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From: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Date: Fri, 2 Dec 2011 21:21:17 +0000
Subject: fix_includes_path.patch
---
src/hits.h | 2 +-
1 files changed, 1 insertions(+), 1 deletions(-)
--- cufflinks.orig/src/hits.h
+++ cufflinks/src/hits.h
@@ -18,7 +18,7 @@
#include <boost/shared_ptr.hpp>
-#include <bam/sam.h>
+#include <samtools/sam.h>
#include "common.h"
#include "multireads.h"
--- cufflinks.orig/ax_check_eigen.m4
+++ cufflinks/ax_check_eigen.m4
@@ -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)
--- cufflinks.orig/src/abundances.cpp
+++ cufflinks/src/abundances.cpp
@@ -50,7 +50,7 @@
#include "negative_binomial_distribution.h"
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
//using Eigen::MatrixXd;
//#ifdef __USE_ISOC99
--- 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>
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
#include "hits.h"
#include "scaffolds.h"
--- cufflinks.orig/src/jensen_shannon.h
+++ cufflinks/src/jensen_shannon.h
@@ -14,7 +14,7 @@
#include <boost/numeric/ublas/io.hpp>
#include <vector>
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
namespace ublas = boost::numeric::ublas;
--- 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>
-#include <Eigen/Dense>
+#include <eigen3/Eigen/Dense>
// Boost Cholesky factorizations in the spirit of lu.hpp
// Written by Robbie Vogt, found at:
|
