Your message dated Tue, 20 Oct 2026 18:49:34 +0000
with message-id <[email protected]>
and subject line Bug#1118526: fixed in kallisto 0.52.0+dfsg-1
has caused the Debian Bug report #1118526,
regarding tests: kallistro: corrupted size vs. prev_size
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.
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--
1118526: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1118526
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: kallisto
Version: 0.48.0+dfsg-3
Severity: serious
Tags: ftbfs
Justification: fails to build from source (but built successfully in the past)
X-Debbugs-Cc: [email protected]
Following up with analysis after the test failure was mentioned by
Andreas in Matrix "Debian Tiny Tasks".
I do not have time to attack it and not familiar with the code-base but
this analysis should help.
Referring to the failed build log:
https://salsa.debian.org/med-team/kallisto/-/jobs/8480324#L2345
"corrupted size vs. prev_size" :- The direct cause is out-of-bounds writes into
malloc control structure fields.
E.g: given `A = calloc(1, 16); B = calloc(1,16)` and A contiguous with B.
If `struct *S = A` and `sizeof(A) == sizeof(*S)` then S[0] is valid but S[1] is
out-of-bounds and a
write may trample on the control structure preamble of B.
>From what I can deduce it occurs in
>`ext/bifrost/src/CompactDBG.tcc::CompactDBG::construct()` template after line
>3323 and before line 3331.
Most likely the reference to `size()` in line 3329.
if (opt.verbose) cout << "CompactedDBG::construct(): After join tips using
mercy k-mers: " << size() << " unitigs" << endl;
https://salsa.debian.org/med-team/kallisto/-/blob/72ff60faebbab43eba75e55fe393d88de42116a5/ext/bifrost/src/CompactedDBG.tcc#L3323
Disabling `opt.verbose` would be an easy way to (dis)prove that.
--- End Message ---
--- Begin Message ---
Source: kallisto
Source-Version: 0.52.0+dfsg-1
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
kallisto, 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 kallisto 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 19:44:13 +0200
Source: kallisto
Architecture: source
Version: 0.52.0+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1118526
Changes:
kallisto (0.52.0+dfsg-1) unstable; urgency=medium
.
* New upstream version
* Adapt patches to new upstream version
* Build the bundled bifrost with the same MAX_KMER_SIZE as kallisto instead
of compiling it with MAX_KMER_SIZE=31. The mismatched k-mer size caused
heap corruption and test failures.
Closes: #1118526
* Drop 'Rules-Requires-Root: no' from d/control (routine-update)
* Reformat the Last-Update date as ISO YYYY-MM-DD.
* Remove unused patch to use Debian packaged bifrost
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