The scripts to upgrade ode-0.12 to ode-0.13 have been attached:

func_collection.sh

@@ -448,17 +448,17 @@ function fetch_ode_mars() {
     pushd . > /dev/null 2>&1
     mkdir -p ${MARS_DEV_ROOT}/external
     cd ${MARS_DEV_ROOT}/external
-    if [ ! -e "ode-0.12.tar.gz" ]; then
-        wget http://sourceforge.net/projects/opende/files/ODE/0.12/ode-0.12.tar.gz
+    if [ ! -e "ode-0.13.1.tar.gz" ]; then
+        wget http://bitbucket.org/odedevs/ode/downloads/ode-0.13.1.tar.gz
         if [ -d "ode_mars" ]; then 
             uninstall_package "external/ode_mars"
             rm -rf ode_mars
         fi
     fi
 
     if [ ! -d "ode_mars" ]; then 
-        tar -xzvf ode-0.12.tar.gz
-        mv ode-0.12 ode_mars
+        tar -xzvf ode-0.13.1.tar.gz
+        mv ode-0.13.1 ode_mars
     fi
     cd ..
     popd > /dev/null 2>&1
@@ -634,18 +634,18 @@ function patch_eigen {
 }
 
 function patch_ode_mars {
-    printBold "patching external/ode_mars version 0.12 ..."
+    printBold "patching external/ode_mars version 0.13.1..."
     setScriptDir
     setupConfig
     # patch was accepted upstream (http://sf.net/p/opende/patches/180) and
     # applied to Rev. 1913 (http://sf.net/p/opende/code/1913) and should be
     # in the next release
-    patch -N -p0 -d ${MARS_DEV_ROOT}/external/ode_mars -i ${MARS_SCRIPT_DIR}/patches/ode-0.12-va_end.patch
-    patch -N -p0 -d ${MARS_DEV_ROOT}/external/ode_mars -i ${MARS_SCRIPT_DIR}/patches/ode-0.12-lambda.patch
-    patch -N -p0 -d ${MARS_DEV_ROOT}/external/ode_mars -i ${MARS_SCRIPT_DIR}/patches/ode-0.12-export_joint_internals.patch
+    #patch -N -p0 -d ${MARS_DEV_ROOT}/external/ode_mars -i ${MARS_SCRIPT_DIR}/patches/ode-0.12-va_end.patch
+    patch -N -p0 -d ${MARS_DEV_ROOT}/external/ode_mars -i ${MARS_SCRIPT_DIR}/patches/ode-0.13.1-lambda.patch
+    patch -N -p0 -d ${MARS_DEV_ROOT}/external/ode_mars -i ${MARS_SCRIPT_DIR}/patches/ode-0.13.1-export_joint_internals.patch
     # patch was submitted upstream (http://sf.net/p/opende/patches/187)
-    patch -N -p0 -d ${MARS_DEV_ROOT}/external/ode_mars -i ${MARS_SCRIPT_DIR}/patches/ode-0.12-abort.patch
-    printBold "... done patching external/ode_mars version 0.12."
+    patch -N -p0 -d ${MARS_DEV_ROOT}/external/ode_mars -i ${MARS_SCRIPT_DIR}/patches/ode-0.13.1-abort.patch
+    printBold "... done patching external/ode_mars version 0.13.1."
 }
 
 
@@ -727,6 +727,7 @@ function install_ode_mars {
       export CFLAGS=-fPIC
       export CXXFLAGS=-fPIC
       # --enable-release
+      ./bootstrap
       ./configure CPPFLAGS="-DdNODEBUG" CXXFLAGS="-O2 -ffast-math -fPIC" CFLAGS="-O2 -ffast-math -fPIC" --enable-double-precision --prefix=$prefix --with-drawstuff=none --disable-demos
       if [ "${platform}" = "linux" ]; then
         if [ x`which libtool` != x ]; then

