[med-svn] [Git][med-team/libgoby-java][master] 6 commits: Adding a Lintian override
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Mon Aug 9 14:33:09 BST 2021
Pierre Gruet pushed to branch master at Debian Med / libgoby-java
Commits:
0af0b403 by Pierre Gruet at 2021-08-08T22:11:46+02:00
Adding a Lintian override
- - - - -
fe63d089 by Pierre Gruet at 2021-08-08T22:13:48+02:00
Preparing to repack to remove a very-long-lines file
- - - - -
5bab00c3 by Pierre Gruet at 2021-08-09T13:48:44+02:00
New upstream version 3.3.1+dfsg1
- - - - -
b71a5c9d by Pierre Gruet at 2021-08-09T14:01:30+02:00
Update upstream source from tag 'upstream/3.3.1+dfsg1'
Update to upstream version '3.3.1+dfsg1'
with Debian dir 0fa2afa1869721787c8e6504b77283b36e06d00a
- - - - -
981d4053 by Pierre Gruet at 2021-08-09T14:54:37+02:00
The lintian override is for the binary package, not the source one
- - - - -
94cb53ed by Pierre Gruet at 2021-08-09T14:55:00+02:00
Fixing issues with undefined macros in the manpage
- - - - -
5 changed files:
- debian/copyright
- + debian/libgoby-io-java.lintian-overrides
- debian/manpages/goby.1
- debian/watch
- − test-data/seq-var-test/seq-var-reads-gsnap.html
Changes:
=====================================
debian/copyright
=====================================
@@ -4,6 +4,9 @@ Upstream-Contact: goby-framework at googlegroups.com
Source: https://github.com/CampagneLaboratory/goby3/releases
Files-Excluded: */*.jar
testsupport/*/lib
+ test-data/seq-var-test/seq-var-reads-gsnap.html
+Comment: We remove jar files that are bundled with the source.
+ Also we remove a html file with very long lines that is unused.
Files: *
Copyright: 2009-2017 Institute for Computational Biomedicine
=====================================
debian/libgoby-io-java.lintian-overrides
=====================================
@@ -0,0 +1,3 @@
+# Surely we follow the Java policy in this package, but it is definitely a
+# science package.
+wrong-section-according-to-package-name
=====================================
debian/manpages/goby.1
=====================================
@@ -174,9 +174,7 @@ within-group-variability (wgv)
Each of the above modes has specific options. The complete list of options for
a given mode <mode> can be get by running
-.Vb 1
.B \& \fBgoby\fP 100m <mode>
-.Ve
which returns a complete list of options for running the mode <mode> as well as
a description of what this mode provides.
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
-opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg[0-9]*//g,repack,compression=xz" \
https://github.com/CampagneLaboratory/goby3/releases (?:.*?/)?r at ANY_VERSION@@ARCHIVE_EXT@
=====================================
test-data/seq-var-test/seq-var-reads-gsnap.html deleted
=====================================
@@ -1,78 +0,0 @@
-<body><head>
-<style type='text/css'>
- body{ font-family: Arial, Helvetica, sans-serif; }
- .odd { background-color: #def; }
- .right {text-align: right;}
- .center {text-align: center;}
- table td {font-size:80%; }
- tfoot input { width:60px; }
- tfoot input.search_init { color:#777777; font-style:italic; }
-</style>
-<link rel='stylesheet' type='text/css' href='http://yui.yahooapis.com/3.3.0/build/cssreset/reset-min.css' />
-<link rel='stylesheet' type='text/css' href='http://yui.yahooapis.com/3.3.0/build/cssreset/reset-context-min.css' />
-<link rel='stylesheet' type='text/css' href='http://ajax.aspnetcdn.com/ajax/jquery.ui/1.8.17/themes/ui-lightness/jquery-ui.css' />
-<link rel='stylesheet' type='text/css' href='http://campagnelab.org/files/cdn/datatables/media/css/jquery.dataTables.css'>
-<script type='text/javascript' charset='utf8' src='http://campagnelab.org/files/cdn/datatables/media/js/jquery.js'></script>
-<script type='text/javascript' charset='utf8' src='http://campagnelab.org/files/cdn/datatables/media/js/jquery.dataTables.min.js'></script>
-<script type='text/javascript' charset='utf8' src='http://campagnelab.org/files/cdn/datatables-plugins/js/fourButtonNavigation.js'></script>
-<script type='text/javascript'>
- var dt;
- jQuery(document).ready(function() {
- dt = jQuery('#alignment').dataTable({
- 'aaData': data,
- 'aoColumns': columns,
- 'bJQueryUI': true,
- 'oLanguage': {
- 'sSearch': 'Search all columns:'
- },
- 'aLengthMenu': [[10, 15, 20, 25, 30, 35, 40, 45, 50, -1], [10, 15, 20, 25, 30, 35, 40, 45, 50, 'All']],
- 'sPaginationType': 'four_button',
- 'sScrollX': '200px',
- 'bSort' : false
- });
- var asInitVals = new Array();
- jQuery('tfoot input').keyup( function () {
- dt.fnFilter( this.value, jQuery('tfoot input').index(this) );
- });
- jQuery('tfoot input').each( function (i) {
- asInitVals[i] = this.value;
- });
