Your message dated Wed, 18 Jan 2017 16:18:36 +0000
with message-id <[email protected]>
and subject line Bug#851764: fixed in hhsuite 3.0~beta2+dfsg-3
has caused the Debian Bug report #851764,
regarding src:hhsuite: type mismatch in printf(3); affects manpage
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
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851764: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=851764
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--- Begin Message ---
Package: hhsuite
Version: 3.0~beta2+dfsg-1
Severity: minor
Tags: upstream patch
User: [email protected]
Usertags: randomness
Dear Maintainer,
hhblits.cpp uses the %i printf(3) conversion to format a 'double' value:
src/hhblits.cpp:333: printf(" -pre_evalue_thresh max E-value
threshold of Smith-Waterman prefilter score (default=%i)\n",
par.prefilter_evalue_thresh);
Formally that's undefined behaviour, although in practice it simply
prints a garbage value. That garbage value is also embedded into the
hhblits_omp(1) man page.
Furthermore, hhsuite-userguide.tex specifies the default value as '0'
whereas the code uses '1000'.
The attached patch should fix both issues.
Cheers,
Daniel
P.S. ViterbiRunner::calculateEarlyStop() puts the return value of log(3)
into a 'float' variable, even though that function returns double. I'm
not sure whether that's intentional or what effect it may have.
--- End Message ---
--- Begin Message ---
Source: hhsuite
Source-Version: 3.0~beta2+dfsg-3
We believe that the bug you reported is fixed in the latest version of
hhsuite, 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 hhsuite 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])
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Hash: SHA256
Format: 1.8
Date: Wed, 18 Jan 2017 16:52:21 +0100
Source: hhsuite
Binary: hhsuite hhsuite-doc hhsuite-data
Architecture: source all amd64
Version: 3.0~beta2+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
hhsuite - sensitive protein sequence searching based on HMM-HMM alignment
hhsuite-data - sensitive protein sequence searching based on HMM-HMM alignment
(
hhsuite-doc - documentation for HHsuite for HMM-HMM comparisons
Closes: 851764
Changes:
hhsuite (3.0~beta2+dfsg-3) unstable; urgency=medium
.
* Specify correct format in printf statement (Thanks for the patch to
Daniel Shahaf <[email protected]>)
Closes: #851764
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