patches/ode-0.13.1-abort.patch

@@ -0,0 +1,38 @@
+--- ode/src/error.cpp	2014-02-04 07:00:58.000000000 +0100
++++ ode/src/error.cpp	2016-01-25 13:14:51.437768604 +0100
+@@ -90,7 +90,8 @@
+     if (error_function) error_function (num,msg,ap);
+     else printMessage (num,"ODE Error",msg,ap);
+     va_end (ap);
+-    exit (1);
++    if (!error_function)
++    exit (1);    
+ }
+
+
+@@ -102,6 +103,7 @@
+     else printMessage (num,"ODE INTERNAL ERROR",msg,ap);
+     va_end (ap);
+     // *((char *)0) = 0;   ... commit SEGVicide
++    if (!debug_function)
+     abort();
+ }
+
+@@ -145,6 +147,7 @@
+         MessageBox(0,s,title,MB_OK | MB_ICONWARNING);
+     }
+     va_end (ap);
++    if (!error_function)
+     exit (1);
+ }
+
+@@ -162,7 +165,8 @@
+         MessageBox(0,s,title,MB_OK | MB_ICONSTOP);
+     }
+     va_end (ap);
+-    abort();
+++   if (!debug_function)
+++   abort();
+ }
+
+

patches/ode-0.12-export_joint_internals.patch → patches/ode-0.13.1-export_joint_internals.patch

@@ -1,9 +1,10 @@
---- ode/src/Makefile.am	Fri Jul 11 08:16:50 2008
-+++ ode/src/Makefile.am	Wed Aug  8 08:43:51 2012
-@@ -14,6 +14,13 @@
- libode_la_LDFLAGS = @EXTRA_LIBTOOL_LDFLAGS@ @ODE_VERSION_INFO@
- libode_la_LIBADD = libfast.la joints/libjoints.la
+--- ode/src/Makefile.am	2014-02-04 07:00:58.000000000 +0100
++++ ode/src/Makefile.am	2016-01-25 13:14:51.545768600 +0100
+@@ -8,7 +8,13 @@
+ noinst_LTLIBRARIES = libfast.la
+ libfast_la_SOURCES = fastldlt.c fastltsolve.c fastdot.c fastlsolve.c
 
+-
 +# to create child classes of dJoint, we need to make more of
 +# the internal data structures accessible.
 +libode_la_includedir = $(includedir)/ode-internals
@@ -12,11 +13,11 @@
 +			obstack.h \
 +			config.h
 
- # please, let's keep the filenames sorted
- libode_la_SOURCES =     array.cpp array.h \
---- ode/src/joints/Makefile.am	Wed Jun  4 23:47:13 2008
-+++ ode/ode/src/joints/Makefile.am	Wed Aug  8 08:43:51 2012
-@@ -2,6 +2,9 @@
+ lib_LTLIBRARIES = libode.la
+
+--- ode/src/joints/Makefile.am	2014-02-04 07:00:58.000000000 +0100
++++ ode/ode/src/joints/Makefile.am	2016-01-25 13:14:51.949768584 +0100
+@@ -4,6 +4,9 @@
 
  noinst_LTLIBRARIES = libjoints.la
 
@@ -26,3 +27,4 @@
  libjoints_la_SOURCES =  joints.h \
                          joint.h joint.cpp \
                          joint_internal.h \
+

patches/ode-0.13.1-lambda.patch

@@ -0,0 +1,23 @@
+--- include/ode/common.h	2014-02-27 21:42:09.000000000 +0100
++++ include/ode/common.h	2016-01-25 13:14:50.297768650 +0100
+@@ -337,6 +337,7 @@
+   dVector3 t1;		/* torque applied to body 1 */
+   dVector3 f2;		/* force applied to body 2 */
+   dVector3 t2;		/* torque applied to body 2 */
++  dReal lambda;
+ } dJointFeedback;
+
+
+--- ode/src/step.cpp	2014-03-05 17:05:14.000000000 +0100
++++ ode/src/step.cpp	2016-01-25 13:14:51.665768595 +0100
+@@ -1293,8 +1293,9 @@
+                         cf2[2] += (fb->f2[2] = data[2]);
+                         cf2[4] += (fb->t2[0] = data[4]);
+                         cf2[5] += (fb->t2[1] = data[5]);
+-                        cf2[6] += (fb->t2[2] = data[6]);
++                        cf2[6] += (fb->t2[2] = data[6]);                        
+                     }
++                    fb->lambda = *(lambdarow+5);
+                 }
+                 else {
+                     // no feedback is required, let's compute cforce the faster way