[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-2-16-gd45e176

[Carlos Borroto]

The following commit has been merged in the master branch:
commit d45e176c658eba50d56eabfb133731850e8edfd3
Author: Carlos Borroto <carlos.borroto at gmail.com>
Date:   Fri Jun 15 16:10:34 2012 -0400

    refresh patches

diff --git a/debian/patches/0001-fix_spelling.patch b/debian/patches/0001-fix_spelling.patch
index fe708dc..c13ba57 100644
--- a/debian/patches/0001-fix_spelling.patch
+++ b/debian/patches/0001-fix_spelling.patch
@@ -9,8 +9,8 @@ Subject: fix_spelling
 
 Index: cufflinks/src/locfit/arith.c
 ===================================================================
---- cufflinks.orig/src/locfit/arith.c	2012-06-08 11:44:22.468790509 -0400
-+++ cufflinks/src/locfit/arith.c	2012-06-08 11:46:41.156792714 -0400
+--- cufflinks.orig/src/locfit/arith.c	2012-06-15 16:08:56.802658315 -0400
++++ cufflinks/src/locfit/arith.c	2012-06-15 16:09:19.150658671 -0400
 @@ -410,7 +410,7 @@
      INT i;
      if (l==NULL) 
@@ -22,8 +22,8 @@ Index: cufflinks/src/locfit/arith.c
      v = createvar("_vvec1",STHIDDEN,l->n,VDOUBLE);
 Index: cufflinks/src/locfit/lfd.c
 ===================================================================
---- cufflinks.orig/src/locfit/lfd.c	2012-06-08 11:44:22.468790509 -0400
-+++ cufflinks/src/locfit/lfd.c	2012-06-08 11:46:41.156792714 -0400
+--- cufflinks.orig/src/locfit/lfd.c	2012-06-15 16:08:56.814658316 -0400
++++ cufflinks/src/locfit/lfd.c	2012-06-15 16:09:19.150658671 -0400
 @@ -78,7 +78,7 @@
          }
        }
@@ -35,9 +35,9 @@ Index: cufflinks/src/locfit/lfd.c
      }
 Index: cufflinks/src/abundances.cpp
 ===================================================================
---- cufflinks.orig/src/abundances.cpp	2012-06-08 11:44:33.688790686 -0400
-+++ cufflinks/src/abundances.cpp	2012-06-08 11:46:41.156792714 -0400
-@@ -1995,7 +1995,7 @@
+--- cufflinks.orig/src/abundances.cpp	2012-06-15 16:08:56.826658315 -0400
++++ cufflinks/src/abundances.cpp	2012-06-15 16:09:19.154658670 -0400
+@@ -1985,7 +1985,7 @@
  	
  	vector<double> gammas;
  	
diff --git a/debian/patches/0003-fix_includes_path.patch b/debian/patches/0003-fix_includes_path.patch
index 469eb58..fb6a052 100644
--- a/debian/patches/0003-fix_includes_path.patch
+++ b/debian/patches/0003-fix_includes_path.patch
@@ -8,8 +8,8 @@ Subject: fix_includes_path.patch
 
 Index: cufflinks/src/hits.h
 ===================================================================
---- cufflinks.orig/src/hits.h	2012-06-08 12:37:48.200841474 -0400
-+++ cufflinks/src/hits.h	2012-06-08 12:37:50.420841510 -0400
+--- cufflinks.orig/src/hits.h	2012-06-15 16:01:29.218651198 -0400
++++ cufflinks/src/hits.h	2012-06-15 16:08:18.626657708 -0400
 @@ -16,7 +16,7 @@
  
  #include <boost/shared_ptr.hpp>
@@ -21,8 +21,8 @@ Index: cufflinks/src/hits.h
  #include "multireads.h"
 Index: cufflinks/ax_check_eigen.m4
 ===================================================================
---- cufflinks.orig/ax_check_eigen.m4	2012-06-08 12:37:25.900841120 -0400
-+++ cufflinks/ax_check_eigen.m4	2012-06-08 12:38:18.984841964 -0400
+--- cufflinks.orig/ax_check_eigen.m4	2012-06-15 16:01:29.194651198 -0400
++++ cufflinks/ax_check_eigen.m4	2012-06-15 16:08:18.626657708 -0400
 @@ -66,7 +66,7 @@
  
