diff -Nru cain-1.9/debian/changelog cain-1.10+dfsg/debian/changelog
--- cain-1.9/debian/changelog	2014-08-25 07:27:25.000000000 +0000
+++ cain-1.10+dfsg/debian/changelog	2015-12-19 06:22:41.000000000 +0000
@@ -1,3 +1,23 @@
+cain (1.10+dfsg-1) unstable; urgency=medium
+
+  [ Ivo Maintz ]
+  * debian/rules:
+    - added patch by Chris Lamb <lamby@debian.org> for
+      repoducible builds
+      Closes: #792684
+  * debian/control:
+    - bumped Standards-Version to 3.9.6
+    - changed description for cain-examples and cain-solvers
+
+  [ Andreas Tille ]
+  * New upstream version
+  * Fixed watch file
+  * debian/copyright rewritten to match DEP5
+  * Moved packaging from SVN to Git
+  * Remove debian/menu
+
+ -- Andreas Tille <tille@debian.org>  Sat, 19 Dec 2015 07:22:11 +0100
+
 cain (1.9-8) unstable; urgency=medium
 
   * Moved debian/upstream to debian/upstream/metadata
diff -Nru cain-1.9/debian/control cain-1.10+dfsg/debian/control
--- cain-1.9/debian/control	2014-08-25 07:25:40.000000000 +0000
+++ cain-1.10+dfsg/debian/control	2015-12-19 06:22:41.000000000 +0000
@@ -9,9 +9,9 @@
                python (<< 3.0),
                libeigen3-dev,
                zip
-Standards-Version: 3.9.5
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/cain/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/cain/trunk/
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/cain.git
+Vcs-Git: git://anonscm.debian.org/debian-med/cain.git
 Homepage: http://cain.sourceforge.net
 
 Package: cain
@@ -54,7 +54,7 @@
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          libeigen3-dev
-Description: simulations of chemical reactions
+Description: solvers for cain
  Cain performs stochastic and deterministic simulations of chemical reactions.
  It can spawn multiple simulation processes to utilize multi-core computers.
  It stores models, methods, and simulation output (populations and reaction
@@ -81,7 +81,7 @@
 Depends: ${shlibs:Depends},
          ${misc:Depends},
          cain
-Description: simulations of chemical reactions
+Description: examples for cain
  Cain performs stochastic and deterministic simulations of chemical reactions.
  It can spawn multiple simulation processes to utilize multi-core computers.
  It stores models, methods, and simulation output (populations and reaction
diff -Nru cain-1.9/debian/copyright cain-1.10+dfsg/debian/copyright
--- cain-1.9/debian/copyright	2013-09-12 08:59:44.000000000 +0000
+++ cain-1.10+dfsg/debian/copyright	2015-12-19 06:22:41.000000000 +0000
@@ -1,28 +1,23 @@
-This work was packaged for Debian by:
-
-    Ivo Maintz <ivo@maintz.de> on Tue, 05 Oct 2010 14:31:33 +0200
-
-It was downloaded from:
-
-    http://cain.sourceforge.net
-
-Upstream Author:
-
-    Sean Mauch <sean@caltech.edu>
-
-Copyright:
-
-    <Copyright (C) 1999-2011, California Institute of Technology>
-
-License:
-
-
-    All rights reserved.
-
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: Cain
+Upstream-Contact: Sean Mauch <sean@caltech.edu>
+Source: http://sourceforge.net/projects/cain/files
+Files-Excluded: __MACOSX
+                */.DS_Store
+                */.sconsign.dblite
+                solvers
+                */*/third-party
+                */*/*.pyc
+                */*.d
+
+Files: *
+Copyright: 1999-2012, California Institute of Technology
+                      Sean Mauch <sean@caltech.edu>
+License: BSD-3-clause
     Redistribution and use in source and binary forms, with or without
     modification, are permitted provided that the following conditions
     are met:
-
+ .
     Redistributions of source code must retain the above copyright notice,
     this list of conditions and the following disclaimer.
     Redistributions in binary form must reproduce the above copyright notice,
@@ -31,7 +26,7 @@
     Neither the name of the California Institute of Technology nor the names
     of its contributors may be used to endorse or promote products derived
     from this software without specific prior written permission.
-    
+ .
     THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
     "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
     LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
@@ -44,10 +39,9 @@
     (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
     OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
-The Debian packaging is:
-
-    Copyright (C) 2010-2011 Ivo Maintz <ivo@maintz.de>
-
-and is licensed under the GPL version 3, see
-/usr/share/common-licenses/GPL-3
+Files: debian/*
+Copyright: 2010-2015 Ivo Maintz <ivo@maintz.de>
+           2015      Andreas Tille <tille@debian.org>
+License: GPL-3+
+ see /usr/share/common-licenses/GPL-3
 
diff -Nru cain-1.9/debian/menu cain-1.10+dfsg/debian/menu
--- cain-1.9/debian/menu	2013-09-12 08:59:44.000000000 +0000
+++ cain-1.10+dfsg/debian/menu	1970-01-01 00:00:00.000000000 +0000
@@ -1,2 +0,0 @@
-?package(cain):needs="X11" section="Applications/Science/Chemistry"\
-  title="cain" command="/usr/bin/cain"
diff -Nru cain-1.9/debian/patches/cain.patch cain-1.10+dfsg/debian/patches/cain.patch
--- cain-1.9/debian/patches/cain.patch	2013-09-12 08:59:44.000000000 +0000
+++ cain-1.10+dfsg/debian/patches/cain.patch	2015-12-19 06:22:41.000000000 +0000
@@ -6,8 +6,8 @@
 Author: Ivo Maintz <ivo@maintz.de>
 Date: Wed, 28 Sep 2011 12:02:11 +0200
 
---- cain-1.9.orig/Makefile
-+++ cain-1.9/Makefile
+--- a/Makefile
++++ b/Makefile
 @@ -2,7 +2,7 @@
  
  # By default make the solvers.
@@ -17,18 +17,9 @@
  
  again: 
  
-@@ -17,6 +17,8 @@
- 	rm -rf Cain.app/Contents/Resources/simulation
- 	rm -rf Cain.app/Contents/Resources/solvers
- 	rm -rf Cain.app/Contents/Resources/state
-+	rm -f solvers/*
-+	rm -f src/solvers/*.d
- 
- test:
- 	nosetests --with-doctest -v simulation state
---- cain-1.9.orig/gui/Application.py
-+++ cain-1.9/gui/Application.py
-@@ -7,6 +7,7 @@
+--- a/gui/Application.py
++++ b/gui/Application.py
+@@ -8,6 +8,7 @@ import os.path
  import wx
  from MainFrame import MainFrame
  from resourcePath import resourcePath
@@ -36,17 +27,8 @@
  
  class Application(wx.App):
      """The application class for Cain."""
-@@ -14,7 +15,7 @@
-     def __init__(self):
-         """Construct the base class and redirect the output."""
-         if not sys.platform in ('win32', 'win64'):
--            wx.App.__init__(self, redirect=True, filename="ErrorLog.txt")
-+            wx.App.__init__(self, redirect=True, filename=join(expanduser('~'),".cain","ErrorLog.txt"))
-         else:
-             # On windows we might not have write permission for the log file.
-             wx.App.__init__(self)
---- cain-1.9.orig/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h
-+++ cain-1.9/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h
+--- a/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h
++++ b/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h
 @@ -9,7 +9,7 @@
  #define __ads_indexedPriorityQueue_IndexedPriorityQueueBinaryHeap_h__
  
@@ -55,14 +37,14 @@
 +#include <stddef.h>
  #include <iostream>
  
- namespace ads {
---- cain-1.9.orig/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h
-+++ cain-1.9/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h
+ #include <cstddef>
+--- a/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h
++++ b/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h
 @@ -9,6 +9,7 @@
  #define __ads_indexedPriorityQueue_IndexedPriorityQueueBinaryHeapPair_h__
  
  #include "IndexedPriorityQueueBase.h"
 +#include <stddef.h>
  
- namespace ads {
+ #include <cstddef>
  
diff -Nru cain-1.9/debian/patches/eigen3.patch cain-1.10+dfsg/debian/patches/eigen3.patch
--- cain-1.9/debian/patches/eigen3.patch	2013-10-14 19:34:56.000000000 +0000
+++ cain-1.10+dfsg/debian/patches/eigen3.patch	2015-12-19 06:22:41.000000000 +0000
@@ -18,7 +18,7 @@
  
 --- a/src/stochastic/TauLeapingImplicit.ipp
 +++ b/src/stochastic/TauLeapingImplicit.ipp
-@@ -153,10 +153,10 @@
+@@ -153,10 +153,10 @@ stepEuler(const double tau) {
        //std::cout << "Jacobian =\n" << jacobian << '\n'
        //<< "f = \n" << f << '\n';
        Eigen::VectorXd delta(N);
diff -Nru cain-1.9/debian/patches/gcc-4.7.patch cain-1.10+dfsg/debian/patches/gcc-4.7.patch
--- cain-1.9/debian/patches/gcc-4.7.patch	2013-09-12 08:59:44.000000000 +0000
+++ cain-1.10+dfsg/debian/patches/gcc-4.7.patch	2015-12-19 06:22:41.000000000 +0000
@@ -2,9 +2,9 @@
 Date: Tue, 22 May 2012 00:23:34 +0000
 Description: Fix FTBFS issue when using gcc-4.7
 
---- cain-1.9.orig/src/stochastic/HistogramsAverageAps.h
-+++ cain-1.9/src/stochastic/HistogramsAverageAps.h
-@@ -159,7 +159,7 @@
+--- a/src/stochastic/HistogramsAverageAps.h
++++ b/src/stochastic/HistogramsAverageAps.h
+@@ -159,7 +159,7 @@ public:
              for (typename array::StaticArrayOfArrays<std::size_t>::const_iterator
                    i = _reactionInfluence.begin(reactionIndex);
                    i != _reactionInfluence.end(reactionIndex); ++i) {
diff -Nru cain-1.9/debian/patches/hardening.patch cain-1.10+dfsg/debian/patches/hardening.patch
--- cain-1.9/debian/patches/hardening.patch	2013-09-12 08:59:44.000000000 +0000
+++ cain-1.10+dfsg/debian/patches/hardening.patch	2015-12-19 06:22:41.000000000 +0000
@@ -2,9 +2,9 @@
 Author: Andreas Tille <tille@debian.org>
 Date: Tue, 22 May 2012 07:59:45 +0200
 
---- cain-1.9.orig/src/solvers/Makefile
-+++ cain-1.9/src/solvers/Makefile
-@@ -51,7 +51,7 @@
+--- a/src/solvers/Makefile
++++ b/src/solvers/Makefile
+@@ -55,7 +55,7 @@ again:
  # Implicit rules.
  
