Your message dated Fri, 12 Jul 2024 12:04:44 +0000
with message-id <[email protected]>
and subject line Bug#1075990: fixed in bamtools 2.5.2+dfsg-6
has caused the Debian Bug report #1075990,
regarding bamtools corrupts output data on bigendian architectures
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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--
1075990: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075990
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: bamtools
Version: 2.5.2+dfsg-4
Severity: normal
Dear Maintainer,
In Ubuntu the autopkgtest fails due to the buffer overflow detected[1]
with the following stack trace:
(gdb) where
#0 __pthread_kill_implementation (threadid=<optimized out>,
signo=signo@entry=6, no_tid=no_tid@entry=0) at pthread_kill.c:44
#1 0x000003fff789fd56 in __pthread_kill_internal (signo=6, threadid=<optimized
out>) at pthread_kill.c:78
#2 0x000003fff784ba90 in __GI_raise (sig=sig@entry=6) at
../sysdeps/posix/raise.c:26
#3 0x000003fff782b4cc in __GI_abort () at abort.c:79
#4 0x000003fff78921f8 in __libc_message_impl (fmt=fmt@entry=0x3fff79a428e "***
%s ***: terminated\n") at ../sysdeps/posix/libc_fatal.c:132
#5 0x000003fff792a50c in __GI___fortify_fail (msg=msg@entry=0x3fff79a424a
"buffer overflow detected") at fortify_fail.c:24
#6 0x000003fff7929d38 in __GI___chk_fail () at chk_fail.c:28
#7 0x000003fff792adae in __GI___memcpy_chk (dstpp=dstpp@entry=0x2aa000ab261,
srcpp=srcpp@entry=0x3ffffff99b4, len=len@entry=4, dstlen=dstlen@entry=3) at
memcpy_chk.c:27
#8 0x000003fff7e2b6ba in memcpy (__len=4, __src=0x3ffffff99b4,
__dest=0x2aa000ab261) at /usr/include/s390x-linux-
gnu/bits/string_fortified.h:29
#9 BamTools::SwapEndian_32p (data=0x2aa000ab261 "") at
/usr/src/bamtools-2.5.2+dfsg-5/src/api/BamAux.h:229
#10 BamTools::Internal::BamWriterPrivate::WriteAlignment (this=0x2aa000890d0,
al=...) at
/usr/src/bamtools-2.5.2+dfsg-5/src/api/internal/bam/BamWriter_p.cpp:353
#11 0x000003fff7e1445c in BamTools::Internal::BamWriterPrivate::SaveAlignment
(al=..., this=0x2aa000890d0) at
/usr/src/bamtools-2.5.2+dfsg-5/src/api/internal/bam/BamWriter_p.cpp:263
#12 BamTools::BamWriter::SaveAlignment (this=<optimized out>, alignment=...) at
/usr/src/bamtools-2.5.2+dfsg-5/src/api/BamWriter.cpp:131
#13 0x000002aa00035f08 in BamTools::RevertTool::RevertToolPrivate::Run() ()
#14 0x000002aa0003e3fe in BamTools::RevertTool::Run(int, char**) ()
#15 0x000002aa0001017a in main ()
(gdb) print i
$1 = 17
This is due to the write loop in src/api/internal/bam/BamWriter_p.cpp using
single byte instead of sizeof(uint32_t) increment to swap bytes in the integer
data.
The output file on s390x is corrupted.
[1]
https://objectstorage.prodstack5.canonical.com/swift/v1/AUTH_0f9aae918d5b4744bf7b827671c86842/autopkgtest-
oracular/oracular/s390x/b/bamtools/20240701_175546_4de2a@/log.gz
-- System Information:
Debian Release: trixie/sid
APT prefers noble-updates
APT policy: (500, 'noble-updates'), (500, 'noble-security'), (500, 'noble'),
(100, 'noble-backports')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 6.8.0-36-generic (SMP w/32 CPU threads; PREEMPT)
Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_OOT_MODULE,
TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en
Shell: /bin/sh linked to /usr/bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
--- End Message ---
--- Begin Message ---
Source: bamtools
Source-Version: 2.5.2+dfsg-6
Done: Andreas Tille <[email protected]>
We believe that the bug you reported is fixed in the latest version of
bamtools, 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 bamtools 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: Fri, 12 Jul 2024 13:46:23 +0200
Source: bamtools
Architecture: source
Version: 2.5.2+dfsg-6
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Closes: 1075990
Changes:
bamtools (2.5.2+dfsg-6) unstable; urgency=medium
.
* Fix output data on bigendian architectures (Thanks a lot for the
patch from Vladimir Petko <[email protected]>!)
Closes: #1075990
* Standards-Version: 4.7.0 (routine-update)
* Build-Depends: s/pkg-config/pkgconf/
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