[med-svn] r21297 - in trunk/packages/rostlab/rate4site/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-01-25 08:43:30 +0000 (Mon, 25 Jan 2016)
New Revision: 21297

Added:
   trunk/packages/rostlab/rate4site/trunk/debian/links
   trunk/packages/rostlab/rate4site/trunk/debian/patches/
   trunk/packages/rostlab/rate4site/trunk/debian/patches/series
   trunk/packages/rostlab/rate4site/trunk/debian/patches/spelling.patch
Modified:
   trunk/packages/rostlab/rate4site/trunk/debian/changelog
Log:
Fix spelling, Same manpage also for rate4site_doublerep



Modified: trunk/packages/rostlab/rate4site/trunk/debian/changelog
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/changelog	2016-01-25 08:34:04 UTC (rev 21296)
+++ trunk/packages/rostlab/rate4site/trunk/debian/changelog	2016-01-25 08:43:30 UTC (rev 21297)
@@ -1,4 +1,4 @@
-rate4site (3.0.0-2) UNRELEASED; urgency=low
+rate4site (3.0.0-2) unstable; urgency=low
 
   * debian/upstream: Fix syntax
   * Moved debian/upstream to debian/upstream/metadata
@@ -6,12 +6,13 @@
   * debhelper 9
   * Priority: optional
   * cme fix dpkg-control
-  * remove empty debian/patches
   * DEP5 fix
   * Remove *-dbg file since this is created automatically
   * Cleanup d/rules
+  * Fix spelling
+  * Same manpage also for rate4site_doublerep
 
- -- Andreas Tille <tille at debian.org>  Mon, 25 Jan 2016 09:06:20 +0100
+ -- Andreas Tille <tille at debian.org>  Mon, 25 Jan 2016 09:15:42 +0100
 
 rate4site (3.0.0-1) unstable; urgency=low
 

Added: trunk/packages/rostlab/rate4site/trunk/debian/links
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/links	                        (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/links	2016-01-25 08:43:30 UTC (rev 21297)
@@ -0,0 +1 @@
+usr/share/man/man1/rate4site.1.gz	usr/share/man/man1/rate4site_doublerep.1.gz

Added: trunk/packages/rostlab/rate4site/trunk/debian/patches/series
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/patches/series	2016-01-25 08:43:30 UTC (rev 21297)
@@ -0,0 +1 @@
+spelling.patch

Added: trunk/packages/rostlab/rate4site/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/rostlab/rate4site/trunk/debian/patches/spelling.patch	                        (rev 0)
+++ trunk/packages/rostlab/rate4site/trunk/debian/patches/spelling.patch	2016-01-25 08:43:30 UTC (rev 21297)
@@ -0,0 +1,39 @@
+Description: Fix spelling
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 25 Jan 2016 09:15:42 +0100
+
+--- a/src/phylogeny/likeDist.cpp
++++ b/src/phylogeny/likeDist.cpp
+@@ -145,10 +145,10 @@ MDOUBLE likeDist::giveDistanceThroughCTC
+ 						const sequence& s2,
+ 						const vector<MDOUBLE>  * weights,
+ 						MDOUBLE* score) const {
+-    // only in the case of homogenous model - work through pairwise EM like
++    // only in the case of homogeneous model - work through pairwise EM like
+     countTableComponentGam ctc;
+     if (_sp.categories() != 1) {
+-	errorMsg::reportError("this function only work for homogenous model.");
++	errorMsg::reportError("this function only work for homogeneous model.");
+     }
+     ctc.countTableComponentAllocatePlace(s1.getAlphabet()->size(),1);
+     for (int i=0; i<s1.seqLen(); ++i) {
+--- a/src/rate4site/rate4site.cpp
++++ b/src/rate4site/rate4site.cpp
+@@ -608,7 +608,7 @@ void rate4site::getStartingNJtreeNjJC_ol
+ 
+ void rate4site::getStartingNJtreeNjMLdis() {
+ 	// note that here ALWAYS, the ML distances are computed using
+-	// an homogenous rate distribution.
++	// an homogeneous rate distribution.
+ 	uniDistribution lUni;
+ 	const pijAccelerator* lpijAcc = _sp->getPijAccelerator();// note this is just a copy of the pointer.
+ 	stochasticProcess lsp(&lUni,lpijAcc);
+@@ -997,7 +997,7 @@ Branch lengths optimization flag:
+ 
+ 	-bn = no Branch lengths optimization
+ 	
+-	-bh = optimization using a homogenous model (no among-site-rate-variation)
++	-bh = optimization using a homogeneous model (no among-site-rate-variation)
+ 	
+ 	-bg = optimization using a Gamma model
+