  .cc.d: 
diff -Nru cain-1.9/debian/patches/help.patch cain-1.10+dfsg/debian/patches/help.patch
--- cain-1.9/debian/patches/help.patch	2013-09-12 08:59:44.000000000 +0000
+++ cain-1.10+dfsg/debian/patches/help.patch	2015-12-19 06:22:41.000000000 +0000
@@ -8,8 +8,8 @@
 Bug-Ubuntu: https://bugs.launchpad.net/bugs/1032304
 Last-Update: Fri, 10 Aug 2012 11:40:11 +0200
 
---- cain-1.9.orig/help/UserSolvers.htm
-+++ cain-1.9/help/UserSolvers.htm
+--- a/help/UserSolvers.htm
++++ b/help/UserSolvers.htm
 @@ -221,14 +221,14 @@ The methods that require exponential dev
  	is generated by a linear search on the groups followed by selecting
  	a reaction within a group with the method of rejection.
diff -Nru cain-1.9/debian/README.Debian-source cain-1.10+dfsg/debian/README.Debian-source
--- cain-1.9/debian/README.Debian-source	2013-09-12 08:59:44.000000000 +0000
+++ cain-1.10+dfsg/debian/README.Debian-source	1970-01-01 00:00:00.000000000 +0000
@@ -1,15 +0,0 @@
-the source package have only .zip file format and a invalid version number
-
-unzip Cain-1_9.zip
-cd Cain
-# remove superfluous files and directories
-rm -rf ../__MACOSX
-find . -iname .DS_Store -exec rm -f {} +
-find . -iname .scons* -exec rm -f {} +
-# clean the solvers directory
-rm -f solvers/*
-# remove third-party files
-rm -rf src/third-party/*
-tar cvzf ../cain_1.9.orig.tar.gz .
-cd ..
-rm -rf Cain/
diff -Nru cain-1.9/debian/rules cain-1.10+dfsg/debian/rules
--- cain-1.9/debian/rules	2013-09-12 08:59:44.000000000 +0000
+++ cain-1.10+dfsg/debian/rules	2015-12-19 06:22:41.000000000 +0000
@@ -12,6 +12,14 @@
 %:
 	dh $@ --with python2
 
+override_dh_auto_clean:
+	dh_auto_clean
+	rm -rf solvers
+
+override_dh_auto_build:
+	mkdir solvers
+	dh_auto_build
+
 override_dh_install-indep:
 	dh_install
 	rm -rf debian/$(pkg)/usr/share/cain/help/* debian/$(pkg)/usr/share/cain/gui/help.htm*
@@ -23,19 +31,7 @@
 override_dh_auto_test:
 	echo "no tests implemented"
 
-override_dh_builddeb:
-	dh_builddeb -- -Z xz
-
 get-orig-source:
-	rm -rf $(SRC_TMP) && mkdir $(SRC_TMP)
-	#[ -f ../cain_$(VERSION).zip ] || wget -O ../cain_$(VERSION).zip http://sf.net/cain/Cain-$(UVERSION).zip # URL did not work
-	[ -f ../cain_$(VERSION).zip ] ||  wget -O ../cain_$(VERSION).zip http://qa.debian.org/watch/sf.php/cain/Cain-$(UVERSION).zip
-	cd $(SRC_TMP) && unzip ../../cain_$(VERSION).zip
-	mv $(SRC_TMP)/Cain $(SRC_TMP)/cain-$(VERSION)
-	find $(SRC_TMP) -name __MACOSX -type d | xargs -r rm -rf
-	find $(SRC_TMP) -iname .DS_Store -exec rm -f {} +
-	find $(SRC_TMP) -iname .scons* -exec rm -f {} +
-	rm -f $(SRC_TMP)/cain-$(VERSION)/solvers/*
-	rm -rf $(SRC_TMP)/cain-$(VERSION)/src/third-party/*
-	cd $(SRC_TMP) && tar cvzf ../../cain_$(VERSION).orig.tar.gz cain-$(VERSION)
-	rm -rf $(SRC_TMP)
+	uscan --verbose --force-download --repack --compression xz
+#	find $(SRC_TMP) -type f -exec chmod 644 {} +
+#	find $(SRC_TMP) -type d -exec chmod 755 {} +
diff -Nru cain-1.9/debian/watch cain-1.10+dfsg/debian/watch
--- cain-1.9/debian/watch	2013-09-12 08:59:44.000000000 +0000
+++ cain-1.10+dfsg/debian/watch	2015-12-19 06:22:41.000000000 +0000
@@ -1,3 +1,3 @@
 version=3
-opts="uversionmangle=s/_/./" \
-http://sf.net/cain/[cC]ain-(\d_\d).zip
+opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,uversionmangle=s/_/./" \
+  http://sf.net/cain/[cC]ain-(\d[\d\._]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip)
diff -Nru cain-1.9/fio/ContentHandler.py cain-1.10+dfsg/fio/ContentHandler.py
--- cain-1.9/fio/ContentHandler.py	2011-09-27 19:44:46.000000000 +0000
+++ cain-1.10+dfsg/fio/ContentHandler.py	2012-07-02 04:07:16.000000000 +0000
@@ -51,7 +51,7 @@
             if 'version' in attributes.keys():
                 self.version = float(attributes['version'])
             else:
-                self.version = 1.9
+                self.version = 1.10
         elif name == 'sbml':
             # Fatal error.
             raise Exception('This is an SBML file. One may only directly open Cain files. Use File->Import SBML instead.')
diff -Nru cain-1.9/gui/About.py cain-1.10+dfsg/gui/About.py
--- cain-1.9/gui/About.py	2011-09-27 19:44:45.000000000 +0000
+++ cain-1.10+dfsg/gui/About.py	2012-07-02 04:07:13.000000000 +0000
@@ -13,7 +13,7 @@
     Cain
     </h1>
     
-    <p>Version 1.9.</p>
+    <p>Version 1.10.</p>
 
     <p>
     Developed at 
diff -Nru cain-1.9/gui/Application.py cain-1.10+dfsg/gui/Application.py
--- cain-1.9/gui/Application.py	2011-09-27 19:44:45.000000000 +0000
+++ cain-1.10+dfsg/gui/Application.py	2012-07-02 04:07:13.000000000 +0000
@@ -3,6 +3,7 @@
 """The script that launches Cain."""
 
 import sys
+import os
 import os.path
 import wx
 from MainFrame import MainFrame
@@ -13,11 +14,17 @@
 
     def __init__(self):
         """Construct the base class and redirect the output."""
-        if not sys.platform in ('win32', 'win64'):
-            wx.App.__init__(self, redirect=True, filename="ErrorLog.txt")
-        else:
-            # On windows we might not have write permission for the log file.
-            wx.App.__init__(self)
+        directory = os.path.join(os.path.expanduser('~'), '.cain')
+        if not os.access(directory, os.W_OK):
+            try:
+                os.mkdir(directory)
+            except:
+                # If we can't get write permissions for the log file, don't
+                # redirect the output.
+                wx.App.__init__(self)
+                return
+        wx.App.__init__(self, redirect=True,
+                        filename=os.path.join(directory, "ErrorLog.txt"))
 
     def OnInit(self):
         # Splash screen.
diff -Nru cain-1.9/gui/GridRowEditor.py cain-1.10+dfsg/gui/GridRowEditor.py
--- cain-1.9/gui/GridRowEditor.py	2011-09-27 19:44:45.000000000 +0000
+++ cain-1.10+dfsg/gui/GridRowEditor.py	2012-07-02 04:07:13.000000000 +0000
@@ -172,6 +172,10 @@
         self.hideDetails()
 
     def getTableData(self):
+        # Save any values being edited in the grid.
+        if self.IsCellEditControlShown(): 
+            self.SaveEditControlValue() 
+            self.HideCellEditControl() 
         data = []
         for row in range(self.GetNumberRows()):
             rowData = []
diff -Nru cain-1.9/help/cain.hhc cain-1.10+dfsg/help/cain.hhc
--- cain-1.9/help/cain.hhc	2011-09-27 19:44:51.000000000 +0000
+++ cain-1.10+dfsg/help/cain.hhc	2012-07-02 04:07:22.000000000 +0000
@@ -38,12 +38,12 @@
           <param name="Local" value="InstallationRedHat-5.6.htm">
           </OBJECT>
       <LI><OBJECT type="text/sitemap">
-          <param name="Name" value="Fedora 15">
-          <param name="Local" value="InstallationFedora-15.htm">
+          <param name="Name" value="Fedora 16">
+          <param name="Local" value="InstallationFedora-16.htm">
           </OBJECT>
       <LI><OBJECT type="text/sitemap">
-          <param name="Name" value="Fedora 14">
-          <param name="Local" value="InstallationFedora.htm">
+          <param name="Name" value="Fedora 15">
+          <param name="Local" value="InstallationFedora-15.htm">
           </OBJECT>
       <LI><OBJECT type="text/sitemap">
           <param name="Name" value="Debian 6">
@@ -54,12 +54,12 @@
           <param name="Local" value="InstallationDebian.htm">
           </OBJECT>
       <LI><OBJECT type="text/sitemap">
-          <param name="Name" value="Ubuntu 11">
-          <param name="Local" value="InstallationUbuntu-11.htm">
+          <param name="Name" value="Ubuntu 12">
+          <param name="Local" value="InstallationUbuntu-12.htm">
           </OBJECT>
       <LI><OBJECT type="text/sitemap">
-          <param name="Name" value="Ubuntu 10">
-          <param name="Local" value="InstallationUbuntu-10.htm">
+          <param name="Name" value="Ubuntu 11">
+          <param name="Local" value="InstallationUbuntu-11.htm">
           </OBJECT>
     </UL>
   </UL>
diff -Nru cain-1.9/help/cain.hhp cain-1.10+dfsg/help/cain.hhp
--- cain-1.9/help/cain.hhp	2011-09-27 19:44:51.000000000 +0000
+++ cain-1.10+dfsg/help/cain.hhp	2012-07-02 04:07:22.000000000 +0000
@@ -20,12 +20,12 @@
 InstallationLinux.htm
 InstallationRedHat-6.0.htm
 InstallationRedHat-5.6.htm
+InstallationFedora-16.htm
 InstallationFedora-15.htm
-InstallationFedora.htm
 InstallationDebian-6.htm
 InstallationDebian.htm
+InstallationUbuntu-12.htm
 InstallationUbuntu-11.htm
-InstallationUbuntu-10.htm
 User.htm
 UserQuick.htm
 UserModel.htm
Binary files /tmp/tmpowQPTK/Alr96NWhxb/cain-1.9/help/cain.htb and /tmp/tmpowQPTK/MhUGwm3H4P/cain-1.10+dfsg/help/cain.htb differ
Binary files /tmp/tmpowQPTK/Alr96NWhxb/cain-1.9/help/cain.wxh and /tmp/tmpowQPTK/MhUGwm3H4P/cain-1.10+dfsg/help/cain.wxh differ
Binary files /tmp/tmpowQPTK/Alr96NWhxb/cain-1.9/help/cain.wxh.bak and /tmp/tmpowQPTK/MhUGwm3H4P/cain-1.10+dfsg/help/cain.wxh.bak differ
diff -Nru cain-1.9/help/Faq.htd cain-1.10+dfsg/help/Faq.htd
--- cain-1.9/help/Faq.htd	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/Faq.htd	2012-07-02 04:07:25.000000000 +0000
@@ -23,8 +23,10 @@
 <p>
 <b>I found an error. What should I do?</b><br>
 Don't panic! Send an email to <img src="seanEmail.png">.  Please include
-any relevant data files and a description of what causes the problem. If
-Cain wrote a file called <tt>ErrorLog.txt</tt>, include that as well.
+any relevant data files and a description of what causes the problem.
+Check the <tt>.cain</tt> directory in your home directory. 
+If Cain wrote a file called <tt>ErrorLog.txt</tt> there,
+include that as well.
 </p>
 
