[med-svn] r20974 - in trunk/packages/genometools/trunk/debian: . patches
Sascha Steinbiss
sascha-guest at moszumanska.debian.org
Thu Jan 7 22:37:54 UTC 2016
Author: sascha-guest
Date: 2016-01-07 22:37:53 +0000 (Thu, 07 Jan 2016)
New Revision: 20974
Added:
trunk/packages/genometools/trunk/debian/patches/spelling
Modified:
trunk/packages/genometools/trunk/debian/changelog
trunk/packages/genometools/trunk/debian/patches/series
Log:
new upstream version
Modified: trunk/packages/genometools/trunk/debian/changelog
===================================================================
--- trunk/packages/genometools/trunk/debian/changelog 2016-01-07 22:37:39 UTC (rev 20973)
+++ trunk/packages/genometools/trunk/debian/changelog 2016-01-07 22:37:53 UTC (rev 20974)
@@ -1,3 +1,11 @@
+genometools (1.5.8-1) unstable; urgency=medium
+
+ * New upstream release.
+ * Ensure that /usr/share/genometools/* is complete.
+ * Fix spelling.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Thu, 07 Jan 2016 22:18:31 +0000
+
genometools (1.5.7-7) unstable; urgency=medium
* build API documentation reproducibly
Modified: trunk/packages/genometools/trunk/debian/patches/series
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/series 2016-01-07 22:37:39 UTC (rev 20973)
+++ trunk/packages/genometools/trunk/debian/patches/series 2016-01-07 22:37:53 UTC (rev 20974)
@@ -1,3 +1,4 @@
+spelling
remove_png_timestamps
adding_soname
libbam-fix
@@ -5,4 +6,3 @@
fix-exports
split-manuals
use-mx32
-sort-inputs
Added: trunk/packages/genometools/trunk/debian/patches/spelling
===================================================================
--- trunk/packages/genometools/trunk/debian/patches/spelling (rev 0)
+++ trunk/packages/genometools/trunk/debian/patches/spelling 2016-01-07 22:37:53 UTC (rev 20974)
@@ -0,0 +1,186 @@
+Description: fix spelling of occurred
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+Forwarded: https://github.com/genometools/genometools/pull/727
+Last-Update: 2016-01-07
+--- a/gtdata/doc/fingerprint.lua
++++ b/gtdata/doc/fingerprint.lua
+@@ -36,5 +36,5 @@
+
+ - 0 everything went fine ('-check': the comparison was successful;
+ '-duplicates': no duplicates found)
+-- 1 an error occured ('-check': the comparison was not successful;
++- 1 an error occurred ('-check': the comparison was not successful;
+ '-duplicates': duplicates found)]])
+--- a/src/core/error_api.h
++++ b/src/core/error_api.h
+@@ -26,7 +26,7 @@
+ This class is used for the handling of ___user errors___ in __GenomeTools__.
+ Thereby, the actual <GtError> object is used to store the __error message__
+ while it is signaled by the return value of the called function, if an error
+- occured.
++ occurred.
+
+ By convention in __GenomeTools__, the <GtError> object is always passed into
+ a function as the last parameter and -1 (or <NULL> for constructors) is used
+--- a/src/core/hashtable.h
++++ b/src/core/hashtable.h
+@@ -81,14 +81,14 @@
+ /**
+ * @brief iterate over the hashtable in key order given by compare
+ * function <cmp>
+- * @return 0 => no error, -1 => error occured
++ * @return 0 => no error, -1 => error occurred
+ */
+ int gt_hashtable_foreach_ordered(GtHashtable *ht, Elemvisitfunc iter,
+ void *data, GtCompare cmp,
+ GtError *err);
+ /**
+ * @brief iterate over the hashtable in implementation-defined order
+- * @return 0 => no error, -1 => error occured
++ * @return 0 => no error, -1 => error occurred
+ */
+ int gt_hashtable_foreach(GtHashtable *ht, Elemvisitfunc iter,
+ void *data, GtError *err);
+--- a/src/core/option_api.h
++++ b/src/core/option_api.h
+@@ -34,14 +34,14 @@
+
+ enum GtOPrval {
+ GT_OPTION_PARSER_OK, /* Everything went fine. */
+- GT_OPTION_PARSER_ERROR, /* An error occured during option parsing. */
++ GT_OPTION_PARSER_ERROR, /* An error occurred during option parsing. */
+ GT_OPTION_PARSER_REQUESTS_EXIT /* The option parser requests an exit, because
+ option -help, -help+, -helpdev, or -version
+ was used. */
+ };
+
+ /* Possible option parser return values. <GT_OPTION_PARSER_OK> denotes that
+- everything went fine, <GT_OPTION_PARSER_ERROR> that an error occured during
++ everything went fine, <GT_OPTION_PARSER_ERROR> that an error occurred during
+ option parsing, and <GT_OPTION_PARSER_REQUESTS_EXIT> that the option parser
+ requests an exit, because option <-help>, <-help+>, <-helpdev> or <-version>
+ was used. */
+--- a/src/core/seq_iterator_api.h
++++ b/src/core/seq_iterator_api.h
+@@ -40,7 +40,7 @@
+ /* Get next <sequence> (of length <len>) and <description> from <seqit>.
+ Note that <seqit> retains ownership of the <sequence> and <description>.
+ Returns 1 if another sequence could be parsed, 0 if all given sequence
+- files are exhausted, And -1 if an error occured (<err> is set
++ files are exhausted, And -1 if an error occurred (<err> is set
+ accordingly). */
+ int gt_seq_iterator_next(GtSeqIterator *seqit,
+ const GtUchar **sequence,
+--- a/src/extended/node_stream_api.h
++++ b/src/extended/node_stream_api.h
+@@ -35,7 +35,7 @@
+ If no error occurs, 0 is returned and <genome_node> contains either the next
+ <GtGenomeNode> or <NULL>, if the <node_stream> is exhausted.
