[med-svn] [pftools] 03/04: Fix spelling
Andreas Tille
tille at debian.org
Fri Mar 31 11:37:24 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository pftools.
commit c68bb38e1ae4e836987d971f096a9a161a728984
Author: Andreas Tille <tille at debian.org>
Date: Fri Mar 31 13:33:59 2017 +0200
Fix spelling
---
debian/patches/series | 1 +
debian/patches/spelling.patch | 294 +++++++++---------------------------------
2 files changed, 63 insertions(+), 232 deletions(-)
diff --git a/debian/patches/series b/debian/patches/series
index 6a9d397..b48767d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@ fix_path_in_test_script.patch
fix_test_output.patch
build_gtop.patch
getopt_for_pgdump.patch
+spelling.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index ee83b24..6f30d82 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -1,236 +1,66 @@
-Description: Fix spelling in manpages
+Description: Fix spelling
Author: Andreas Tille <tille at debian.org>
-Last-Update: 2017-03-22
+Last-Update: 2017-03-31
---- a/man/2ft.1
-+++ b/man/2ft.1
-@@ -120,6 +120,6 @@ manual pages of pftools program
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/6ft.1
-+++ b/man/6ft.1
-@@ -122,6 +122,6 @@ manual pages of pftools program
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/gtop.1
-+++ b/man/gtop.1
-@@ -256,6 +256,6 @@ operations.
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/htop.1
-+++ b/man/htop.1
-@@ -370,6 +370,6 @@ documentation
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/pfmake.1
-+++ b/man/pfmake.1
-@@ -142,7 +142,7 @@ format.
- Optional profile file.
- .br
- If a filename is specified, the profile will be parsed and
--those parameters mentionned in the
-+those parameters mentioned in the
- .I description
- section will be kept for the computation of the output profile.
- .\" --- 0 ---
-@@ -341,7 +341,7 @@ Default: 0.333
- .BI \-S\ matrix_multiplier
- Score matrix multiplier.
- .br
--On input, the numbers of the score matrix are multipled by this factor.
-+On input, the numbers of the score matrix are multiplied by this factor.
- .br
- Default: 0.1
- .\" --- T ---
-@@ -532,6 +532,6 @@ Comput. Appl. Biosci.
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/pfscale.1
-+++ b/man/pfscale.1
-@@ -319,6 +319,6 @@ Trends Biochem. Sci.
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/pfscan.1
-+++ b/man/pfscan.1
-@@ -49,7 +49,7 @@ pfscan \- scan a protein or DNA sequence
- compares a protein or nucleic acid sequence against a profile library.
- The result is an unsorted list of profile-sequence matches written to
- the standard output.
--A variety of output formats containing different informations can be specified
-+A variety of output formats containing different information can be specified
- via the options
- .BR \-l , \ \-L , \ \-r , \ \-k , \ \-s , \ \-x , \ \-y
- and
-@@ -222,7 +222,7 @@ Default: lowest priority mode defined in
- .\" ------------------------------------------------
- .\" Output modifiers subsection
- .\" ------------------------------------------------
--.SS Ouput modifiers
-+.SS Output modifiers
- .\" --- d ---
- .TP
- .B \-d
-@@ -411,6 +411,6 @@ the raw score is above or equal to the s
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/pfsearch.1
-+++ b/man/pfsearch.1
-@@ -49,7 +49,7 @@ matching a profile
- .B pfsearch
- compares a query profile against a DNA or protein sequence library.
- The result is an unsorted list of profile-sequence matches written to the standard output.
--A variety of output formats containing different informations can be specified
-+A variety of output formats containing different information can be specified
- via the options
- .BR \-l , \ \-L , \ \-r , \ \-k , \ \-s , \ \-x , \ \-y
- and
-@@ -95,7 +95,7 @@ This file should contain one or several
- .SM EMBL/SWISS-PROT
- (default) or Pearson/Fasta (option
- .BR \-f )
--formated DNA or protein sequences. The program
-+formatted DNA or protein sequences. The program
- .B pfsearch
- tries to identify matches between the input profile and all individual
- sequences of this library. If the filename is replaced by a
-@@ -219,7 +219,7 @@ Default: lowest priority mode defined in
- .\" ------------------------------------------------
- .\" Output modifiers subsection
- .\" ------------------------------------------------
--.SS Ouput modifiers
-+.SS Output modifiers
- .\" --- d ---
- .TP
- .B \-d
-@@ -410,6 +410,6 @@ problem.
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/pfw.1
-+++ b/man/pfw.1
-@@ -217,6 +217,6 @@ J. Mol. Biol.