 <p>
diff -Nru cain-1.9/help/Faq.htm cain-1.10+dfsg/help/Faq.htm
--- cain-1.9/help/Faq.htm	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/Faq.htm	2012-07-02 04:07:25.000000000 +0000
@@ -24,8 +24,10 @@
 <p>
 <b>I found an error. What should I do?</b><br>
 Don't panic! Send an email to <img src="seanEmail.png">.  Please include
-any relevant data files and a description of what causes the problem. If
-Cain wrote a file called <tt>ErrorLog.txt</tt>, include that as well.
+any relevant data files and a description of what causes the problem.
+Check the <tt>.cain</tt> directory in your home directory. 
+If Cain wrote a file called <tt>ErrorLog.txt</tt> there,
+include that as well.
 </p>
 
 <p>
diff -Nru cain-1.9/help/index.html cain-1.10+dfsg/help/index.html
--- cain-1.9/help/index.html	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/index.html	2012-07-02 04:07:25.000000000 +0000
@@ -18,13 +18,13 @@
     <ul>
       <li> <a href="InstallationRedHat-6.0.htm">RedHat/CentOS 6.0</a>
       <li> <a href="InstallationRedHat-5.6.htm">RedHat/CentOS 5.6</a>
+      <li> <a href="InstallationFedora-16.htm">Fedora 16</a>
       <li> <a href="InstallationFedora-15.htm">Fedora 15</a>
-      <li> <a href="InstallationFedora.htm">Fedora 14</a>
       <li> <a href="InstallationDebian-6.htm">Debian 6</a>
       <li> <a href="InstallationDebian.htm">Debian 5</a>
+      <li> <a href="InstallationUbuntu-12.htm">Ubuntu 12</a>
       <li> <a href="InstallationUbuntu-11.htm">Ubuntu 11</a>
-      <li> <a href="InstallationUbuntu-10.htm">Ubuntu 10</a>
- </ul>
+    </ul>
   </ul>
   <li> <a href="User.htm">User's Guide</a>
   <ul>
diff -Nru cain-1.9/help/InstallationFedora-16.htd cain-1.10+dfsg/help/InstallationFedora-16.htd
--- cain-1.9/help/InstallationFedora-16.htd	1970-01-01 00:00:00.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationFedora-16.htd	2012-07-02 04:07:25.000000000 +0000
@@ -0,0 +1,37 @@
+<html>
+<head>
+<title>Installation on Fedora 16</title>
+</head>
+<body>
+<h1>Installation on Fedora 16</h1>
+
+<!--
+Follow the instructions in the User Manual.
+Install the kernel development packages.
+Reboot.
+cd /media/VBOX...
+su
+sh ./VBoxLinuxAdditions-x86.run
+Building the kernel modules fails.
+-->
+
+
+<p>
+Select System&rarr;Administration&rarr;Add/Remove Software. Install the following packages:
+<ul>
+  <li> gcc-c++: C++ support for GCC.
+  <li> wxPython: GUI toolkit for the Python programming language.
+  <li> python-matplotlib: Python plotting library.
+  <li> python-matplotlib-wx: wxPython backend for python-matplotlib.
+  <li> Scipy: Scientific Tools for Python
+  <li> sympy: A Python library for symbolic mathematics.
+  <!--
+  <li> python-matplotlib-tk: Tk backend for python-matplotlib.
+  -->
+</ul>
+Then follow the <a href="InstallationLinux.htm">installation instructions</a>
+to compile the solvers and launch the application.
+</p>
+
+</body>
+</html>
\ No newline at end of file
diff -Nru cain-1.9/help/InstallationFedora-16.htm cain-1.10+dfsg/help/InstallationFedora-16.htm
--- cain-1.9/help/InstallationFedora-16.htm	1970-01-01 00:00:00.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationFedora-16.htm	2012-07-02 04:07:25.000000000 +0000
@@ -0,0 +1,38 @@
+
+<html>
+<head>
+<title>Installation on Fedora 16</title>
+</head>
+<body>
+<h1>Installation on Fedora 16</h1>
+
+<!--
+Follow the instructions in the User Manual.
+Install the kernel development packages.
+Reboot.
+cd /media/VBOX...
+su
+sh ./VBoxLinuxAdditions-x86.run
+Building the kernel modules fails.
+-->
+
+
+<p>
+Select System&rarr;Administration&rarr;Add/Remove Software. Install the following packages:
+<ul>
+  <li> gcc-c++: C++ support for GCC.
+  <li> wxPython: GUI toolkit for the Python programming language.
+  <li> python-matplotlib: Python plotting library.
+  <li> python-matplotlib-wx: wxPython backend for python-matplotlib.
+  <li> Scipy: Scientific Tools for Python
+  <li> sympy: A Python library for symbolic mathematics.
+  <!--
+  <li> python-matplotlib-tk: Tk backend for python-matplotlib.
+  -->
+</ul>
+Then follow the <a href="InstallationLinux.htm">installation instructions</a>
+to compile the solvers and launch the application.
+</p>
+
+</body>
+</html>
\ No newline at end of file
diff -Nru cain-1.9/help/InstallationFedora.htd cain-1.10+dfsg/help/InstallationFedora.htd
--- cain-1.9/help/InstallationFedora.htd	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationFedora.htd	1970-01-01 00:00:00.000000000 +0000
@@ -1,36 +0,0 @@
-<html>
-<head>
-<title>Installation on Fedora 14</title>
-</head>
-<body>
-<h1>Installation on Fedora 14</h1>
-
-<!--
-Follow the instructions in the User Manual.
-Install the kernel development packages.
-Reboot.
-cd /media/VBOX...
-su
-sh ./VBoxLinuxAdditions-x86.run
-Building the kernel modules fails.
--->
-
-
-<p>
-Select System&rarr;Administration&rarr;Add/Remove Software. Install the following packages:
-<ul>
-  <li> gcc-c++: C++ support for GCC.
-  <li> wxPython: GUI toolkit for the Python programming language.
-  <li> python-matplotlib: Python plotting library.
-  <li> Scipy: Scientific Tools for Python
-  <li> sympy: A Python library for symbolic mathematics.
-  <!--
-  <li> python-matplotlib-tk: Tk backend for python-matplotlib.
-  -->
-</ul>
-Then follow the <a href="InstallationLinux.htm">installation instructions</a>
-to compile the solvers and launch the application.
-</p>
-
-</body>
-</html>
\ No newline at end of file
diff -Nru cain-1.9/help/InstallationFedora.htm cain-1.10+dfsg/help/InstallationFedora.htm
--- cain-1.9/help/InstallationFedora.htm	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationFedora.htm	1970-01-01 00:00:00.000000000 +0000
@@ -1,37 +0,0 @@
-
-<html>
-<head>
-<title>Installation on Fedora 14</title>
-</head>
-<body>
-<h1>Installation on Fedora 14</h1>
-
-<!--
-Follow the instructions in the User Manual.
-Install the kernel development packages.
-Reboot.
-cd /media/VBOX...
-su
-sh ./VBoxLinuxAdditions-x86.run
-Building the kernel modules fails.
--->
-
-
-<p>
-Select System&rarr;Administration&rarr;Add/Remove Software. Install the following packages:
-<ul>
-  <li> gcc-c++: C++ support for GCC.
-  <li> wxPython: GUI toolkit for the Python programming language.
-  <li> python-matplotlib: Python plotting library.
-  <li> Scipy: Scientific Tools for Python
-  <li> sympy: A Python library for symbolic mathematics.
-  <!--
-  <li> python-matplotlib-tk: Tk backend for python-matplotlib.
-  -->
-</ul>
-Then follow the <a href="InstallationLinux.htm">installation instructions</a>
-to compile the solvers and launch the application.
-</p>
-
-</body>
-</html>
\ No newline at end of file
diff -Nru cain-1.9/help/InstallationLinux.htd cain-1.10+dfsg/help/InstallationLinux.htd
--- cain-1.9/help/InstallationLinux.htd	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationLinux.htd	2012-07-02 04:07:25.000000000 +0000
@@ -9,6 +9,13 @@
 <!--OS X as the host. Use the 32-bit versions instead.-->
 
