLA,FVGT_m_MULTI_ODD, HAS_BUG_NUMBER,MD5_SHA1_SUM,MEDS2,PGPSIGNATURE,RCVD_IN_DNSWL_MED, SPF_HELO_PASS,SPF_PASS,USER_IN_DKIM_WELCOMELIST autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 124; hammy, 150; neutral, 262; spammy, 0. spammytokens: hammytokens:0.000-+--HX-Debian:DAK, 0.000-+--H*rp:D*ftp-master.debian.org, 0.000-+--HX-DAK:process-upload, 0.000-+--UD:debian.tar.xz, 0.000-+--H*r:sk:fasolo. Return-path: <envelope@ftp-master.debian.org> Received: from mitropoulos.debian.org ([2001:648:2ffc:deb:216:61ff:fe9d:958d]:48288) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <envelope@ftp-master.debian.org>) id 1x8cxF-00DmvY-1j for 1114084-close@bugs.debian.org; Mon, 21 Sep 2026 12:17:05 +0000 Received: via submission from C=NA, ST=NA, L=Ankh Morpork, O=Debian SMTP, OU=Debian SMTP CA, CN=fasolo.debian.org, EMAIL=hostmaster@fasolo.debian.org (verified) by mitropoulos.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <envelope@ftp-master.debian.org>) id 1x8cxD-002wTP-1r for 1114084-close@bugs.debian.org; Mon, 21 Sep 2026 12:17:03 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=ftp-master.debian.org; s=smtpauto.fasolo; h=Date:Message-Id:Content-Type: Subject:MIME-Version:To:Reply-To:From:Cc:Content-Transfer-Encoding:Content-ID :Content-Description:In-Reply-To:References; bh=XD88GSunTfZZv3MQHtUd0rv+Cgy40lqZNmjMBisEArk=; b=E/HKynfUNq1Zj/C0lnwupU8cGc aFYs1/ZgJ5OxcC8pbCduVF6pOz315jo4i0S+XWWohytgi2JJz6bcSZLI+CYpgbmupNC8PHiRePMLA REW2yvicsXReh3VZPbJXmvOpqFnzGRMUWJTWBzQHEYssU/Wyn59imvZBRG6QbYfvPiYhp6RdCrP9A DS4Wq/vQSzjffcKVRT8EiWQgmg5If2YsGQgYKH+G6zbfpztdOctLy4XQANWHqS0FH2d0IKEXGwDOv 8CvRgnbySFOAHAJqlHnEiMIYHg5TERYaLvAVAIGA0WFEl2EwMM8v63GDWd5WZqVnoV8DWTd/aGt46 P0m3gu4g==; Received: from dak by fasolo.debian.org with local (Exim 4.98.2) (envelope-from <envelope@ftp-master.debian.org>) id 1x8cxC-00000007neP-1hBR; Mon, 21 Sep 2026 12:17:02 +0000 From: Debian FTP Masters <ftpmaster@ftp-master.debian.org> Reply-To: Andreas Tille <tille@debian.org> To: 1114084-close@bugs.debian.org X-DAK: dak process-upload X-Debian: DAK X-Debian-Package: cufflinks Debian: DAK Debian-Changes: cufflinks_2.2.1+git20190706.dc3b0cb+dfsg-1_source.changes Debian-Source: cufflinks Debian-Version: 2.2.1+git20190706.dc3b0cb+dfsg-1 Debian-Architecture: source Debian-Suite: unstable Debian-Archive-Action: accept MIME-Version: 1.0 Subject: Bug#1114084: fixed in cufflinks 2.2.1+git20190706.dc3b0cb+dfsg-1 Content-Type: multipart/signed; micalg="pgp-sha256"; protocol="application/pgp-signature"; boundary="===============8831161969127448853==" Message-Id: <E1x8cxC-00000007neP-1hBR@fasolo.debian.org> Date: Mon, 21 Sep 2026 12:17:02 +0000 --===============8831161969127448853== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Source: cufflinks Source-Version: 2.2.1+git20190706.dc3b0cb+dfsg-1 Done: Andreas Tille <tille@debian.org> We believe that the bug you reported is fixed in the latest version of cufflinks, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 1114084@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <tille@debian.org> (supplier of updated cufflinks package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmaster@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Mon, 21 Sep 2026 13:33:58 +0200 Source: cufflinks Architecture: source Version: 2.2.1+git20190706.dc3b0cb+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debi= an.org> Changed-By: Andreas Tille <tille@debian.org> Closes: 1114084 1127186 Changes: cufflinks (2.2.1+git20190706.dc3b0cb+dfsg-1) unstable; urgency=3Dmedium . * New upstream version (latest commit) * Build with gcc-15 - Force -std=3Dgnu11 when compiling the legacy locfit C code so that old-style "extern f();" declarations keep their pre-C23 meaning of "unspecified arguments" instead