Your message dated Sat, 03 Dec 2011 19:06:27 +0000
with message-id <[email protected]>
and subject line Bug#650475: fixed in mlv-smile 1.47-2
has caused the Debian Bug report #650475,
regarding mlv-smile: 'man mlv-smile' typos: "infering" x 2, "palindrom" x 2,
"criterias" x 10, "ipossible", "repecting", "susbtitutions", etc.
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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--
650475: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=650475
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: mlv-smile
Version: 1.47-1
Severity: minor
Tags: patch
Dear Maintainer,
Found some typos in '/usr/share/man/man1/mlv-smile.1.gz', see attached '.diff'.
Hope this helps...
-- System Information:
Debian Release: wheezy/sid
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: i386 (i686)
Kernel: Linux 3.0.0-2-686-pae (SMP w/2 CPU cores)
Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968) (ignored: LC_ALL set to C)
Shell: /bin/sh linked to /bin/dash
Versions of packages mlv-smile depends on:
ii libc6 2.13-21
ii perl 5.14.2-6
mlv-smile recommends no packages.
mlv-smile suggests no packages.
-- no debconf information
--- mlv-smile.1 2011-06-01 19:17:39.000000000 -0400
+++ /tmp/mlv-smile.1 2011-11-29 20:50:07.511654397 -0500
@@ -21,8 +21,8 @@
several motifs (called boxes) that respects distance constraints. The user has
to write in a
.IR "parameter_file"
-the list of criterias that he wants the signal to respect. In a first
-step of extraction, all signals respecting these criterias are found.
+the list of criteria that he wants the signal to respect. In a first
+step of extraction, all signals respecting these criteria are found.
In a second step, they are all statistically evaluated, aiming to detect
the ones that are exceptionally represented in the original sequences.
Since the 1.4 version
@@ -30,7 +30,7 @@
allows one to extract such signals on any alphabet in any kind of sequences.
.SH OPTIONS
-The program usually waits for a parameter file that contains all the criterias
+The program usually waits for a parameter file that contains all the criteria
needed. The only option is:
.TP
.B \-g number
@@ -200,7 +200,7 @@
.fi
-.SH PARAMETER FILE CRITERIAS
+.SH PARAMETER FILE CRITERIA
.TP
.B "FASTA File <filename>"
The name of the file which contains the sequences to use for inference.
@@ -251,8 +251,8 @@
.TP
.B "Boxes <number>"
The number of boxes that compose the motifs to infer.
-When infering simple one box motifs, it's not necessary to use local
-criterias as global and local criterias will be the same.
+When inferring simple one box motifs, it's not necessary to use local
+criteria as global and local criteria will be the same.
.TP
.B "Composition in <symbol> <number> [OPTIONAL]"
@@ -261,7 +261,7 @@
.TP
.B "BOX <number>"
-Begin the description of the criterias of a given box of the motif.
+Begin the description of the criteria of a given box of the motif.
.TP
.B "Min length <number>"
@@ -283,7 +283,7 @@
.B "Min spacer length <number>"
Minimum number of symbols between the end of the current box and the
beginning of the next one. This parameter mustn't appear in the last box's
-criterias, which has no next box!
+criteria, which has no next box!
.TP
.B "Max spacer length <number>"
@@ -294,16 +294,16 @@
This criteria allows one to infer motifs composed of several boxes without
really knowing the distance between these boxes. The min and max spacer length
will be used as a "large" interval, and the delta's value will define the size
-of smalls intervals into this large one. An inference of two boxes motifs
+of small intervals into this large one. An inference of two box motifs
with a [10-20] range of distance between the boxes will produce motifs whose
occurrences respect this range. A "Delta" criteria fixed to 2, for instance,
-will realize the same inference in all the ipossible ranges [i-delta, i+delta]
+will realize the same inference in all the possible ranges [i-delta, i+delta]
(here: [10-14], [11-15], ...). As many output files as different ranges
will be produced.
.TP
-.B "Palindrom of box <number> [OPTIONAL]"
-Indicate that the concerned box must be the biological palindrom of one of
+.B "Palindrome of box <number> [OPTIONAL]"
+Indicate that the concerned box must be the biological palindrome of one of
the previous boxes.
.TP
@@ -327,15 +327,15 @@
.SH WARNING
mlv-smile is an exact combinatorial algorithm. It is not made to infer any
kind of motifs. The amount of data where the extraction is made can be very
-large, but some criterias (in particular the number of substitutions) must
+large, but some criteria (in particular the number of substitutions) must
be restrained to reasonable values: one or two substitutions allowed in a
10 length motif is ok, but not 6 or 8 substitutions. The notion of spacers
-is made to avoid the use of to much susbtitutions.
+is made to avoid the use of to much substitutions.
.SH BUGS
A bug has been found in the 1.46 version, which could generate wrong results
in some particular cases. In particular, results may be wrong for incoherent
-length criterias.
+length criteria.
There are still probably a lot of bugs in mlv-smile. This 1.47 version is
quite stable, but do not hesitate to report any bug to <lama AT prism.uvsq DOT fr>.
@@ -349,7 +349,7 @@
You should refer to these paper for algorithmic details. If bored by such
things, just notice that the extraction step of
.BR mlv-smile
-is exact, which means that all motifs repecting the given criterias are found.
+is exact, which means that all motifs respecting the given criteria are found.
Please quote this article if you produce some results given by
.BR mlv-smile.
@@ -364,7 +364,7 @@
.PP
and
.PP
-.I A. Vanet and L. Marsan and A. Labigne and M.-F. Sagot, "Infering regulatory
+.I A. Vanet and L. Marsan and A. Labigne and M.-F. Sagot, "Inferring regulatory
.I elements from a whole genome. An application to the analysis of genome of
.I Helicobacter Pylori Sigma 80 family of promoter signals", J. Mol. Biol. 297,
.I 2000, 335-353
--- End Message ---
--- Begin Message ---
Source: mlv-smile
Source-Version: 1.47-2
We believe that the bug you reported is fixed in the latest version of
mlv-smile, which is due to be installed in the Debian FTP archive:
mlv-smile_1.47-2.debian.tar.gz
to main/m/mlv-smile/mlv-smile_1.47-2.debian.tar.gz
mlv-smile_1.47-2.dsc
to main/m/mlv-smile/mlv-smile_1.47-2.dsc
mlv-smile_1.47-2_i386.deb
to main/m/mlv-smile/mlv-smile_1.47-2_i386.deb
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.
Thorsten Alteholz <[email protected]> (supplier of updated mlv-smile 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: SHA1
Format: 1.8
Date: Sat, 03 Dec 2011 19:20:00 +0100
Source: mlv-smile
Binary: mlv-smile
Architecture: source i386
Version: 1.47-2
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Thorsten Alteholz <[email protected]>
Description:
mlv-smile - Find statistically significant patterns in sequences
Closes: 650475
Changes:
mlv-smile (1.47-2) unstable; urgency=low
.
* Spellchecked manual pages (Closes: #650475, thanks to A. Costa).
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