 <p>
+On Ubuntu, you may simply search for cain in the Software Center
+application, and then install it. Of course, you can also get the source
+distribution from <a href="http://cain.sourceforge.net/">sourceforge</a>
+and follow the instruction below.
+</p>
+
+<p>
 For Linux or Unix, use the platform-independent distribution. You will
 need appropriate versions of
 <a href="http://www.python.org/">Python</a>,
@@ -29,8 +36,8 @@
   Debian <a href="InstallationDebian-6.htm">6</a> and
   <a href="InstallationDebian.htm">5</a>
   <li>
-  Ubuntu <a href="InstallationUbuntu-11.htm">11</a> and
-  <a href="InstallationUbuntu-10.htm">10</a>
+  Ubuntu <a href="InstallationUbuntu-12.htm">12</a> and
+  <a href="InstallationUbuntu-11.htm">11</a>
 </ul>
 I recommend using
 the current version of <a href="http://gcc.gnu.org/">GNU GCC</a>.
@@ -42,7 +49,7 @@
 <p>
 Download the platform-independent distribution and place it in a convenient
 location. Then uncompress the zip file.<br>
-<tt>unzip Cain-1.9.zip</tt><br>
+<tt>unzip Cain-1_10.zip</tt><br>
 Build the mass action solvers.<br>
 <tt>cd Cain</tt><br>
 <tt>make</tt><br>
diff -Nru cain-1.9/help/InstallationLinux.htm cain-1.10+dfsg/help/InstallationLinux.htm
--- cain-1.9/help/InstallationLinux.htm	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationLinux.htm	2012-07-02 04:07:25.000000000 +0000
@@ -10,6 +10,13 @@
 <!--OS X as the host. Use the 32-bit versions instead.-->
 
 <p>
+On Ubuntu, you may simply search for cain in the Software Center
+application, and then install it. Of course, you can also get the source
+distribution from <a href="http://cain.sourceforge.net/">sourceforge</a>
+and follow the instruction below.
+</p>
+
+<p>
 For Linux or Unix, use the platform-independent distribution. You will
 need appropriate versions of
 <a href="http://www.python.org/">Python</a>,
@@ -30,8 +37,8 @@
   Debian <a href="InstallationDebian-6.htm">6</a> and
   <a href="InstallationDebian.htm">5</a>
   <li>
-  Ubuntu <a href="InstallationUbuntu-11.htm">11</a> and
-  <a href="InstallationUbuntu-10.htm">10</a>
+  Ubuntu <a href="InstallationUbuntu-12.htm">12</a> and
+  <a href="InstallationUbuntu-11.htm">11</a>
 </ul>
 I recommend using
 the current version of <a href="http://gcc.gnu.org/">GNU GCC</a>.
@@ -43,7 +50,7 @@
 <p>
 Download the platform-independent distribution and place it in a convenient
 location. Then uncompress the zip file.<br>
-<tt>unzip Cain-1.9.zip</tt><br>
+<tt>unzip Cain-1_10.zip</tt><br>
 Build the mass action solvers.<br>
 <tt>cd Cain</tt><br>
 <tt>make</tt><br>
diff -Nru cain-1.9/help/InstallationMac.htd cain-1.10+dfsg/help/InstallationMac.htd
--- cain-1.9/help/InstallationMac.htd	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationMac.htd	2012-07-02 04:07:25.000000000 +0000
@@ -16,14 +16,13 @@
 
 
 <p>
-<b>Leopard.</b>
 To use Cain you will need 
 <a href="http://www.python.org/">Python</a>,
 <a href="http://www.wxpython.org/">wxPython</a>,
 <a href="http://numpy.scipy.org/">numpy</a>,
 <a href="http://matplotlib.sourceforge.net/">matplotlib</a>, and
 <a href="http://sympy.org/">sympy</a>.
-Unfortunately, Leopard (10.5) comes with rather old versions of the first
+Unfortunately, Mac OS X comes with rather old versions of the first
 three and does not have matplotlib or SymPy.
 There are several ways of obtaining the
 necessary software to run Cain. The easiest solution is to install the
@@ -33,19 +32,6 @@
 </p>
 
 <p>
-<b>Lion or Snow Leopard.</b>
-There is a complication with using the system version of Python.
-The default version of Python is a 64-bit
-application and the wxPython libraries will only work with the 32-bit
-version. The easiest solution is to install the Enthought Python
-Distribution. Otherwise you can either install a 32-bit version of
-Python from the <a href="http://www.python.org/">Python web site</a>,
-or you can configure the system version of Python to run in 32-bit
-mode. For instructions on the latter search for
-&quot;wxpython snow leopard.&quot;
-</p>
-
-<p>
 <b>Enthought Python Distribution.</b>
 As mentioned above the easiest way to get appropriate versions of
 python and the required packages is to 
@@ -78,6 +64,19 @@
 </p>
 
 <p>
+<b>Lion or Snow Leopard.</b>
+There is a complication with using the system version of Python.
+The default version of Python is a 64-bit
+application and the wxPython libraries will only work with the 32-bit
+version. The easiest solution is to install the Enthought Python
+Distribution. Otherwise you can either install a 32-bit version of
+Python from the <a href="http://www.python.org/">Python web site</a>,
+or you can configure the system version of Python to run in 32-bit
+mode. For instructions on the latter search for
+&quot;wxpython snow leopard.&quot;
+</p>
+
+<p>
 <b>C++ compiler.</b>
 In order to compile custom executables (either for kinetic laws that are
 not mass-action or to speed up simulations that use mass-action kinetics)
diff -Nru cain-1.9/help/InstallationMac.htm cain-1.10+dfsg/help/InstallationMac.htm
--- cain-1.9/help/InstallationMac.htm	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationMac.htm	2012-07-02 04:07:25.000000000 +0000
@@ -17,14 +17,13 @@
 
 
 <p>
-<b>Leopard.</b>
 To use Cain you will need 
 <a href="http://www.python.org/">Python</a>,
 <a href="http://www.wxpython.org/">wxPython</a>,
 <a href="http://numpy.scipy.org/">numpy</a>,
 <a href="http://matplotlib.sourceforge.net/">matplotlib</a>, and
 <a href="http://sympy.org/">sympy</a>.
-Unfortunately, Leopard (10.5) comes with rather old versions of the first
+Unfortunately, Mac OS X comes with rather old versions of the first
 three and does not have matplotlib or SymPy.
 There are several ways of obtaining the
 necessary software to run Cain. The easiest solution is to install the
@@ -34,19 +33,6 @@
 </p>
 
 <p>
-<b>Lion or Snow Leopard.</b>
-There is a complication with using the system version of Python.
-The default version of Python is a 64-bit
-application and the wxPython libraries will only work with the 32-bit
-version. The easiest solution is to install the Enthought Python
-Distribution. Otherwise you can either install a 32-bit version of
-Python from the <a href="http://www.python.org/">Python web site</a>,
-or you can configure the system version of Python to run in 32-bit
-mode. For instructions on the latter search for
-&quot;wxpython snow leopard.&quot;
-</p>
-
-<p>
 <b>Enthought Python Distribution.</b>
 As mentioned above the easiest way to get appropriate versions of
 python and the required packages is to 
@@ -79,6 +65,19 @@
 </p>
 
 <p>
+<b>Lion or Snow Leopard.</b>
+There is a complication with using the system version of Python.
+The default version of Python is a 64-bit
+application and the wxPython libraries will only work with the 32-bit
+version. The easiest solution is to install the Enthought Python
+Distribution. Otherwise you can either install a 32-bit version of
+Python from the <a href="http://www.python.org/">Python web site</a>,
+or you can configure the system version of Python to run in 32-bit
+mode. For instructions on the latter search for
+&quot;wxpython snow leopard.&quot;
+</p>
+
+<p>
 <b>C++ compiler.</b>
 In order to compile custom executables (either for kinetic laws that are
 not mass-action or to speed up simulations that use mass-action kinetics)
diff -Nru cain-1.9/help/InstallationUbuntu-10.htd cain-1.10+dfsg/help/InstallationUbuntu-10.htd
--- cain-1.9/help/InstallationUbuntu-10.htd	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationUbuntu-10.htd	1970-01-01 00:00:00.000000000 +0000
@@ -1,30 +0,0 @@
-<html>
-<head>
-<title>Installation on Ubuntu 10</title>
-</head>
-<body>
-<h1>Installation on Ubuntu 10</h1>
-
-<!--
-Update packages with Update Manager.
-sudo apt-get install dkms
-cd /media/VBOX...
-sudo sh ./VBoxLinuxAdditions-x86.run
--->
-
-<p>
-Select Applications&rarr;Ubuntu Software Center.
-<ul>
-  <li> g++: The GNU C++ compiler.
-  <li> python-wxversion: wxWidgets cross-platform C++ GUI toolkit.
-  <li> python-matplotlib: Python based plotting system in style
-  similar to Matlab.
-  <li> python-scipy: Scientific Tools for Python.
-  <li> python-sympy: Computer Algebra System (CAS) in Python.
-</ul>
-Then follow the <a href="InstallationLinux.htm">installation instructions</a>
-to compile the solvers and launch the application.
-</p>
-
-</body>
-</html>
diff -Nru cain-1.9/help/InstallationUbuntu-10.htm cain-1.10+dfsg/help/InstallationUbuntu-10.htm
--- cain-1.9/help/InstallationUbuntu-10.htm	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationUbuntu-10.htm	1970-01-01 00:00:00.000000000 +0000
@@ -1,31 +0,0 @@
-
-<html>
-<head>
-<title>Installation on Ubuntu 10</title>
-</head>
-<body>
-<h1>Installation on Ubuntu 10</h1>
-
-<!--
-Update packages with Update Manager.
-sudo apt-get install dkms
-cd /media/VBOX...
-sudo sh ./VBoxLinuxAdditions-x86.run
--->
-
-<p>
-Select Applications&rarr;Ubuntu Software Center.
-<ul>
-  <li> g++: The GNU C++ compiler.
-  <li> python-wxversion: wxWidgets cross-platform C++ GUI toolkit.
-  <li> python-matplotlib: Python based plotting system in style
-  similar to Matlab.
-  <li> python-scipy: Scientific Tools for Python.
-  <li> python-sympy: Computer Algebra System (CAS) in Python.
-</ul>
-Then follow the <a href="InstallationLinux.htm">installation instructions</a>
-to compile the solvers and launch the application.
-</p>
-
-</body>
-</html>
diff -Nru cain-1.9/help/InstallationUbuntu-11.htd cain-1.10+dfsg/help/InstallationUbuntu-11.htd
--- cain-1.9/help/InstallationUbuntu-11.htd	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationUbuntu-11.htd	2012-07-02 04:07:25.000000000 +0000
@@ -15,6 +15,12 @@
 -->
 