of "no arguments" - gcc15.patch: fix broken function signatures (prresp, compbandwid, wdexpand, compsda, widthsj, kdecri, ar_setfunction, extern INT fact[]) - cxxstandard.patch: force -std=3Dgnu++17 instead of upstream's -std=3Dc= ++03 (C++03 no longer works with GCC 16's libstdc++, Boost 1.90 and Eigen 5, while the compiler default C++23 breaks the bundled LEMON library which still uses std::allocator::construct/destroy) - byte.patch: use uint8_t instead of the bare 'byte' type (collides with std::byte under C++17) in gff.cpp, codons.cpp and gdna.cpp Closes: #1114084 * d/watch: - version=3D5 - Fetch latest Git commit * Do not Build-Depend libboost-system-dev + d/rules: exclude boost-system Closes: #1127186 * Build-Depends: - libboost-filesystem-dev - s/dh-python/dh-sequence-python3/ * Fix doc installation * Reformat the Last-Update date as ISO YYYY-MM-DD. * Remove redundant Priority: optional from source stanza. * Update standards version to 4.7.4, no changes needed. * Reflow Uploaders field (cme) * Drop 'Rules-Requires-Root: no' from d/control (routine-update) * debputy lint --auto-fix (routine-update) * Add autopkgtest Checksums-Sha1: a1b1ebdcf7bfa7842464f0a57bc870543d6d1866 2415 cufflinks_2.2.1+git20190706.dc= 3b0cb+dfsg-1.dsc e357c2b02deeab3d3296c40845fabecd697263ee 480884 cufflinks_2.2.1+git20190706.= dc3b0cb+dfsg.orig.tar.xz 28e0ba5273427736cfc6125cb14a4fa227a7d056 31676 cufflinks_2.2.1+git20190706.d= c3b0cb+dfsg-1.debian.tar.xz 86085abd1a6937e751f30c350a286b50c4389ad1 7818 cufflinks_2.2.1+git20190706.dc= 3b0cb+dfsg-1_amd64.buildinfo Checksums-Sha256: 4fae0087b3a9e179777c89fc50dcbd5d0d10f5641729705fb3dd331f327a98b7 2415 cuffli= nks_2.2.1+git20190706.dc3b0cb+dfsg-1.dsc d90f7286f79a20d942ddb59f67f5a516ae9a48b673cb9442c1aa135b954161ea 480884 cuff= links_2.2.1+git20190706.dc3b0cb+dfsg.orig.tar.xz acf038ef51af05c8cd11f6017c828ab0bf6d5eb2a617f4071b01d4e0f71ca055 31676 cuffl= inks_2.2.1+git20190706.dc3b0cb+dfsg-1.debian.tar.xz 1eed7f83cc53623d7eabf988e48944ab69df964ce2e820d3b767f88277445822 7818 cuffli= nks_2.2.1+git20190706.dc3b0cb+dfsg-1_amd64.buildinfo Files: 3ffdf62db9937e9367e9766e61185ca0 2415 non-free/science optional cufflinks_2.= 2.1+git20190706.dc3b0cb+dfsg-1.dsc 0a567f914ca5bd4409f0b1a1077ef69a 480884 non-free/science optional cufflinks_= 2.2.1+git20190706.dc3b0cb+dfsg.orig.tar.xz 2a9fff904eca76d96587852d65e091e3 31676 non-free/science optional cufflinks_2= .2.1+git20190706.dc3b0cb+dfsg-1.debian.tar.xz 8f3dad9a20e98fba3f43de51d688b198 7818 non-free/science optional cufflinks_2.= 2.1+git20190706.dc3b0cb+dfsg-1_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmqxGUkRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtGf7A/7BrZTJoO7q+d/wxHXeEWCpjox4j/MvBl/ 3WafNCXjP+LR2FcaAxrP6gIi+jco0AitPmITGNbSl11EeVn3LrCgxxrM90ZYdNkI g8Krq8PIAJO0jbUxm6qA7Y14fLHEQmHu53RSOgMJCXxY2HWaq3h8tU0Ny6KThxBE NHxhOoYV/g1xWDCIQc+73fcCGW5J6sRzfHslf+TcAGFV3kD8Audz6OUQiTarqzzV 7xBJTUN34W1sF7qHgf9ArzPtkb0PdsIJ7yR6i+1vzdSM/cqbshh533dCED5ACMIb WuPbxr+61TNAOmIxyOhSVEn0fzqZr4aNn/8QYYHQQ1HvuYwI6OvXmOIPWdyCGLBA 29pRc0i2srh6AkNJW572Gfps5thM7bHCs64Bu6dXgpocElLQDWMUB+xaxlr+AqST z9ShfUxiiakNN8x7llOpdurawTBEfdlSKdtlZ+w+W9uG0+s0Y8u8uLaGN/Pp8VFD nh9kSBHAq03W6uuKVGxP241XDLnUtnmBDC7ie1icV9G4zQFMPC6ZtaECgOUR5ST1 RSaLywKPUcTh54kS5zMVUiuIHHHGJhb23ypZ2KAlWNz6tuP95CtdoKmMAVjmBQap NqMB3LR5iT77XtYHUvKP5k1EMYny1ePZRg6gCtSoR21yMwkrr8uKDtnd2foV1CXN cuxs22nf+Yc=3D =3DucFZ -----END PGP SIGNATURE----- --===============8831161969127448853== Content-Type: application/pgp-signature -----BEGIN PGP SIGNATURE----- iHUEABYIAB0WIQTziqJOuF8J+ZI8pJSb9qggYcy5IQUCarEgPgAKCRCb9qggYcy5 IRd6AQCHB2W4gQVLvbrNkUXjI63EFcf6fe07smf8EJfiKPVVrAEAtJ6h2U7m9YXP 3/eJtIxLhGxZhCO8qim6VBHVdk7UjQM= =1zCF -----END PGP SIGNATURE----- --===============8831161969127448853==-- ]