Debian Bug report logs - #851764
src:hhsuite: type mismatch in printf(3); affects manpage

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Daniel Shahaf <danielsh@apache.org>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: src:hhsuite: type mismatch in printf(3); affects manpage

Date: Wed, 18 Jan 2017 15:22:26 +0000

Package: hhsuite
Version: 3.0~beta2+dfsg-1
Severity: minor
Tags: upstream patch
User: reproducible-builds@lists.alioth.debian.org
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.

Message #10 received at 851764@bugs.debian.org (full text, mbox, reply):

From: Daniel Shahaf <danielsh@apache.org>

To: Debian Bug Tracking System <851764@bugs.debian.org>

Subject: Re: Bug#851764: src:hhsuite: type mismatch in printf(3); affects manpage

Date: Wed, 18 Jan 2017 15:27:48 +0000

Daniel Shahaf wrote on Wed, Jan 18, 2017 at 15:22:26 +0000:
> The attached patch should fix both issues.

--- a/doc/hhsuite-userguide.tex
+++ b/doc/hhsuite-userguide.tex
@@ -1466,7 +1466,7 @@
  -maxfilt                  max number of hits allowed to pass 2nd prefilter (default=20000)   
  -min_prefilter_hits       min number of hits to pass prefilter (default=100)               
  -prepre_smax_thresh       min score threshold of ungapped prefilter (default=10)               
- -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=0)
+ -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=1000.0)
  -pre_bitfactor            prefilter scores are in units of 1 bit / pre_bitfactor (default=4)
  -pre_gap_open             gap open penalty in prefilter Smith-Waterman alignment (default=20)
  -pre_gap_extend           gap extend penalty in prefilter Smith-Waterman alignment (default=4)
--- a/src/hhblits.cpp
+++ b/src/hhblits.cpp
@@ -330,7 +330,7 @@
     printf(" -maxfilt                  max number of hits allowed to pass 2nd prefilter (default=%i)   \n", par.maxnumdb);
     printf(" -min_prefilter_hits       min number of hits to pass prefilter (default=%i)               \n", par.min_prefilter_hits);
     printf(" -prepre_smax_thresh       min score threshold of ungapped prefilter (default=%i)               \n", par.preprefilter_smax_thresh);
-    printf(" -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=%i)\n", par.prefilter_evalue_thresh);
+    printf(" -pre_evalue_thresh        max E-value threshold of Smith-Waterman prefilter score (default=%.1f)\n", par.prefilter_evalue_thresh);
     printf(" -pre_bitfactor            prefilter scores are in units of 1 bit / pre_bitfactor (default=%i)\n", par.prefilter_bit_factor);
     printf(" -pre_gap_open             gap open penalty in prefilter Smith-Waterman alignment (default=%i)\n", par.prefilter_gap_open);
     printf(" -pre_gap_extend           gap extend penalty in prefilter Smith-Waterman alignment (default=%i)\n", par.prefilter_gap_extend);

Message #15 received at 851764-close@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <tille@debian.org>

To: 851764-close@bugs.debian.org

Subject: Bug#851764: fixed in hhsuite 3.0~beta2+dfsg-3

Date: Wed, 18 Jan 2017 16:18:36 +0000

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 851764@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <tille@debian.org> (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 ftpmaster@ftp-master.debian.org)


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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 <debian-med-packaging@lists.alioth.debian.org>
Changed-By: Andreas Tille <tille@debian.org>
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 <danielsh@apache.org>)
     Closes: #851764
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Files:
 dde7c43cd6a64e7849ed7a4c85d02785 2282 science optional hhsuite_3.0~beta2+dfsg-3.dsc
 ea3a333ce35e1b37ebb0f36a2110597a 14552 science optional hhsuite_3.0~beta2+dfsg-3.debian.tar.xz
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