 <p>
+The easy way to install is to search for cain in the Software Center
+application, and then install it. Use the instructions below if
+you are installing from the source distribution.
+</p>
+
+<p>
 Select Applications&rarr;Ubuntu Software Center and install the
 following packages.
 <ul>
diff -Nru cain-1.9/help/InstallationUbuntu-11.htm cain-1.10+dfsg/help/InstallationUbuntu-11.htm
--- cain-1.9/help/InstallationUbuntu-11.htm	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationUbuntu-11.htm	2012-07-02 04:07:25.000000000 +0000
@@ -16,6 +16,12 @@
 -->
 
 <p>
+The easy way to install is to search for cain in the Software Center
+application, and then install it. Use the instructions below if
+you are installing from the source distribution.
+</p>
+
+<p>
 Select Applications&rarr;Ubuntu Software Center and install the
 following packages.
 <ul>
diff -Nru cain-1.9/help/InstallationUbuntu-12.htd cain-1.10+dfsg/help/InstallationUbuntu-12.htd
--- cain-1.9/help/InstallationUbuntu-12.htd	1970-01-01 00:00:00.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationUbuntu-12.htd	2012-07-02 04:07:25.000000000 +0000
@@ -0,0 +1,39 @@
+<html>
+<head>
+<title>Installation on Ubuntu 12</title>
+</head>
+<body>
+<h1>Installation on Ubuntu 12</h1>
+
+<!--
+Use 1024 MB of RAM and a 16 GB hard drive.
+Update packages with Update Manager.
+Install dkms in the software manager.
+sudo apt-get install dkms
+cd /media/VBOX...
+sudo sh ./VBoxLinuxAdditions-x86.run
+-->
+
+<p>
+The easy way to install is to search for cain in the Software Center
+application, and then install it. Use the instructions below if
+you are installing from the source distribution.
+</p>
+
+<p>
+Select Applications&rarr;Ubuntu Software Center and install the
+following packages.
+<ul>
+  <li> g++: The GNU C++ compiler.
+  <li> python-wxversion: wxWidgets cross-platform C++ GUI toolkit.
+  <li> python-matplotlib: Python based plotting system in style
+  similar to Matlab.
+  <li> python-scipy: Scientific Tools for Python.
+  <li> python-sympy: Computer Algebra System (CAS) in Python.
+</ul>
+Then follow the <a href="InstallationLinux.htm">installation instructions</a>
+to compile the solvers and launch the application.
+</p>
+
+</body>
+</html>
diff -Nru cain-1.9/help/InstallationUbuntu-12.htm cain-1.10+dfsg/help/InstallationUbuntu-12.htm
--- cain-1.9/help/InstallationUbuntu-12.htm	1970-01-01 00:00:00.000000000 +0000
+++ cain-1.10+dfsg/help/InstallationUbuntu-12.htm	2012-07-02 04:07:25.000000000 +0000
@@ -0,0 +1,40 @@
+
+<html>
+<head>
+<title>Installation on Ubuntu 12</title>
+</head>
+<body>
+<h1>Installation on Ubuntu 12</h1>
+
+<!--
+Use 1024 MB of RAM and a 16 GB hard drive.
+Update packages with Update Manager.
+Install dkms in the software manager.
+sudo apt-get install dkms
+cd /media/VBOX...
+sudo sh ./VBoxLinuxAdditions-x86.run
+-->
+
+<p>
+The easy way to install is to search for cain in the Software Center
+application, and then install it. Use the instructions below if
+you are installing from the source distribution.
+</p>
+
+<p>
+Select Applications&rarr;Ubuntu Software Center and install the
+following packages.
+<ul>
+  <li> g++: The GNU C++ compiler.
+  <li> python-wxversion: wxWidgets cross-platform C++ GUI toolkit.
+  <li> python-matplotlib: Python based plotting system in style
+  similar to Matlab.
+  <li> python-scipy: Scientific Tools for Python.
+  <li> python-sympy: Computer Algebra System (CAS) in Python.
+</ul>
+Then follow the <a href="InstallationLinux.htm">installation instructions</a>
+to compile the solvers and launch the application.
+</p>
+
+</body>
+</html>
diff -Nru cain-1.9/help/License.htd cain-1.10+dfsg/help/License.htd
--- cain-1.9/help/License.htd	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/License.htd	2012-07-02 04:07:25.000000000 +0000
@@ -6,7 +6,7 @@
 <h1><a name="License">License</a></h1>
 
 <p>
-Copyright (c) 1999-2011, California Institute of Technology
+Copyright (c) 1999 to the present, California Institute of Technology
 </p>
 
 <p>
diff -Nru cain-1.9/help/License.htm cain-1.10+dfsg/help/License.htm
--- cain-1.9/help/License.htm	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/License.htm	2012-07-02 04:07:25.000000000 +0000
@@ -7,7 +7,7 @@
 <h1><a name="License">License</a></h1>
 
 <p>
-Copyright (c) 1999-2011, California Institute of Technology
+Copyright (c) 1999 to the present, California Institute of Technology
 </p>
 
 <p>
diff -Nru cain-1.9/help/Links.htd cain-1.10+dfsg/help/Links.htd
--- cain-1.9/help/Links.htd	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/Links.htd	2012-07-02 04:07:25.000000000 +0000
@@ -25,7 +25,11 @@
   provides software and test models at his web site.
   <li>
   <a href="http://dsmts.googlecode.com/">DSMTS</a>
-  (Discrete Stochastic Models Test Suite) is a test suite in SBML format.
+  (Discrete Stochastic Models Test Suite) is a test suite in SBML
+  format.
+  <li>
+  <a href="http://www.sbos.eu/">SB.OS</a> is a live DVD based on
+  Ubuntu Linux that comes with a comprehensive list of Systems Biology Software.
   <li>
   <a href="http://magnet.systemsbiology.net/software/Dizzy/">Dizzy</a>
   is a chemical kinetics stochastic simulation software package written in
diff -Nru cain-1.9/help/Links.htm cain-1.10+dfsg/help/Links.htm
--- cain-1.9/help/Links.htm	2011-09-27 19:44:52.000000000 +0000
+++ cain-1.10+dfsg/help/Links.htm	2012-07-02 04:07:25.000000000 +0000
@@ -26,7 +26,11 @@
   provides software and test models at his web site.
   <li>
   <a href="http://dsmts.googlecode.com/">DSMTS</a>
-  (Discrete Stochastic Models Test Suite) is a test suite in SBML format.
+  (Discrete Stochastic Models Test Suite) is a test suite in SBML
+  format.
+  <li>
+  <a href="http://www.sbos.eu/">SB.OS</a> is a live DVD based on
+  Ubuntu Linux that comes with a comprehensive list of Systems Biology Software.
   <li>
   <a href="http://magnet.systemsbiology.net/software/Dizzy/">Dizzy</a>
   is a chemical kinetics stochastic simulation software package written in
diff -Nru cain-1.9/help/Welcome.htd cain-1.10+dfsg/help/Welcome.htd
--- cain-1.9/help/Welcome.htd	2011-09-27 19:44:54.000000000 +0000
+++ cain-1.10+dfsg/help/Welcome.htd	2012-07-02 04:07:28.000000000 +0000
@@ -9,7 +9,7 @@
 <h1>Welcome</h1>
 
 <p>
-This is version 1.9 of Cain, developed by Sean Mauch,
+This is version 1.10 of Cain, developed by Sean Mauch,
 <img src="seanEmail.png">, at the <a href="http://www.cacr.caltech.edu/">
 Center for Advanced Computing Research</a>, at the 
 <a href="http://www.caltech.edu/">California Institute of Technology</a>.
diff -Nru cain-1.9/help/Welcome.htm cain-1.10+dfsg/help/Welcome.htm
--- cain-1.9/help/Welcome.htm	2011-09-27 19:44:54.000000000 +0000
+++ cain-1.10+dfsg/help/Welcome.htm	2012-07-02 04:07:28.000000000 +0000
@@ -10,7 +10,7 @@
 <h1>Welcome</h1>
 
 <p>
-This is version 1.9 of Cain, developed by Sean Mauch,
+This is version 1.10 of Cain, developed by Sean Mauch,
 <img src="seanEmail.png">, at the <a href="http://www.cacr.caltech.edu/">
 Center for Advanced Computing Research</a>, at the 
 <a href="http://www.caltech.edu/">California Institute of Technology</a>.
diff -Nru cain-1.9/Makefile cain-1.10+dfsg/Makefile
--- cain-1.9/Makefile	2011-09-27 19:44:45.000000000 +0000
+++ cain-1.10+dfsg/Makefile	2012-07-02 04:07:13.000000000 +0000
@@ -17,6 +17,8 @@
 	rm -rf Cain.app/Contents/Resources/simulation
 	rm -rf Cain.app/Contents/Resources/solvers
 	rm -rf Cain.app/Contents/Resources/state
+	rm -f solvers/*
+	rm -f src/solvers/*.d
 
 test:
 	nosetests --with-doctest -v simulation state
diff -Nru cain-1.9/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h cain-1.10+dfsg/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h
--- cain-1.9/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeap.h	2012-07-02 04:07:29.000000000 +0000
@@ -12,6 +12,8 @@
 
 #include <iostream>
 
+#include <cstddef>
+
 namespace ads {
 
 //! Indexed priority queue that partitions the active and inactive elements.
diff -Nru cain-1.9/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h cain-1.10+dfsg/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h
--- cain-1.9/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/ads/indexedPriorityQueue/IndexedPriorityQueueBinaryHeapPair.h	2012-07-02 04:07:29.000000000 +0000
@@ -10,6 +10,8 @@
 
 #include "IndexedPriorityQueueBase.h"
 
