[med-svn] [SCM] cufflinks branch, master, updated. debian/1.3.0-2-7-g2fb02e8

[Carlos Borroto]

The following commit has been merged in the master branch:
commit 2fb02e8323fc1b0888e6b26ec0b2b825d7392a3e
Author: Carlos Borroto <carlos.borroto at gmail.com>
Date:   Fri Jun 8 12:40:33 2012 -0400

    refreshs 0003-fix_includes_path.patch to proper include Eigen library

diff --git a/debian/patches/0003-fix_includes_path.patch b/debian/patches/0003-fix_includes_path.patch
index dfd5a55..469eb58 100644
--- a/debian/patches/0003-fix_includes_path.patch
+++ b/debian/patches/0003-fix_includes_path.patch
@@ -6,10 +6,10 @@ Subject: fix_includes_path.patch
  src/hits.h |    2 +-
  1 files changed, 1 insertions(+), 1 deletions(-)
 
-diff --git a/src/hits.h b/src/hits.h
-index ee1331e..6aefc9c 100644
---- a/src/hits.h
-+++ b/src/hits.h
+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
 @@ -16,7 +16,7 @@
  
  #include <boost/shared_ptr.hpp>
@@ -19,4 +19,81 @@ index ee1331e..6aefc9c 100644
  
  #include "common.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
+@@ -66,7 +66,7 @@
+ 
+ AC_LANG_PUSH(C++)
+ AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
+-@%:@include <Eigen/Dense>
++@%:@include <eigen3/Eigen/Dense>
+ ]], [[
+ ]])],[
+ 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
+ /* end confdefs.h.  */
+ 
+-#include <Eigen/Dense>
++#include <eigen3/Eigen/Dense>
+ 
+ int
+ 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
+@@ -41,7 +41,7 @@
+ #include <boost/random/negative_binomial_distribution.hpp>
+ 
+ 
+-#include <Eigen/Dense>
++#include <eigen3/Eigen/Dense>
+ //using Eigen::MatrixXd;
+ 
+ 
+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
+@@ -18,7 +18,7 @@
+ #include <boost/numeric/ublas/matrix.hpp>
+ #include <boost/numeric/ublas/vector.hpp>
+ 
+-#include <Eigen/Dense>
++#include <eigen3/Eigen/Dense>
+ 
+ #include "hits.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
+@@ -14,7 +14,7 @@
+ #include <boost/numeric/ublas/io.hpp>
+ 
+ #include <vector>
+-#include <Eigen/Dense>
++#include <eigen3/Eigen/Dense>
+ 
+ namespace ublas = boost::numeric::ublas;
+ 
+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
+@@ -35,7 +35,7 @@
+ #include <boost/random/variate_generator.hpp>
+ #include <boost/math/constants/constants.hpp>
+ 
+-#include <Eigen/Dense>
++#include <eigen3/Eigen/Dense>
+ 
+ // Boost Cholesky factorizations in the spirit of lu.hpp
+ // Written by Robbie Vogt, found at: 

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