[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-2-20-g5793b68

[Carlos Borroto]

The following commit has been merged in the master branch:
commit 5793b688c8b26fc08fc81602e64b1f0b41453d07
Author: Carlos Borroto <carlos.borroto at gmail.com>
Date:   Thu Jul 12 15:35:45 2012 -0400

    refresh patches

diff --git a/debian/patches/0001-fix_spelling.patch b/debian/patches/0001-fix_spelling.patch
index c13ba57..4308e78 100644
--- a/debian/patches/0001-fix_spelling.patch
+++ b/debian/patches/0001-fix_spelling.patch
@@ -7,10 +7,8 @@ Subject: fix_spelling
  src/locfit/lfd.c   |    2 +-
  2 files changed, 2 insertions(+), 2 deletions(-)
 
-Index: cufflinks/src/locfit/arith.c
-===================================================================
---- 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
+--- cufflinks.orig/src/locfit/arith.c
++++ cufflinks/src/locfit/arith.c
 @@ -410,7 +410,7 @@
      INT i;
      if (l==NULL) 
@@ -20,10 +18,8 @@ Index: cufflinks/src/locfit/arith.c
          return NULL;
      }
      v = createvar("_vvec1",STHIDDEN,l->n,VDOUBLE);
-Index: cufflinks/src/locfit/lfd.c
-===================================================================
---- 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
+--- cufflinks.orig/src/locfit/lfd.c
++++ cufflinks/src/locfit/lfd.c
 @@ -78,7 +78,7 @@
          }
        }
@@ -33,11 +29,9 @@ Index: cufflinks/src/locfit/lfd.c
          return(0);
        }
      }
-Index: cufflinks/src/abundances.cpp
-===================================================================
---- 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 @@
+--- cufflinks.orig/src/abundances.cpp
++++ cufflinks/src/abundances.cpp
+@@ -2019,7 +2019,7 @@
  	
  	vector<double> gammas;
  	
diff --git a/debian/patches/0003-fix_includes_path.patch b/debian/patches/0003-fix_includes_path.patch
index fb6a052..141b5f0 100644
--- a/debian/patches/0003-fix_includes_path.patch
+++ b/debian/patches/0003-fix_includes_path.patch
@@ -6,10 +6,8 @@ Subject: fix_includes_path.patch
  src/hits.h |    2 +-
  1 files changed, 1 insertions(+), 1 deletions(-)
 
-Index: cufflinks/src/hits.h
-===================================================================
---- 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
+--- cufflinks.orig/src/hits.h
++++ cufflinks/src/hits.h
 @@ -16,7 +16,7 @@
  
  #include <boost/shared_ptr.hpp>
@@ -19,10 +17,8 @@ Index: cufflinks/src/hits.h
  
  #include "common.h"
  #include "multireads.h"
-Index: cufflinks/ax_check_eigen.m4
-===================================================================
---- 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
+--- cufflinks.orig/ax_check_eigen.m4
++++ cufflinks/ax_check_eigen.m4
 @@ -66,7 +66,7 @@
  
  AC_LANG_PUSH(C++)
@@ -32,12 +28,10 @@ Index: cufflinks/ax_check_eigen.m4
  ]], [[
  ]])],[
  AC_MSG_RESULT(yes)
-Index: cufflinks/configure
-===================================================================
---- 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.$ac_ext
+--- cufflinks.orig/configure
++++ cufflinks/configure
+@@ -5674,7 +5674,7 @@
+ cat >>conftest.$ac_ext <<_ACEOF
  /* end confdefs.h.  */
  
 -#include <Eigen/Dense>
@@ -45,10 +39,8 @@ Index: cufflinks/configure
  
  int
  main ()
-Index: cufflinks/src/abundances.cpp
-===================================================================
---- 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
+--- cufflinks.orig/src/abundances.cpp
++++ cufflinks/src/abundances.cpp
 @@ -41,7 +41,7 @@
  #include <boost/random/negative_binomial_distribution.hpp>
  
@@ -58,10 +50,8 @@ Index: cufflinks/src/abundances.cpp
  //using Eigen::MatrixXd;
  
  
-Index: cufflinks/src/abundances.h
-===================================================================
---- 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
+--- cufflinks.orig/src/abundances.h
++++ cufflinks/src/abundances.h
 @@ -18,7 +18,7 @@
  #include <boost/numeric/ublas/matrix.hpp>
  #include <boost/numeric/ublas/vector.hpp>
@@ -71,10 +61,8 @@ Index: cufflinks/src/abundances.h
  
  #include "hits.h"
  #include "scaffolds.h"
-Index: cufflinks/src/jensen_shannon.h
-===================================================================
---- 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
+--- cufflinks.orig/src/jensen_shannon.h
++++ cufflinks/src/jensen_shannon.h
 @@ -14,7 +14,7 @@
  #include <boost/numeric/ublas/io.hpp>
  
@@ -84,10 +72,8 @@ Index: cufflinks/src/jensen_shannon.h
  
  namespace ublas = boost::numeric::ublas;
  
-Index: cufflinks/src/sampling.h
-===================================================================
---- 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
+--- cufflinks.orig/src/sampling.h
++++ cufflinks/src/sampling.h
 @@ -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.