+#include <cstddef>
+
 namespace ads {
 
 //! Indexed priority queue that partitions the active and inactive elements.
diff -Nru cain-1.9/src/ads/timer/Timer.h cain-1.10+dfsg/src/ads/timer/Timer.h
--- cain-1.9/src/ads/timer/Timer.h	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/ads/timer/Timer.h	2012-07-02 04:07:30.000000000 +0000
@@ -35,10 +35,10 @@
   \code
   Timer timer;
   for (std::size_t i = 0; i != 100; ++i) {
-     timer.start();
-     // Code to time.
-     ...
-     timer.stop();
+  timer.start();
+  // Code to time.
+  ...
+  timer.stop();
   }
   std::cout << "Elapsed time = " << timer << " seconds.\n";
 
@@ -64,6 +64,9 @@
    uint64_t _start;
    uint64_t _elapsed;
    mach_timebase_info_data_t _timeBaseInfo;
+#elif defined __linux__
+   timespec _start;
+   timespec _elapsed;
 #else
    clock_t _start;
    clock_t _elapsed;
diff -Nru cain-1.9/src/ads/timer/Timer.ipp cain-1.10+dfsg/src/ads/timer/Timer.ipp
--- cain-1.9/src/ads/timer/Timer.ipp	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/ads/timer/Timer.ipp	2012-07-02 04:07:30.000000000 +0000
@@ -52,6 +52,80 @@
    return 1e-9 *(_elapsed * _timeBaseInfo.numer / _timeBaseInfo.denom);
 }
 
+#elif defined __linux__
+// stolen from
+// http://www.guyrutenberg.com/2007/09/22/profiling-code-using-clock_gettime/
+timespec diff(timespec start, timespec end) {
+   //printf("diff called on \nend   = (%3ld, %10ld)\nstart = (%3ld, %10ld)\n",
+   //end.tv_sec, end.tv_nsec, start.tv_sec, start.tv_nsec);
+   timespec temp;
+   if ((end.tv_nsec-start.tv_nsec)<0) {
+      temp.tv_sec = end.tv_sec-start.tv_sec-1;
+      temp.tv_nsec = 1000000000+end.tv_nsec-start.tv_nsec;
+   }
+   else {
+      temp.tv_sec = end.tv_sec-start.tv_sec;
+      temp.tv_nsec = end.tv_nsec-start.tv_nsec;
+   }
+   return temp;
+}
+
+inline
+Timer::
+Timer() :
+   // Initialize with an invalid start time.
+   _start(),
+   _elapsed() {
+   _start.tv_sec = std::numeric_limits<time_t>::max();
+   _start.tv_nsec = std::numeric_limits<long>::max();
+   _elapsed.tv_sec = 0;
+   _elapsed.tv_nsec = 0;
+}
+
+inline
+void
+Timer::
+start() {
+   clock_gettime(CLOCK_REALTIME, &_start);
+}
+
+inline
+void
+Timer::
+stop() {
+#ifdef DEBUG_stlib
+   // Check that the clock was started.
+   assert(_start.tv_sec != std::numeric_limits<time_t>::max() &&
+          _start.tv_nsec != std::numeric_limits<long>::max());
+#endif
+   timespec temp;
+   clock_gettime(CLOCK_REALTIME, &temp);
+   temp = diff(_start, temp);
+   _elapsed.tv_sec += temp.tv_sec;
+   _elapsed.tv_nsec += temp.tv_nsec;
+   if (_elapsed.tv_nsec > 1000000000) {
+      _elapsed.tv_sec++;
+      _elapsed.tv_nsec -= 1000000000;
+   }
+}
+
+inline
+void
+Timer::
+reset() {
+   _start.tv_sec = std::numeric_limits<time_t>::max();
+   _start.tv_nsec = std::numeric_limits<long>::max();
+   _elapsed.tv_sec = 0;
+   _elapsed.tv_nsec = 0;
+}
+
+inline
+Timer::
+operator double() const {
+   return double(_elapsed.tv_sec + _elapsed.tv_nsec / 1e9);
+}
+
+
 #else
 //----------------------------------------------------------------------------
 
diff -Nru cain-1.9/src/ads/utility/ParseOptionsArguments.h cain-1.10+dfsg/src/ads/utility/ParseOptionsArguments.h
--- cain-1.9/src/ads/utility/ParseOptionsArguments.h	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/ads/utility/ParseOptionsArguments.h	2012-07-02 04:07:30.000000000 +0000
@@ -223,7 +223,7 @@
    /*!
      \pre The number of remaining arguments must not be zero.
 
-     The object of type T must be able to read its' state from a stream
+     The object of type T must be able to read its state from a stream
      with \c operator>>().
 
      \return true if the argument could be read.
diff -Nru cain-1.9/src/array/all.h cain-1.10+dfsg/src/array/all.h
--- cain-1.9/src/array/all.h	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/array/all.h	2012-07-02 04:07:30.000000000 +0000
@@ -6,6 +6,7 @@
 #include "Array.h"
 #include "EquilateralArray.h"
 #include "MultiArray.h"
+#include "PackedArrayOfArrays.h"
 #include "SparseVector.h"
 #include "StaticArrayOfArrays.h"
 #include "SymmetricArray2D.h"
@@ -94,6 +95,8 @@
 - array::SparseVector is a sparse 1-D vector. It stores index/value pairs.
 - array::StaticArrayOfArrays is a static %array of arrays (no, really).
 It is an efficient way to represent static, sparse, 2-D arrays.
+- array::PackedArrayOfArrays is like array::StaticArrayOfArrays, 
+but supports building on the fly by manipulating the last array.
 - array::TriangularArray is a 2-D triangular %array.
 - array::SymmetricArray2D is a symmetric 2-D %array with or without the
 diagonal elements.
diff -Nru cain-1.9/src/array/EquilateralArrayImp.h cain-1.10+dfsg/src/array/EquilateralArrayImp.h
--- cain-1.9/src/array/EquilateralArrayImp.h	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/array/EquilateralArrayImp.h	2012-07-02 04:07:30.000000000 +0000
@@ -100,7 +100,7 @@
    typename Base::const_reference
    operator()(const typename Base::size_type i0) const {
       LOKI_STATIC_CHECK(_D == 1, BadDimension);
-      return operator[](i0);
+      return Base::operator[](i0);
    }
 
    //! Return a const reference to the specified element in the 1-D array.
@@ -115,7 +115,7 @@
    operator()(const typename Base::size_type i0,
               const typename Base::size_type i1) const {
       LOKI_STATIC_CHECK(_D == 2, BadDimension);
-      return operator[](i0 + i1 * _N);
+      return Base::operator[](i0 + i1 * _N);
    }
 
    //! Return a const reference to the specified element in the 2-D array.
@@ -132,7 +132,7 @@
               const typename Base::size_type i2)
    const {
       LOKI_STATIC_CHECK(_D == 3, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N);
    }
 
    //! Return a const reference to the specified element in the 3-D array.
@@ -149,7 +149,7 @@
               const typename Base::size_type i2,
               const typename Base::size_type i3) const {
       LOKI_STATIC_CHECK(_D == 4, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N);
    }
 
    //! Return a const reference to the specified element in the 4-D array.
@@ -167,8 +167,8 @@
               const typename Base::size_type i3,
               const typename Base::size_type i4) const {
       LOKI_STATIC_CHECK(_D == 5, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N);
    }
 
    //! Return a const reference to the specified element in the 5-D array.
@@ -187,8 +187,8 @@
               const typename Base::size_type i4,
               const typename Base::size_type i5) const {
       LOKI_STATIC_CHECK(_D == 6, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N);
    }
 
    //! Return a const reference to the specified element in the 6-D array.
@@ -208,9 +208,9 @@
               const typename Base::size_type i5,
               const typename Base::size_type i6) const {
       LOKI_STATIC_CHECK(_D == 7, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
-                        i6 * _N * _N * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
+                              i6 * _N * _N * _N * _N * _N * _N);
    }
 
    //! Return a const reference to the specified element in the 7-D array.
@@ -231,10 +231,10 @@
               const typename Base::size_type i6,
               const typename Base::size_type i7) const {
       LOKI_STATIC_CHECK(_D == 8, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
-                        i6 * _N * _N * _N * _N * _N * _N +
-                        i7 * _N * _N * _N * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
+                              i6 * _N * _N * _N * _N * _N * _N +
+                              i7 * _N * _N * _N * _N * _N * _N * _N);
    }
 
    //! Return a const reference to the specified element in the 8-D array.
@@ -256,11 +256,11 @@
               const typename Base::size_type i7,
               const typename Base::size_type i8) const {
       LOKI_STATIC_CHECK(_D == 9, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
-                        i6 * _N * _N * _N * _N * _N * _N +
-                        i7 * _N * _N * _N * _N * _N * _N * _N +
-                        i8 * _N * _N * _N * _N * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
+                              i6 * _N * _N * _N * _N * _N * _N +
+                              i7 * _N * _N * _N * _N * _N * _N * _N +
+                              i8 * _N * _N * _N * _N * _N * _N * _N * _N);
    }
 
    //! Return a const reference to the specified element in the 9-D array.
@@ -283,12 +283,12 @@
               const typename Base::size_type i8,
               const typename Base::size_type i9) const {
       LOKI_STATIC_CHECK(_D == 10, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
-                        i6 * _N * _N * _N * _N * _N * _N +
-                        i7 * _N * _N * _N * _N * _N * _N * _N +
-                        i8 * _N * _N * _N * _N * _N * _N * _N * _N +
-                        i9 * _N * _N * _N * _N * _N * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
+                              i6 * _N * _N * _N * _N * _N * _N +
+                              i7 * _N * _N * _N * _N * _N * _N * _N +
+                              i8 * _N * _N * _N * _N * _N * _N * _N * _N +
+                              i9 * _N * _N * _N * _N * _N * _N * _N * _N * _N);
    }
 
    //! Return a const reference to the specified element in the 10-D array.
@@ -323,7 +323,7 @@
    typename Base::reference
    operator()(const typename Base::size_type i0) {
       LOKI_STATIC_CHECK(_D == 1, BadDimension);
-      return operator[](i0);
+      return Base::operator[](i0);
    }
 
    //! Return a reference to the specified element in the 1-D array.
@@ -338,7 +338,7 @@
    operator()(const typename Base::size_type i0,
               const typename Base::size_type i1) {
       LOKI_STATIC_CHECK(_D == 2, BadDimension);
-      return operator[](i0 + i1 * _N);
+      return Base::operator[](i0 + i1 * _N);
    }
 