  AC_LANG_PUSH(C++)
@@ -34,10 +34,10 @@ Index: cufflinks/ax_check_eigen.m4
  AC_MSG_RESULT(yes)
 Index: cufflinks/configure
 ===================================================================
---- cufflinks.orig/configure	2012-06-08 12:37:25.900841120 -0400
-+++ cufflinks/configure	2012-06-08 12:38:34.120842204 -0400
-@@ -6438,7 +6438,7 @@
- cat >>conftest.$ac_ext <<_ACEOF
+--- cufflinks.orig/configure	2012-06-15 16:06:07.302655620 -0400
++++ cufflinks/configure	2012-06-15 16:08:18.630657708 -0400
+@@ -5973,7 +5973,7 @@
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
  /* end confdefs.h.  */
  
 -#include <Eigen/Dense>
@@ -47,8 +47,8 @@ Index: cufflinks/configure
  main ()
 Index: cufflinks/src/abundances.cpp
 ===================================================================
---- cufflinks.orig/src/abundances.cpp	2012-06-08 12:37:50.396841509 -0400
-+++ cufflinks/src/abundances.cpp	2012-06-08 12:39:07.760842740 -0400
+--- cufflinks.orig/src/abundances.cpp	2012-06-15 16:08:18.598657707 -0400
++++ cufflinks/src/abundances.cpp	2012-06-15 16:08:18.630657708 -0400
 @@ -41,7 +41,7 @@
  #include <boost/random/negative_binomial_distribution.hpp>
  
@@ -60,8 +60,8 @@ Index: cufflinks/src/abundances.cpp
  
 Index: cufflinks/src/abundances.h
 ===================================================================
---- cufflinks.orig/src/abundances.h	2012-06-08 12:34:20.772838177 -0400
-+++ cufflinks/src/abundances.h	2012-06-08 12:39:43.096843302 -0400
+--- cufflinks.orig/src/abundances.h	2012-06-15 16:01:29.206651200 -0400
++++ cufflinks/src/abundances.h	2012-06-15 16:08:18.634657708 -0400
 @@ -18,7 +18,7 @@
  #include <boost/numeric/ublas/matrix.hpp>
  #include <boost/numeric/ublas/vector.hpp>
@@ -73,8 +73,8 @@ Index: cufflinks/src/abundances.h
  #include "scaffolds.h"
 Index: cufflinks/src/jensen_shannon.h
 ===================================================================
---- cufflinks.orig/src/jensen_shannon.h	2012-06-08 11:44:33.696790687 -0400
-+++ cufflinks/src/jensen_shannon.h	2012-06-08 12:39:28.712843073 -0400
+--- cufflinks.orig/src/jensen_shannon.h	2012-06-15 16:01:29.218651198 -0400
++++ cufflinks/src/jensen_shannon.h	2012-06-15 16:08:18.634657708 -0400
 @@ -14,7 +14,7 @@
  #include <boost/numeric/ublas/io.hpp>
  
@@ -86,8 +86,8 @@ Index: cufflinks/src/jensen_shannon.h
  
 Index: cufflinks/src/sampling.h
 ===================================================================
---- cufflinks.orig/src/sampling.h	2012-06-08 11:44:33.696790687 -0400
-+++ cufflinks/src/sampling.h	2012-06-08 12:38:03.992841726 -0400
+--- cufflinks.orig/src/sampling.h	2012-06-15 16:01:29.234651199 -0400
++++ cufflinks/src/sampling.h	2012-06-15 16:08:18.634657708 -0400
 @@ -35,7 +35,7 @@
  #include <boost/random/variate_generator.hpp>
  #include <boost/math/constants/constants.hpp>

-- 
Transcript assembly, differential expression, and differential regulation for RNA-Seq.