[From nobody Wed Oct 21 10:03:06 2026 Received: (at submit) by bugs.debian.org; 31 Jan 2026 09:03:31 +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=-15.0 required=4.0 tests=BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FOURLA,FVGT_m_MULTI_ODD,HAS_PACKAGE, RCVD_IN_DNSWL_MED,SPF_HELO_PASS,SPF_PASS autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 64; hammy, 150; neutral, 211; spammy, 0. spammytokens: hammytokens:0.000-+--H*UA:sk:x86_64-, 0.000-+--forky, 0.000-+--HTo:N*Debian, 0.000-+--H*Ad:N*Bug, 0.000-+--H*Ad:N*Tracking Return-path: <yavor@gnu.org> Received: from eggs.gnu.org ([2001:470:142:3::10]:45132) by buxtehude.debian.org with esmtps (TLS1.2:ECDHE_SECP256R1__RSA_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <yavor@gnu.org>) id 1vm6On-00Az9A-1W for submit@bugs.debian.org; Sat, 31 Jan 2026 08:32:10 +0000 Received: from fencepost.gnu.org ([2001:470:142:3::e]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from <yavor@gnu.org>) id 1vm4gM-0000Y1-VQ for submit@bugs.debian.org; Sat, 31 Jan 2026 01:42:10 -0500 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=gnu.org; s=fencepost-gnu-org; h=MIME-Version:Subject:To:From:Date:in-reply-to: references; bh=D2nMln4aIJAGB9qQgj5hzUu4LE0GmAUsVAeW/LI1IAo=; b=c+gBEigG2av9GP 1IwrizXh60eq9I0U9Hta5+mnXmp7ruQwhC9ClZqKGPXcfaNpY6e6A81p8Y2/sTYgZ0JWi/O1AnNzZ +43IXlfshfkADgs6NEu/y9mD4NKhKyhsTlUWDfT9Zz58K1CwPebws0MKyXyvcpinkEm7qBZSG7nhO fPhYuIj/MEUWod6ZkcZWjPEh5Zl9ua0vHGlKwnxpIzGWvk7ohzbMh/3uizL2Xv6zi/lRGTWULnXYY GN/Fl+H6xifUIYBk4z5+IH4s1s+hlRqVYdtJrGYmao/xal0pD5K1WV9wHUDlLOooYTBtaXmmNcp5D us0ZYRgcJSWSE+ls4NAQ==; Date: Sat, 31 Jan 2026 08:42:03 +0200 Message-ID: <874io29tc4.GNU's_not_UNIX!-yavor@gnu.org> From: Yavor Doganov <yavor@gnu.org> To: Debian Bug Tracking System <submit@bugs.debian.org> Subject: ltrsift: Crashes when creating a new project User-Agent: Wanderlust/2.15.9 (Almost Unreal) SEMI-EPG/1.14.7 (Harue) FLIM-LB/1.14.9 (=?UTF-8?B?R29qxY0=?=) APEL-LB/10.8 EasyPG/1.0.0 Emacs/30.2 (x86_64-pc-linux-gnu) MULE/6.0 (HANACHIRUSATO) Organization: The GNU Emacs Church (Bulgarian Eparchy) MIME-Version: 1.0 (generated by SEMI-EPG 1.14.7 - "Harue") Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Delivered-To: submit@bugs.debian.org Package: ltrsift Version: 1.0.2-11 Severity: normal While working on #967603, I noticed that the program crashes when creating a new project. Steps to reproduce: $ apt source ltrsift $ cd ltrsift-1.0.2/sample_data/ $ ./prepare_encseqs $ gdb ltrsift Select File -> New... Press the first "Browse..." button and set a project name Press the "Add files..." button and select "dmel58.ltrd.gff3" Press the second "Browse..." button and select "dmel58.esq" Press the "Forward" button Press the "Apply button Thread 17 "ltrsift" received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7fffdbfff6c0 (LWP 123425)] 0x00007ffff7305ebc in gt_genome_node_accept (gn=<optimized out>, nv=<optimized out>, err=err@entry=0x0) at src/extended/genome_node.c:326 warning: 326 src/extended/genome_node.c: Няма такъв файл или директория (gdb) bt #0 0x00007ffff7305ebc in gt_genome_node_accept (gn=<optimized out>, nv=<optimized out>, err=err@entry=0x0) at src/extended/genome_node.c:326 #1 0x000055555557beee in ltrgui_preprocess_stream_next (gs=<optimized out>, gn=0x7fffdbffeb40, err=0x0) at src/preprocess_stream.c:44 #2 0x00007ffff733a31b in gt_node_stream_next (ns=ns@entry=0x7fffc40541f0, gn=gn@entry=0x7fffdbffeb98, err=<optimized out>) at src/extended/node_stream.c:94 #3 0x0000555555578c5f in save_and_reload_data_start (data=0x555555b665a0) at src/menubar.c:831 #4 0x00007ffff7713126 in g_thread_proxy (data=0x555555b0f980) at ../../../glib/gthread.c:893 #5 0x00007ffff709f489 in start_thread (arg=<optimized out>) at ./nptl/pthread_create.c:448 #6 0x00007ffff711dd38 in __GI___clone3 () at ../sysdeps/unix/sysv/linux/x86_64/clone3.S:78 (gdb) up #1 0x000055555557beee in ltrgui_preprocess_stream_next (gs=<optimized out>, gn=0x7fffdbffeb40, err=0x0) at src/preprocess_stream.c:44 44 (void) gt_genome_node_accept(*gn, (GtNodeVisitor*) ps->pv, err); (gdb) p *gn $1 = (GtGenomeNode *) 0x7fffc4044c70 (gdb) p *gn->c_class Cannot access memory at address 0x20 If I enable the "Perform clustering?" checkbox on the assistant's first page and "Perform classification?" on the second one, the crash doesn't happen. -- System Information: Debian Release: forky/sid APT prefers unstable-debug APT policy: (500, 'unstable-debug'), (500, 'testing-debug'), (500, 'unstable'), (500, 'testing') Architecture: amd64 (x86_64) Foreign Architectures: i386, x32 Kernel: Linux 6.18.5+deb14-amd64 (SMP w/6 CPU threads; PREEMPT) Locale: LANG=bg_BG.UTF-8, LC_CTYPE=bg_BG.UTF-8 (charmap=UTF-8), LANGUAGE=bg:ru:mk Shell: /bin/sh linked to /usr/bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages ltrsift depends on: ii libc6 2.42-11 ii libcairo2 1.18.4-3 ii libgdk-pixbuf-2.0-0 2.44.4+dfsg-1 ii libgenometools0t64 1.6.6+ds-2 ii libglib2.0-0t64 2.86.3-5 ii libgtk2.0-0t64 2.24.33-10 ii libpango-1.0-0 1.57.0-1 Versions of packages ltrsift recommends: ii last-align 1645-1 ii ncbi-blast+ 2.17.0+ds-6 ltrsift suggests no packages. -- no debconf information ]