    //! Return a reference to the specified element in the 2-D array.
@@ -354,7 +354,7 @@
               const typename Base::size_type i1,
               const typename Base::size_type i2) {
       LOKI_STATIC_CHECK(_D == 3, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N);
    }
 
    //! Return a reference to the specified element in the 3-D array.
@@ -371,7 +371,7 @@
               const typename Base::size_type i2,
               const typename Base::size_type i3) {
       LOKI_STATIC_CHECK(_D == 4, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N);
    }
 
    //! Return a reference to the specified element in the 4-D array.
@@ -389,8 +389,8 @@
               const typename Base::size_type i3,
               const typename Base::size_type i4) {
       LOKI_STATIC_CHECK(_D == 5, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N);
    }
 
    //! Return a reference to the specified element in the 5-D array.
@@ -409,8 +409,8 @@
               const typename Base::size_type i4,
               const typename Base::size_type i5) {
       LOKI_STATIC_CHECK(_D == 6, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N);
    }
 
    //! Return a reference to the specified element in the 6-D array.
@@ -430,9 +430,9 @@
               const typename Base::size_type i5,
               const typename Base::size_type i6) {
       LOKI_STATIC_CHECK(_D == 7, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
-                        i6 * _N * _N * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
+                              i6 * _N * _N * _N * _N * _N * _N);
    }
 
    //! Return a reference to the specified element in the 7-D array.
@@ -453,10 +453,10 @@
               const typename Base::size_type i6,
               const typename Base::size_type i7) {
       LOKI_STATIC_CHECK(_D == 8, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
-                        i6 * _N * _N * _N * _N * _N * _N +
-                        i7 * _N * _N * _N * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
+                              i6 * _N * _N * _N * _N * _N * _N +
+                              i7 * _N * _N * _N * _N * _N * _N * _N);
    }
 
    //! Return a reference to the specified element in the 8-D array.
@@ -478,11 +478,11 @@
               const typename Base::size_type i7,
               const typename Base::size_type i8) {
       LOKI_STATIC_CHECK(_D == 9, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
-                        i6 * _N * _N * _N * _N * _N * _N +
-                        i7 * _N * _N * _N * _N * _N * _N * _N +
-                        i8 * _N * _N * _N * _N * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
+                              i6 * _N * _N * _N * _N * _N * _N +
+                              i7 * _N * _N * _N * _N * _N * _N * _N +
+                              i8 * _N * _N * _N * _N * _N * _N * _N * _N);
    }
 
    //! Return a reference to the specified element in the 9-D array.
@@ -505,12 +505,12 @@
               const typename Base::size_type i8,
               const typename Base::size_type i9) {
       LOKI_STATIC_CHECK(_D == 10, BadDimension);
-      return operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
-                        i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
-                        i6 * _N * _N * _N * _N * _N * _N +
-                        i7 * _N * _N * _N * _N * _N * _N * _N +
-                        i8 * _N * _N * _N * _N * _N * _N * _N * _N +
-                        i9 * _N * _N * _N * _N * _N * _N * _N * _N * _N);
+      return Base::operator[](i0 + i1 * _N + i2 * _N * _N + i3 * _N * _N * _N +
+                              i4 * _N * _N * _N * _N + i5 * _N * _N * _N * _N * _N +
+                              i6 * _N * _N * _N * _N * _N * _N +
+                              i7 * _N * _N * _N * _N * _N * _N * _N +
+                              i8 * _N * _N * _N * _N * _N * _N * _N * _N +
+                              i9 * _N * _N * _N * _N * _N * _N * _N * _N * _N);
    }
 
    //! Return a reference to the specified element in the 10-D array.
diff -Nru cain-1.9/src/array/EquilateralArrayRef.h cain-1.10+dfsg/src/array/EquilateralArrayRef.h
--- cain-1.9/src/array/EquilateralArrayRef.h	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/array/EquilateralArrayRef.h	2012-07-02 04:07:30.000000000 +0000
@@ -45,7 +45,7 @@
    //! Construct from a pointer to the array data.
    EquilateralArrayRef(typename Base::iterator data) :
       Base() {
-      setData(data);
+      Base::setData(data);
    }
 
