[Debian-med-packaging] Bug#1126708: ltrsift: Crashes when creating a new project

[Yavor Doganov]

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 at 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 at 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 at entry=0x7fffc40541f0, gn=gn at 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