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/psa.5
-+++ b/man/psa.5
-@@ -191,7 +191,7 @@ This manual page was originally written
- .br
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
+--- a/src/C/include/system.h
++++ b/src/C/include/system.h
+@@ -835,7 +835,7 @@ printSystemInfo(const SystemInfo * const
+ const size_t Length = strlen(Template);
+ const char * LastCharacter = &Buffer[Length - 2];
+
+- fputs("| System informations |\n"
++ fputs("| System information |\n"
+ "%----------------------------------------------------------------------------%\n", stderr);
+
+ #define WRITE(LeftSpace, Title, Value) {\
+@@ -947,4 +947,4 @@ int main (int argc, char * argv[])
+ }
---- a/man/psa2msa.1
-+++ b/man/psa2msa.1
-@@ -242,6 +242,6 @@ will be issued on standard error.
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/ptof.1
-+++ b/man/ptof.1
-@@ -312,6 +312,6 @@ will be issued on standard error.
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/ptoh.1
-+++ b/man/ptoh.1
-@@ -290,6 +290,6 @@ Comput. Chem.
- .SH AUTHOR
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
---- a/man/xpsa.5
-+++ b/man/xpsa.5
-@@ -43,7 +43,7 @@ Nevertheless the keywords defined here c
- to store and transfer information.
- .PP
- None of the defined keywords are mandatory and analysis tools have often a length limit imposed
--on the header line. In order to keep the header line reasonnably short and user readable,
-+on the header line. In order to keep the header line reasonably short and user readable,
- these tools can easily remove individual
- .IR keyword = value
- pairs which are not important to the specific task at hand.
-@@ -241,7 +241,7 @@ negative offset from the end of the alig
- .br
- In combination with the information given by
- .I seq_pos
--this allows to deduce the length of the query sequence.
-+this allows one to deduce the length of the query sequence.
- .\" --- strand ---
- .TP
- .I strand
-@@ -354,7 +354,7 @@ The total circular motif has at least 2
- .RI ' PEX7 '
- sequence, because this single repeat is part of the second match as described by the
- .I match_parent
--keyword. The parental matches have been ommited from this example, they would be numbered using the
-+keyword. The parental matches have been omitted from this example, they would be numbered using the
- .I match_nb
- keyword.
- .br
-@@ -390,7 +390,7 @@ This manual page was originally written
- .br
- The
- .B pftools
--package was developped by Philipp Bucher.
-+package was developed by Philipp Bucher.
- .br
- Any comments or suggestions should be addressed to <pftools at isb-sib.ch>.
+ #endif
+-#endif
+\ No newline at end of file
++#endif
+--- a/src/C/prg/pfsearch.c
++++ b/src/C/prg/pfsearch.c
+@@ -209,12 +209,12 @@ static void __attribute__((noreturn)) Us
+ " --output-method [-o] : printing output method\n"
+ " == 0 replicates the pfseach output without\n"
+ " options (DEFAULT)\n"
+- " == 1 simple ouput\n"
++ " == 1 simple output\n"
+ " == 2 replicates pfsearch -lxz output\n"
+ " == 3 replicates pfscan -lxz output\n"
+ " == 4 tsv output (single line tab delimited)\n"
+ " --output-length [-W] : maximum number of column for sequence\n"
+- " ouput printing\n"
++ " output printing\n"
+ " Other\n"
+ " --verbose [-v] : verbose on stderr\n"
+ " --help [-h] : output command help\n",
+@@ -388,7 +388,7 @@ int main (int argc, char *argv[])
+ } else if (method == 4) {
+ PrintFunction = &PrintTSV;
+ } else {
+- fputs("Unrecognized ouput method.\n", stderr);
++ fputs("Unrecognized output method.\n", stderr);
+ exit(1);
+ }
+ }
+--- a/src/C/utils/ReadSequence.c
++++ b/src/C/utils/ReadSequence.c
+@@ -35,13 +35,13 @@ int AnalyzeFASTAStructure(char * const F
+
+ const int FileDescriptor = open(FileName, O_RDONLY);
+ if ( FileDescriptor == -1) {
+- fprintf(stderr, "Error occured while accessing file %s\n", FileName);
++ fprintf(stderr, "Error occurred while accessing file %s\n", FileName);
+ perror("The error reads ");
+ return 1;
+ }
+ if (fstat(FileDescriptor, &FileStat) == -1 ) {
+- fprintf(stderr, "Error occured while accessing file %s\n", FileName);
++ fprintf(stderr, "Error occurred while accessing file %s\n", FileName);
+ perror("The error reads ");
+ return 1;
+ }
--
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