Your message dated Wed, 21 Oct 2026 09:00:19 +0000
with message-id <[email protected]>
and subject line Bug#1126708: fixed in ltrsift 1.0.2-12
has caused the Debian Bug report #1126708,
regarding ltrsift: Crashes when creating a new project
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
1126708: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1126708
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: ltrsift
Source-Version: 1.0.2-12
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
ltrsift, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated ltrsift 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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 20 Oct 2026 20:25:55 +0200
Source: ltrsift
Binary: ltrsift ltrsift-dbgsym ltrsift-sample
Architecture: source amd64 all
Version: 1.0.2-12
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
ltrsift - postprocessing and classification of LTR retrotransposons
ltrsift-sample - postprocessing and classification of LTR retrotransposons
(sample
Closes: 967603 1105470 1126708
Changes:
ltrsift (1.0.2-12) unstable; urgency=medium
.
* Team upload.
* d/watch: version=5
* Standards-Version: 4.7.4 (routine-update)
* Reflow Uploaders field (cme)
* Port from GTK+ 2 to GTK+ 3. Closes: #967603
* Add autopkgtest checking the GTK+ 3 port.
* Create ltrsift-sample package containing upstream sample data to enable
running more decent autopkgtest and enable users verifying functionality
easily
* Fix use-after-free when creating a project. Closes: #1126708
* Add autopkgtest reproducing the project creation crash.
* Fix build failure with make --shuffle=reverse by creating output
directories before compiling and linking. Closes: #1105470
Checksums-Sha1:
bbddb0f5f2515448c87893d414764d17c949e821 2162 ltrsift_1.0.2-12.dsc
1fb7cf26017d24e250a180e8c80733c9bb9347f5 19624 ltrsift_1.0.2-12.debian.tar.xz
c843a668fafdc2b47d9146eccec56c1306cb2174 307588
ltrsift-dbgsym_1.0.2-12_amd64.deb
aff4a59516da4f71045d3375a49f9cf1717d8165 7193056
ltrsift-sample_1.0.2-12_all.deb
06f840fd83b08eaa46b17f03bd0a5b8ddbbea41b 14776 ltrsift_1.0.2-12_amd64.buildinfo
69c7ed273f469ead426fc7c4a55f5039846425f5 101800 ltrsift_1.0.2-12_amd64.deb
Checksums-Sha256:
4ea264661da338dcd56a37ae9034cab0722a0c8d255469c6c346917ec1a267fb 2162
ltrsift_1.0.2-12.dsc
7499f5cc7260e3459e6beb8a52be5294d6746f9868671064b2a37c03024c7b07 19624
ltrsift_1.0.2-12.debian.tar.xz
2ae01e077cdb40e84f09123e855298926edac3d8c771c6927f5571a91fbf7cad 307588
ltrsift-dbgsym_1.0.2-12_amd64.deb
d5bc03cfdc2cc56946a02c413c65852d2ddfb25398d351bf5c3081aeff09706c 7193056
ltrsift-sample_1.0.2-12_all.deb
1f3b704a54244d55477eeb464e8ee73aa9110de6797c988fbcda0e322c71f093 14776
ltrsift_1.0.2-12_amd64.buildinfo
5cb4bc32a48592faa9747f9bf7cdcf891cf97fd60863e5795bae66d6dc29089d 101800
ltrsift_1.0.2-12_amd64.deb
Files:
89eb7c134dc808a0ee448aca72560277 2162 science optional ltrsift_1.0.2-12.dsc
d1d4885963338e96d0f567f916aa50b4 19624 science optional
ltrsift_1.0.2-12.debian.tar.xz
53fbff00548e72f529d56dc97a8c567c 307588 debug optional
ltrsift-dbgsym_1.0.2-12_amd64.deb
906945a594ad8d799574bb014c63cbd8 7193056 science optional
ltrsift-sample_1.0.2-12_all.deb
c68e9957b04c148ffec504a077620356 14776 science optional
ltrsift_1.0.2-12_amd64.buildinfo
aedb92a7078e824d18d474b4fbd281fc 101800 science optional
ltrsift_1.0.2-12_amd64.deb
-----BEGIN PGP SIGNATURE-----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=0has
-----END PGP SIGNATURE-----
pgplI0kdHPcC_.pgp
Description: PGP signature
--- End Message ---
