[med-svn] [cufflinks] 11/12: Try to build against Debian packaged liblemon but failed

[Andreas Tille]

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tille pushed a commit to branch master
in repository cufflinks.

commit 0601d0dd82cf2d9035b416101569ba6e6c914486
Author: Andreas Tille <tille at debian.org>
Date:   Fri Aug 5 22:12:14 2016 +0200

    Try to build against Debian packaged liblemon but failed
---
 debian/control                                    |  3 +-
 debian/patches/0003-fix_includes_path.patch       | 37 +++++++------------
 debian/patches/use_debian_packaged_liblemon.patch | 44 +++++++++++++++++++++++
 3 files changed, 59 insertions(+), 25 deletions(-)

diff --git a/debian/control b/debian/control
index 6bf4e21..896d86b 100644
--- a/debian/control
+++ b/debian/control
@@ -17,7 +17,8 @@ Build-Depends: debhelper (>= 9),
                zlib1g-dev,
                dh-autoreconf,
                python,
-               libeigen3-dev
+               libeigen3-dev,
+               liblemon-dev
 Standards-Version: 3.9.8
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/cufflinks.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/cufflinks.git
diff --git a/debian/patches/0003-fix_includes_path.patch b/debian/patches/0003-fix_includes_path.patch
index c6aa5f9..4451ef0 100644
--- a/debian/patches/0003-fix_includes_path.patch
+++ b/debian/patches/0003-fix_includes_path.patch
@@ -6,8 +6,8 @@ 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
+--- a/src/hits.h
++++ b/src/hits.h
 @@ -18,7 +18,7 @@
  
  #include <boost/shared_ptr.hpp>
@@ -17,9 +17,9 @@ Subject: fix_includes_path.patch
  
  #include "common.h"
  #include "multireads.h"
---- cufflinks.orig/ax_check_eigen.m4
-+++ cufflinks/ax_check_eigen.m4
-@@ -66,7 +66,7 @@
+--- a/ax_check_eigen.m4
++++ b/ax_check_eigen.m4
+@@ -66,7 +66,7 @@ export EIGEN_CPPFLAGS
  
  AC_LANG_PUSH(C++)
  AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
@@ -28,19 +28,8 @@ Subject: fix_includes_path.patch
  ]], [[
  ]])],[
  AC_MSG_RESULT(yes)
---- cufflinks.orig/configure
-+++ cufflinks/configure
-@@ -6723,7 +6723,7 @@
- cat >>conftest.$ac_ext <<_ACEOF
- /* end confdefs.h.  */
- 
--#include <Eigen/Dense>
-+#include <eigen3/Eigen/Dense>
- 
- int
- main ()
---- cufflinks.orig/src/abundances.cpp
-+++ cufflinks/src/abundances.cpp
+--- a/src/abundances.cpp
++++ b/src/abundances.cpp
 @@ -50,7 +50,7 @@
  #include "negative_binomial_distribution.h"
  
@@ -50,8 +39,8 @@ Subject: fix_includes_path.patch
  //using Eigen::MatrixXd;
  
  //#ifdef  __USE_ISOC99
---- cufflinks.orig/src/abundances.h
-+++ cufflinks/src/abundances.h
+--- a/src/abundances.h
++++ b/src/abundances.h
 @@ -18,7 +18,7 @@
  #include <boost/numeric/ublas/matrix.hpp>
  #include <boost/numeric/ublas/vector.hpp>
@@ -61,8 +50,8 @@ Subject: fix_includes_path.patch
  
  #include "hits.h"
  #include "scaffolds.h"
---- cufflinks.orig/src/jensen_shannon.h
-+++ cufflinks/src/jensen_shannon.h
+--- a/src/jensen_shannon.h
++++ b/src/jensen_shannon.h
 @@ -14,7 +14,7 @@
  #include <boost/numeric/ublas/io.hpp>
  
@@ -72,8 +61,8 @@ Subject: fix_includes_path.patch
  
  namespace ublas = boost::numeric::ublas;
  
---- cufflinks.orig/src/sampling.h
-+++ cufflinks/src/sampling.h
+--- a/src/sampling.h
++++ b/src/sampling.h
 @@ -35,7 +35,7 @@
  #include <boost/random/variate_generator.hpp>
  #include <boost/math/constants/constants.hpp>
diff --git a/debian/patches/use_debian_packaged_liblemon.patch b/debian/patches/use_debian_packaged_liblemon.patch
index 7e0fac0..7f23927 100644
--- a/debian/patches/use_debian_packaged_liblemon.patch
+++ b/debian/patches/use_debian_packaged_liblemon.patch
@@ -54,3 +54,47 @@
  cufflinks_LDFLAGS =  $(LDFLAGS) $(BOOST_LDFLAGS) $(BAM_LDFLAGS) #$(ZLIB_LDFLAGS) 
  
  cuffcompare_SOURCES = cuffcompare.cpp
+--- a/src/graph_optimize.cpp
++++ b/src/graph_optimize.cpp
+@@ -13,9 +13,10 @@
+ #include "graph_optimize.h"
+ // for graph optimization only
+ 
+-#include <lemon/topology.h>
++// #include <lemon/topology.h>
+ #include <lemon/smart_graph.h>
+-#include <lemon/bipartite_matching.h>
++// #include <lemon/bipartite_matching.h>
++#include <lemon/connectivity.h>
+ 
+ #include "scaffold_graph.h"
+ #include "scaffolds.h"
+--- a/src/assemble.cpp
++++ b/src/assemble.cpp
+@@ -16,10 +16,12 @@
+ #include <vector>
+ #include <iostream>
+ 
+-#include <lemon/topology.h>
++//#include <lemon/topology.h>
+ 
+ //#include <lemon/graph_utils.h>
+-#include <lemon/bipartite_matching.h>
++//#include <lemon/bipartite_matching.h>
++#include <lemon/connectivity.h>
++#include <lemon/smart_graph.h>
+ 
+ #include <boost/ref.hpp>
+ // DON'T move this, or mystery compiler errors will result. Affects gcc >= 4.1
+--- a/src/matching_merge.h
++++ b/src/matching_merge.h
+@@ -14,7 +14,8 @@
+ 
+ //#include <lemon/topology.h>
+ #include <lemon/smart_graph.h>
+-#include <lemon/bipartite_matching.h>
++//#include <lemon/bipartite_matching.h>
++#include <lemon/connectivity.h>
+ 
+ #include "scaffold_graph.h"
+ #include "scaffolds.h"

-- 
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