+ If an error occurs, -1 is returned and <err> is set accordingly (the status
+- of <genome_node> is undefined, but no ownership transfer occured). */
++ of <genome_node> is undefined, but no ownership transfer occurred). */
+ int gt_node_stream_next(GtNodeStream *node_stream,
+ GtGenomeNode **genome_node,
+ GtError *err);
+--- a/src/external/lua-5.1.5/src/lbaselib.c
++++ b/src/external/lua-5.1.5/src/lbaselib.c
+@@ -501,7 +501,7 @@
+ else
+ return CO_SUS; /* initial state */
+ }
+- default: /* some error occured */
++ default: /* some error occurred */
+ return CO_DEAD;
+ }
+ }
+--- a/src/gth/intermediate.c
++++ b/src/gth/intermediate.c
+@@ -515,7 +515,7 @@
+ if (XML_Parse(parser, gt_str_get(line), gt_str_length(line), false) ==
+ XML_STATUS_ERROR) {
+ error = XML_GetErrorCode(parser);
+- gt_error_set(err, "an error occured parsing line "GT_WU
++ gt_error_set(err, "an error occurred parsing line "GT_WU
+ " of file \"%s\": %s",
+ parseinfo.linenumber, outputfilename,
+ XML_ErrorString(error));
+@@ -530,7 +530,7 @@
+ /* finish parsing */
+ if (XML_Parse(parser, NULL, 0, true) == XML_STATUS_ERROR) {
+ error = XML_GetErrorCode(parser);
+- gt_error_set(err, "an error occured while finishing the parsing of file "
++ gt_error_set(err, "an error occurred while finishing the parsing of file "
+ "\"%s\": %s", outputfilename, XML_ErrorString(error));
+ had_err = -1;
+ }
+--- a/src/match/eis-encidxseq-construct.h
++++ b/src/match/eis-encidxseq-construct.h
+@@ -118,7 +118,7 @@
+ * suffix-array data structure to read construction from and progress
+ * information
+ * @param alphabet encoding to use for the built sequence, "ownership"
+- * of alphabet will pass to the returned object if no error occured.
++ * of alphabet will pass to the returned object if no error occurred.
+ * @param totalLen length of indexed sequence (including terminator
+ * and separators)
+ * @param projectName base name of corresponding suffixerator project
+--- a/src/match/eis-encidxseq.h
++++ b/src/match/eis-encidxseq.h
+@@ -50,7 +50,7 @@
+ * pass information that is kept across individual calls
+ * @param err genometools error object reference
+ * @return number of bits actually written, or (BitOffset)-1 if an
+- * error occured
++ * error occurred
+ */
+ typedef BitOffset (*bitInsertFunc)(BitString cwDest, BitOffset cwOffset,
+ BitString varDest, BitOffset varOffset,
+@@ -436,7 +436,7 @@
+ * @param pos position for which to print context
+ * @param fp print diagnostics to this file pointer
+ * @param hint use this structure for hinting
+- * @return 0 if an I/O error occured wrt fp
++ * @return 0 if an I/O error occurred wrt fp
+ */
+ static inline int
+ EISPrintDiagsForPos(const EISeq *seqIdx, GtUword pos, FILE *fp,
+--- a/www/genometools.org/htdocs/libgenometools.html
++++ b/www/genometools.org/htdocs/libgenometools.html
+@@ -3197,7 +3197,7 @@
+ This class is used for the handling of <strong>user errors</strong> in <em>GenomeTools</em>.
+ Thereby, the actual <code>GtError</code> object is used to store the <em>error message</em>
+ while it is signaled by the return value of the called function, if an error
+- occured.</p><p> By convention in <em>GenomeTools</em>, the <code>GtError</code> object is always passed into
++ occurred.</p><p> By convention in <em>GenomeTools</em>, the <code>GtError</code> object is always passed into
+ a function as the last parameter and -1 (or <code>NULL</code> for constructors) is used
+ as return value to indicate that an error occurred.
+ Success is usually indicated by 0 as return value or via a non-<code>NULL</code> object
+@@ -5879,7 +5879,7 @@
+ If no error occurs, 0 is returned and <code>genome_node</code> contains either the next
+ <code>GtGenomeNode</code> or <code>NULL</code>, if the <code>node_stream</code> is exhausted.
+ If an error occurs, -1 is returned and <code>err</code> is set accordingly (the status
+- of <code>genome_node</code> is undefined, but no ownership transfer occured).
++ of <code>genome_node</code> is undefined, but no ownership transfer occurred).
+ </p>
+ <hr>
+ <a name="gt_node_stream_pull"></a>
+@@ -7430,7 +7430,7 @@
+ Get next <code>sequence</code> (of length <code>len</code>) and <code>description</code> from <code>seqit</code>.
+ Note that <code>seqit</code> retains ownership of the <code>sequence</code> and <code>description</code>.
+ Returns 1 if another sequence could be parsed, 0 if all given sequence
+- files are exhausted, And -1 if an error occured (<code>err</code> is set
++ files are exhausted, And -1 if an error occurred (<code>err</code> is set
+ accordingly).
+ </p>
+ <hr>
+--- a/www/genometools.org/htdocs/tools/gt_fingerprint.html
++++ b/www/genometools.org/htdocs/tools/gt_fingerprint.html
+@@ -176,7 +176,7 @@
+ </li>
+ <li>
+ <p>
+-1 an error occured (<em>-check</em>: the comparison was not successful;
++1 an error occurred (<em>-check</em>: the comparison was not successful;
+ <em>-duplicates</em>: duplicates found)
+ </p>
+ </li>
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