[med-svn] r21084 - in trunk/packages/exonerate/trunk/debian: . patches

Mon Jan 11 08:49:49 UTC 2016

Author: tille
Date: 2016-01-11 08:49:48 +0000 (Mon, 11 Jan 2016)
New Revision: 21084

Added:
   trunk/packages/exonerate/trunk/debian/patches/manpagesyntax.patch
   trunk/packages/exonerate/trunk/debian/patches/spelling.patch
Modified:
   trunk/packages/exonerate/trunk/debian/changelog
   trunk/packages/exonerate/trunk/debian/patches/series
Log:
fix spelling and manpage syntax issues


Modified: trunk/packages/exonerate/trunk/debian/changelog
===================================================================

--- trunk/packages/exonerate/trunk/debian/changelog	2016-01-11 08:18:56 UTC (rev 21083)
+++ trunk/packages/exonerate/trunk/debian/changelog	2016-01-11 08:49:48 UTC (rev 21084)
@@ -16,6 +16,7 @@
   * cme fix dpkg-control
   * debhelper 9
   * DEP5
+  * fix spelling and manpage syntax issues
 
  -- Andreas Tille <tille at debian.org>  Fri, 09 May 2014 13:17:32 +0200
 

Added: trunk/packages/exonerate/trunk/debian/patches/manpagesyntax.patch
===================================================================
--- trunk/packages/exonerate/trunk/debian/patches/manpagesyntax.patch	                        (rev 0)
+++ trunk/packages/exonerate/trunk/debian/patches/manpagesyntax.patch	2016-01-11 08:49:48 UTC (rev 21084)
@@ -0,0 +1,92 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 09 May 2014 13:17:32 +0200
+Description: Fix manpage syntax
+
+--- a/doc/man/man1/exonerate-server.1
++++ b/doc/man/man1/exonerate-server.1
+@@ -75,7 +75,7 @@ The default port number for the exonerat
+ 
+ .RE
+ .SH OPTIONS
+-.T
++.TP
+ Some of the command line options for the exonerate-server are the same as for the
+ exonerate client, and these are documented in the man page for
+ .B exonerate.
+--- a/doc/man/man1/exonerate.1
++++ b/doc/man/man1/exonerate.1
+@@ -45,13 +45,13 @@ rather than on the symbols.
+ This numbering scheme starts from zero.
+ This numbering is shown below for the sequence "ACGT":
+ .\"
+-.SP
++.sp
+ .nf
+ 
+  A C G T
+ 0 1 2 3 4
+ 
+-.SP
++.sp
+ .fi
+ .\"
+ Hence the subsequence "CG" would have start=1,
+@@ -1194,7 +1194,7 @@ show the observed relative frequencies o
+ the splice sites in the chosen organism (in ACGT order).
+ 
+ .B Example 5' splice data file:
+-.SP
++.sp
+ .nf
+ 
+  # start of example 5' splice data
+@@ -1210,11 +1210,11 @@ the splice sites in the chosen organism
+   5  6  85   4
+  16 18  21  45
+  # end of test 5' splice data
+-.SP
++.sp
+ .fi
+ 
+ .B Example 3' splice data file:
+-.SP
++.sp
+ .nf
+ 
+  # start of example 3' splice data
+@@ -1236,7 +1236,7 @@ the splice sites in the chosen organism
+  splice
+   28  14  47  11
+  # end of example 3' splice data
+-.SP
++.sp
+ .fi
+ 
+ .TP
+--- a/doc/man/man1/fastautils.1
++++ b/doc/man/man1/fastautils.1
+@@ -72,7 +72,7 @@ This documentation accompanies version 2
+ .\"
+ .SH AUTHOR
+ Guy St.C. Slater.  <guy at ebi.ac.uk>.
+-.L
++.P
+ See the AUTHORS file accompanying the source code
+ for a list of contributors.
+ .SH AVAILABILITY
+--- a/doc/man/man1/ipcress.1
++++ b/doc/man/man1/ipcress.1
+@@ -67,11 +67,11 @@ Maximum product length to report
+ .RE
+ .P
+ Here is an example line in this format:
+-.SP
++.sp
+ .nf
+ 
+ ID0001 CATGCATGCATGC CGATGCANGCATGCT 900 1100
+-.SP
++.sp
+ .fi
+ .\"
+ .RE

Modified: trunk/packages/exonerate/trunk/debian/patches/series
===================================================================
--- trunk/packages/exonerate/trunk/debian/patches/series	2016-01-11 08:18:56 UTC (rev 21083)
+++ trunk/packages/exonerate/trunk/debian/patches/series	2016-01-11 08:49:48 UTC (rev 21084)
@@ -1,3 +1,4 @@
-autoreconf.patch
 fix_build-as-needed.patch
 manpages.patch
+spelling.patch
+manpagesyntax.patch

Added: trunk/packages/exonerate/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/exonerate/trunk/debian/patches/spelling.patch	                        (rev 0)
+++ trunk/packages/exonerate/trunk/debian/patches/spelling.patch	2016-01-11 08:49:48 UTC (rev 21084)
@@ -0,0 +1,46 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 09 May 2014 13:17:32 +0200
+Description: Fix spelling
+
+--- a/src/database/dataset.c
++++ b/src/database/dataset.c
+@@ -114,7 +114,7 @@ static Dataset_Header *Dataset_Header_re
+         g_error("Bad magic number in dataset file");
+     header->version = BitArray_read_int(fp);
+     if(header->version != DATASET_HEADER_VERSION)
+-        g_error("Incompatable dataset file version");
++        g_error("Incompatible dataset file version");
+     header->type = BitArray_read_int(fp);
+     header->line_length = BitArray_read_int(fp);
+     /**/
+--- a/doc/man/man1/exonerate-server.1
++++ b/doc/man/man1/exonerate-server.1
+@@ -261,7 +261,7 @@ the external id (eg. from fasta header)
+ .TP 16
+ .B <def>
+ a description line for the sequence (also from the fasta header),
+-this field is optional an may be ommitted.
++this field is optional an may be omitted.
+ .RE
+ 
+ .TP 10
+--- a/doc/man/man1/exonerate.1
++++ b/doc/man/man1/exonerate.1
+@@ -357,7 +357,7 @@ It is currently only available when usin
+ This model allows alignment of a protein sequence to genomic
+ DNA.   This is similar to the protein2dna model,
+ with the addition of modelling of introns and intron phases.
+-This model is simliar to those used by genewise.
++This model is similar to those used by genewise.
+ .\"
+ .TP
+ .B protein2genome:bestfit
+@@ -737,7 +737,7 @@ subject to alignment during refinement b
+ .\"
+ .RE
+ 
+-.SH VITERBI ALGORITM OPTIONS
++.SH VITERBI ALGORITHM OPTIONS
+ .TP
+ .B "\-D | \--dpmemory" <Mb>
+ The exhaustive alignment traceback routines use a Hughey-style