- jQuery('tfoot input').focus( function () {
- if (this.className == 'search_init') {
- this.className = '';
- this.value = '';
- }
- });
- jQuery('tfoot input').blur( function (i) {
- if ( this.value == '' ) {
- this.className = 'search_init';
- this.value = asInitVals[jQuery('tfoot input').index(this)];
- }
- });
- });
- jQuery(window).bind('resize', function() {
- dt.fnAdjustColumnSizing();
- });
-</script>
-</head>
-<html>
-<script type='text/javascript'>
- function formatNumber(o, val) {
- x1 = val + '';
- var rgx = /(\d+)(\d{3})/;
- while (rgx.test(x1)) {
- x1 = x1.replace(rgx, '$1' + ',' + '$2');
- }
- return x1;
- }
- var columns = [
-{'sTitle':'queryIndex','fnRender':formatNumber,'sClass':'right'},{'sTitle':'targetIdentifier'},{'sTitle':'position','fnRender':formatNumber,'sClass':'right'},{'sTitle':'queryLength','fnRender':formatNumber,'sClass':'right'},{'sTitle':'alignmentLength','fnRender':formatNumber,'sClass':'right'},{'sTitle':'strand'},{'sTitle':'score','fnRender':formatNumber,'sClass':'right'},{'sTitle':'mappingQuality','fnRender':formatNumber,'sClass':'right'},{'sTitle':'pairFlags','sClass':'right'},{'sTitle':'readFragmentIndex','sClass':'center'},{'sTitle':'pairFragmentIndex','sClass':'center'},{'sTitle':'pairTarget'},{'sTitle':'pairPosition','fnRender':formatNumber,'sClass':'right'},{'sTitle':'spliceFlags','sClass':'right'},{'sTitle':'spliceForwardFragmentIndex','sClass':'center'},{'sTitle':'spliceForwardTarget'},{'sTitle':'spliceForwardPosition','fnRender':formatNumber,'sClass':'right'},{'sTitle':'spliceBackwardFragmentIndex','sClass':'center'},{'sTitle':'spliceBackwardTarget'},{'sTitle':'spliceBackwardPosition','fnRender':formatNumber,'sClass':'right'},{'sTitle':'referenceLength','fnRender':formatNumber,'sClass':'right'},{'sTitle':'numIndels','fnRender':formatNumber,'sClass':'right'},{'sTitle':'numMismatches','fnRender':formatNumber,'sClass':'right'}];
-</script>
-<table cellpadding='0' cellspacing='0' border='0' class='display' id='alignment'>
-<tfoot><tr>
-<td><input type='text' name='search_queryIndex' value='filter' class='search_init'/></td><td><input type='text' name='search_targetIdentifier' value='filter' class='search_init'/></td><td><input type='text' name='search_position' value='filter' class='search_init'/></td><td><input type='text' name='search_queryLength' value='filter' class='search_init'/></td><td><input type='text' name='search_alignmentLength' value='filter' class='search_init'/></td><td><input type='text' name='search_strand' value='filter' class='search_init'/></td><td><input type='text' name='search_score' value='filter' class='search_init'/></td><td><input type='text' name='search_mappingQuality' value='filter' class='search_init'/></td><td><input type='text' name='search_pairFlags' value='filter' class='search_init'/></td><td><input type='text' name='search_readFragmentIndex' value='filter' class='search_init'/></td><td><input type='text' name='search_pairFragmentIndex' value='filter' class='search_init'/></td><td><input type='text' name='search_pairTarget' value='filter' class='search_init'/></td><td><input type='text' name='search_pairPosition' value='filter' class='search_init'/></td><td><input type='text' name='search_spliceFlags' value='filter' class='search_init'/></td><td><input type='text' name='search_spliceForwardFragmentIndex' value='filter' class='search_init'/></td><td><input type='text' name='search_spliceForwardTarget' value='filter' class='search_init'/></td><td><input type='text' name='search_spliceForwardPosition' value='filter' class='search_init'/></td><td><input type='text' name='search_spliceBackwardFragmentIndex' value='filter' class='search_init'/></td><td><input type='text' name='search_spliceBackwardTarget' value='filter' class='search_init'/></td><td><input type='text' name='search_spliceBackwardPosition' value='filter' class='search_init'/></td><td><input type='text' name='search_referenceLength' value='filter' class='search_init'/></td><td><input type='text' name='search_numIndels' value='filter' class='search_init'/></td><td><input type='text' name='search_numMismatches' value='filter' class='search_init'/></td></tr></tfoot>
-</table>
-<script type='text/javascript'>
- var data = [
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-</script></body></html>
View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/6c8ca392327222d46119ac507f8094e35449cc58...94cb53edc0174d900c2c90aef495ad4209cf37a8
--
View it on GitLab: https://salsa.debian.org/med-team/libgoby-java/-/compare/6c8ca392327222d46119ac507f8094e35449cc58...94cb53edc0174d900c2c90aef495ad4209cf37a8
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