[med-svn] r22675 - in trunk/packages/hhsuite/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2016-08-13 05:48:31 +0000 (Sat, 13 Aug 2016)
New Revision: 22675

Added:
   trunk/packages/hhsuite/trunk/debian/patches/spelling.patch
Modified:
   trunk/packages/hhsuite/trunk/debian/changelog
   trunk/packages/hhsuite/trunk/debian/patches/series
Log:
Fix spelling


Modified: trunk/packages/hhsuite/trunk/debian/changelog
===================================================================
--- trunk/packages/hhsuite/trunk/debian/changelog	2016-08-13 05:44:01 UTC (rev 22674)
+++ trunk/packages/hhsuite/trunk/debian/changelog	2016-08-13 05:48:31 UTC (rev 22675)
@@ -3,6 +3,7 @@
   * Use system defined log2 and log10 to enable build using gcc-6.1
     Closes: #831115
   * cme fix dpkg-control
+  * fix spelling
 
  -- Andreas Tille <tille at debian.org>  Sat, 13 Aug 2016 07:27:28 +0200
 

Modified: trunk/packages/hhsuite/trunk/debian/patches/series
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/series	2016-08-13 05:44:01 UTC (rev 22674)
+++ trunk/packages/hhsuite/trunk/debian/patches/series	2016-08-13 05:48:31 UTC (rev 22675)
@@ -9,3 +9,4 @@
 version_bump
 add_Makefile_in_data.patch
 gcc-6.1.patch
+spelling.patch

Added: trunk/packages/hhsuite/trunk/debian/patches/spelling.patch
===================================================================
--- trunk/packages/hhsuite/trunk/debian/patches/spelling.patch	                        (rev 0)
+++ trunk/packages/hhsuite/trunk/debian/patches/spelling.patch	2016-08-13 05:48:31 UTC (rev 22675)
@@ -0,0 +1,57 @@
+Description: Fix spelling
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Sat, 13 Aug 2016 07:27:28 +0200
+
+--- a/src/hhblits.C
++++ b/src/hhblits.C
+@@ -398,7 +398,7 @@ void help(char all=0)
+   printf(" -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=%i)      \n",cpu);
+ #endif
+   if (all) {
+-  printf(" -scores <file> write scores for all pairwise comparisions to file               \n");
++  printf(" -scores <file> write scores for all pairwise comparisons to file               \n");
+   printf(" -atab   <file> write all alignments in tabular layout to file                   \n");
+   printf(" -maxres <int>  max number of HMM columns (def=%5i)             \n",par.maxres);
+   printf(" -maxmem [1,inf[ max available memory in GB (def=%.1f)          \n",par.maxmem);
+--- a/src/hhsearch.C
++++ b/src/hhsearch.C
+@@ -325,7 +325,7 @@ void help(char all=0)
+   if (all) {
+   printf(" -maxres <int>  max number of HMM columns (def=%5i)             \n",par.maxres);
+   printf(" -maxmem [1,inf[ max available memory in GB (def=%.1f)          \n",par.maxmem);
+-  printf(" -scores <file> write scores for all pairwise comparisions to file         \n");
++  printf(" -scores <file> write scores for all pairwise comparisons to file         \n");
+   printf(" -calm {0,..,3} empirical score calibration of 0:query 1:template 2:both   \n");
+   printf("                default 3: neural network-based estimation of EVD params   \n");
+   // printf(" -opt  <file>   parameter optimization mode (def=off): return sum of ranks \n");
+--- a/src/hhsuite-userguide.tex
++++ b/src/hhsuite-userguide.tex
+@@ -1542,7 +1542,7 @@ Other options:
+  -neffmax ]1,20] skip further search iterations when diversity Neff of query MSA 
+                 becomes larger than neffmax (default=10.0)
+  -cpu <int>     number of CPUs to use (for shared memory SMPs) (default=2)      
+- -scores <file> write scores for all pairwise comparisions to file               
++ -scores <file> write scores for all pairwise comparisons to file               
+  -atab   <file> write all alignments in tabular layout to file                   
+  -maxres <int>  max number of HMM columns (def=15002)             
+  -maxmem [1,inf[ max available memory in GB (def=3.0)          
+@@ -1663,7 +1663,7 @@ Other options:
+  -v <int>       verbose mode: 0:no screen output  1:only warings  2: verbose   
+  -maxres <int>  max number of HMM columns (def=15002)             
+  -maxmem [1,inf[ max available memory in GB (def=3.0)          
+- -scores <file> write scores for all pairwise comparisions to file         
++ -scores <file> write scores for all pairwise comparisons to file         
+  -calm {0,..,3} empirical score calibration of 0:query 1:template 2:both   
+                 default 3: neural network-based estimation of EVD params   
+ 
+--- a/src/cs/context_profile-inl.h
++++ b/src/cs/context_profile-inl.h
+@@ -36,7 +36,7 @@ void ContextProfile<Abc>::Read(FILE* fin
+     assert(len & 1);
+     if (nalph != Abc::kSize)
+         throw Exception("Alphabet size of serialized context profile should be %d"
+-                        "but is acutally %d!", Abc::kSize, nalph);
++                        "but is actually %d!", Abc::kSize, nalph);
+ 
+     // If everything went fine we can resize our data memmbers
+     probs.Resize(len);