    // @}
diff -Nru cain-1.9/src/array/PackedArrayOfArrays.h cain-1.10+dfsg/src/array/PackedArrayOfArrays.h
--- cain-1.9/src/array/PackedArrayOfArrays.h	1970-01-01 00:00:00.000000000 +0000
+++ cain-1.10+dfsg/src/array/PackedArrayOfArrays.h	2012-07-02 04:07:30.000000000 +0000
@@ -0,0 +1,465 @@
+// -*- C++ -*-
+
+/*!
+  \file PackedArrayOfArrays.h
+  \brief A class for a packed %array of arrays.
+*/
+
+#if !defined(__array_PackedArrayOfArrays_h__)
+#define __array_PackedArrayOfArrays_h__
+
+#include "../ext/vector.h"
+
+namespace array {
+
+//! A packed %array of arrays.
+/*!
+  \param _T is the value type.
+
+  This is an array of arrays that have varying sizes. One may think of it as 
+  as two dimensional array where the rows have varying numbers of columns.
+  This data structure is useful where one might think of using a container
+  of containers like \c std::vector<std::vector<double> >. 
+
+  This class packs all of the elements of all of the arrays into a 
+  contigous storage. This gives it better cache utilization than a 
+  container of containers. The downside is that it has limited ability 
+  to modify the sizes of the component arrays. You can only manipulate 
+  the last array. We will talk more about that later.
+  In addition to packed elements, this class stores a vector of array 
+  delimiters that define the begining and end of each array.
+
+  There are a number of ways to construct this class. The default 
+  constructor makes an empty data structure. There are no arrays and
+  no elements. Below we construct the class and verify this.
+  \code
+  array::PackedArrayOfArrays<double> x;
+  assert(x.numArrays() == 0);
+  assert(x.empty());
+  \endcode
+  You can also construct it from a container of containers. You may use
+  any container that satisfies the STL interface for a sequence.
+  \code
+  std::vector<std::vector<double> > a;
+  ...
+  array::PackedArrayOfArrays<double> x(a);
+  \endcode
+  \code
+  std::list<std::list<double> > a;
+  ...
+  array::PackedArrayOfArrays<double> x(a);
+  \endcode
+  If you know the sizes of the arrays but do not yet know the element values,
+  you can construct a PackedArrayOfArrays with the range of sizes.
+  \code
+  std::vector<std::size_t> sizes;
+  ...
+  array::PackedArrayOfArrays<double> x(sizes.begin(), sizes.end());
+  \endcode
+  You can also construct a PackedArrayOfArrays from a range of array sizes
+  and the range for the packed elements.
+  \code
+  std::vector<std::size_t> sizes;
+  std::vector<double> packedData;
+  ...
+  array::PackedArrayOfArrays<double> x(sizes.begin(), sizes.end(),
+                                       packedData.begin(), packedData.end());
+  \endcode
+
+  This class inherits from std::vector to store the elements, and 
+  it retains the accessors. Thus you can use \c operator[], \c size(),
+  \c empty(), \c begin(), \c end(), \c rbegin(), and \c rend() to work 
+  with the packed array of elements. For example, below we compute the
+  sum of the elements in three different ways.
+  \code
+  array::PackedArrayOfArrays<double> x;
+  ...
+  // Indexing.
+  double sum = 0;
+  for (std::size_t i = 0; i != x.size(); ++i) {
+     sum += x[i];
+  }
+  // Iterator.
+  sum = 0;
+  for (array::PackedArrayOfArrays<double>::const_iterator i = x.begin();
+       i != x.end(); ++i) {
+     sum += *i;
+  }
+  // Accumulate.
+  sum = std::accumulate(x.begin(), x.end(), 0.)
+  \endcode
+
+  Of course, you can also work with the component arrays. There are 
+  versions of \c size(), \c empty(), \c begin(), \c end(), \c rbegin(),
+  and \c rend() that take the component array index as an argument and 
+  return information about that array.
+  \code
+  array::PackedArrayOfArrays<double> x;
+  ...
+  // Make a vector of the array sizes.
+  std::vector<std::size_t> sizes(x.numArrays());
+  for (std::size_t i = 0; i != x.numArrays(); ++i) {
+     sizes[i] = x.size(i);
+  }
+  // Calculate the sum of each array.
+  std::vector<double> sums(x.numArrays());
+  for (std::size_t i = 0; i != x.numArrays(); ++i) {
+     sums[i] = std::accumulate(x.begin(i), x.end(i), 0.);
+  }
+  \endcode
+  
+  \c operator() with a single argument will give you the beginning of 
+  the specified array. This \c x(i) is equivalent to \c x.begin(i).
+  With two arguments it gives you the specified element of the
+  specified array. That is, \c x(m,n) is the nth element of the mth array.
+
+  Note that in inheriting from std::vector, the modifier functions
+  \c assign(), \c insert(), and \c erase() have been disabled.
+  This is because (for the sake of efficiency) PackedArrayOfArrays
+  only supports changing the size of the last array.
+  Use \c push_back() and pop_back() to append an element to the last array
+  and remove the last element from the last array, respectively.
+  \c pushArray() appends an empty array, while \c popArray() 
+  erases the last array (which need not be empty).
+*/
+template<typename _T>
+class PackedArrayOfArrays :
+      public std::vector<_T> {
+   //
+   // Types.
+   //
+private:
+
+   typedef std::vector<_T> Base;
+
+   //
+   // Data.
+   //
+private:
+
+   //! Delimiters that determine the beginning and end of each %array.
+   std::vector<typename Base::size_type> _delimiters;
+
+   //
+   // Disable the following functions from the base class:
+   // assign(), insert(), and erase().
+   //
+private:
+   template<typename _InputIterator>
+   void
+   assign(_InputIterator first, _InputIterator last);
+
+   void
+   assign(typename Base::size_type n, typename Base::const_reference x);
+
+   typename Base::iterator
+   insert(typename Base::iterator position, typename Base::const_reference x);
+
+   void
+   insert(typename Base::iterator position, typename Base::size_type n,
+          typename Base::const_reference x);
+
+   template<typename _InputIterator>
+   void
+   insert(typename Base::iterator position, _InputIterator first,
+          _InputIterator last);
+
+   typename Base::iterator
+   erase(typename Base::iterator position);
+
+   typename Base::iterator
+   erase(typename Base::iterator first, typename Base::iterator last);
+
+   //
+   // Use from the base class.
+   //
+public:
+   using Base::size;
+   using Base::empty;
+   using Base::begin;
+   using Base::end;
+   using Base::rbegin;
+   using Base::rend;
+
+public:
+
+   //--------------------------------------------------------------------------
+   /*! \name Constructors etc.
+     Use the synthesized copy constructor, assignment operator, and destructor.
+   */
+   // @{
+
+   //! Default constructor. Empty data structure.
+   PackedArrayOfArrays() :
+      Base(),
+      _delimiters(1) {
+      _delimiters[0] = 0;
+   }
+
+   //! Construct from a container of containers.
+   template<typename _Container>
+   PackedArrayOfArrays(const _Container& cOfC);
+
+   //! Construct from the %array sizes and the values.
+   template<typename SizeForwardIter, typename ValueForwardIter>
+   PackedArrayOfArrays(SizeForwardIter sizesBeginning, SizeForwardIter sizesEnd,
+                       ValueForwardIter valuesBeginning,
+                       ValueForwardIter valuesEnd);
+
+   //! Rebuild from the component %array sizes.
+   template<typename SizeForwardIter>
+   void
+   rebuild(SizeForwardIter sizesBeginning, SizeForwardIter sizesEnd);
+
+   //! Rebuild from the %array sizes and the values.
+   template<typename SizeForwardIter, typename ValueForwardIter>
+   void
+   rebuild(SizeForwardIter sizesBeginning, SizeForwardIter sizesEnd,
+           ValueForwardIter valuesBeginning, ValueForwardIter valuesEnd) {
+      rebuild(sizesBeginning, sizesEnd);
+      std::copy(valuesBeginning, valuesEnd, begin());
+   }
+
+   //! Swap with the argument.
+   void
+   swap(PackedArrayOfArrays& other) {
+      Base::swap(other);
+      _delimiters.swap(other._delimiters);
+   }
+
+   // @}
+   //--------------------------------------------------------------------------
+   //! \name Accessors for the whole set of elements.
+   // @{
+
+   //! Return the number of arrays.
+   typename Base::size_type
+   numArrays() const {
+      return _delimiters.size() - 1;
+   }
+
+   // @}
+   //--------------------------------------------------------------------------
+   //! \name Accessors for individual arrays.
+   // @{
+
+   //! Return the number of elements in the n<sup>th</sup> %array.
+   typename Base::size_type
+   size(const typename Base::size_type n) const {
+      return _delimiters[n + 1] - _delimiters[n];
+   }
+
+   //! Return true if the n<sup>th</sup> %array is empty.
+   bool
+   empty(const typename Base::size_type n) const {
+      return size(n) == 0;
+   }
+
+   //! Return a const iterator to the first value in the n<sup>th</sup> %array.
+   typename Base::const_iterator
+   begin(const typename Base::size_type n) const {
+      return Base::begin() + _delimiters[n];
+   }
+
+   //! Return a const iterator to one past the last value in the n<sup>th</sup> %array.
+   typename Base::const_iterator
+   end(const typename Base::size_type n) const {
+      return Base::begin() + _delimiters[n + 1];
+   }
+
+   //! Return a const reverse iterator to the last value in the n<sup>th</sup> %array.
+   typename Base::const_reverse_iterator
+   rbegin(const typename Base::size_type n) const {
+      return typename Base::const_reverse_iterator(end(n));
+   }
+
+   //! Return a const reverse iterator to one before the first value in the n<sup>th</sup> %array.
+   typename Base::const_reverse_iterator
+   rend(const typename Base::size_type n) const {
+      return typename Base::const_reverse_iterator(begin(n));
+   }
+
+   //! Return a const iterator to the first element of the n<sup>th</sup> %array.
+   typename Base::const_iterator
+   operator()(const typename Base::size_type n) const {
+      return begin(n);
+   }
+
+   //! Return the m<sup>th</sup> element of the n<sup>th</sup> %array.
+   typename Base::const_reference
+   operator()(const std::size_t n, const std::size_t m) const {
+#ifdef DEBUG_stlib
+      assert(m < size(n));
+#endif
+      return Base::operator[](_delimiters[n] + m);
+   }
+
+   // @}
+   //--------------------------------------------------------------------------
+   //! \name Manipulators for the whole set of elements.
+   // @{
+
+   //! Clear the %array of arrays.
+   void
+   clear() {
+      Base::clear();
+      _delimiters.resize(1);
+      _delimiters[0] = 0;
+   }
+
+   // @}
+   //--------------------------------------------------------------------------
+   //! \name Manipulators for individual arrays.
+   // @{
+
+   //! Return an iterator to the first value in the n<sup>th</sup> %array.
+   typename Base::iterator
+   begin(const typename Base::size_type n) {
+      return Base::begin() + _delimiters[n];
+   }
+
+   //! Return an iterator to one past the last value in the n<sup>th</sup> %array.
+   typename Base::iterator
+   end(const typename Base::size_type n) {
+      return Base::begin() + _delimiters[n + 1];
+   }
+
+   //! Return an iterator to the first element of the n<sup>th</sup> %array.
+   typename Base::iterator
+   operator()(const typename Base::size_type n) {
+      return begin(n);
+   }
+
+   //! Return the m<sup>th</sup> element of the n<sup>th</sup> %array.
+   typename Base::reference
+   operator()(const typename Base::size_type n, const typename Base::size_type m) {
+#ifdef DEBUG_stlib
+      assert(m < size(n));
+#endif
+      return Base::operator[](_delimiters[n] + m);
+   }
+
+   //! Append an empty array.
+   void
+   pushArray() {
+      _delimiters.push_back(_delimiters.back());
+   }
+
+   //! Append an array with elements defined by the sequence.
+   template<typename _InputIterator>
+   void
+   pushArray(_InputIterator begin, _InputIterator end) {
+      pushArray();
+      while (begin != end) {
+         push_back(*begin++);
+      }
+   }
+
+   //! Pop the last array.
+   void
+   popArray() {
+      Base::erase(begin(numArrays() - 1), end(numArrays() - 1));
+      _delimiters.pop_back();
+   }
+
+   //! Append an element to the last array.
+   void
+   push_back(typename Base::const_reference x) {
+      Base::push_back(x);
+      ++_delimiters.back();
+   }
+
+   //! Pop an element from the last array.
+   void
+   pop_back() {
+      Base::pop_back();
+      --_delimiters.back();
+   }
+
+   // @}
+   //--------------------------------------------------------------------------
+   //! \name Equality.
+   // @{
+
+   //! Return true if the arrays are equal.
+   bool
+   operator==(const PackedArrayOfArrays& x) const {
+      return static_cast<const Base&>(*this) == static_cast<const Base&>(x) &&
+         _delimiters == x._delimiters;
+   }
+
+   //! Return true if the arrays are not equal.
+   bool
+   operator!=(const PackedArrayOfArrays& x) const {
+      return ! operator==(x);
+   }
+
+   // @}
+   //--------------------------------------------------------------------------
+   //! \name File I/O.
+   // @{
+
+   //! Write to a file stream in ascii format.
+   void
+   put(std::ostream& out) const;
+
+   //! Read from a file stream in ascii format.
+   void
+   get(std::istream& in);
+
+   // @}
+};
+
+//
+// File I/O.
+//
+
+//! Write a PackedArrayOfArrays in ascii format.
+/*!
+  \relates PackedArrayOfArrays
+
+  Below is the file format.
+  \verbatim
+  number_of_arrays number_of_elements
+  array_0_size
+  array_0_value_0 array_0_value_1 ...
+  array_1_size
+  array_1_value_0 array_1_value_1 ...
+  ... \endverbatim
+*/
+template<typename _T>
+inline
+std::ostream&
+operator<<(std::ostream& out, const PackedArrayOfArrays<_T>& x) {
+   x.put(out);
+   return out;
+}
+
+//! Read a PackedArrayOfArrays in ascii format.
+/*!
+  \relates PackedArrayOfArrays
+
+  Below is the file format.
+  \verbatim
+  number_of_arrays number_of_elements
+  array_0_size
+  array_0_value_0 array_0_value_1 ...
+  array_1_size
+  array_1_value_0 array_1_value_1 ...
+  ... \endverbatim
+*/
+template<typename _T>
+inline
+std::istream&
+operator>>(std::istream& in, PackedArrayOfArrays<_T>& x) {
+   x.get(in);
+   return in;
+}
+
+} // namespace array
+
+#define __array_PackedArrayOfArrays_ipp__
+#include "PackedArrayOfArrays.ipp"
+#undef __array_PackedArrayOfArrays_ipp__
+
+#endif
diff -Nru cain-1.9/src/array/PackedArrayOfArrays.ipp cain-1.10+dfsg/src/array/PackedArrayOfArrays.ipp
--- cain-1.9/src/array/PackedArrayOfArrays.ipp	1970-01-01 00:00:00.000000000 +0000
+++ cain-1.10+dfsg/src/array/PackedArrayOfArrays.ipp	2012-07-02 04:07:30.000000000 +0000
@@ -0,0 +1,91 @@
+// -*- C++ -*-
+
+#if !defined(__array_PackedArrayOfArrays_ipp__)
+#error This file is an implementation detail of the class PackedArrayOfArrays.
+#endif
+
+namespace array {
+
+
+// Construct from a container of containers.
+template<typename _T>
+template<typename _Container>
+inline
+PackedArrayOfArrays<_T>::
+PackedArrayOfArrays(const _Container& cOfC) :
+   Base(),
+   _delimiters(1) {
+   _delimiters[0] = 0;
+   typedef typename _Container::const_iterator ArrayIter;
+   typedef typename _Container::value_type::const_iterator ElementIter;
+   for (ArrayIter i = cOfC.begin(); i != cOfC.end(); ++i) {
+      pushArray();
+      for (ElementIter j = i->begin(); j != i->end(); ++j) {
+         push_back(*j);
+      }
+   }
+}
+
+
+template<typename _T>
+template<typename SizeForwardIter, typename ValueForwardIter>
+inline
+PackedArrayOfArrays<_T>::
+PackedArrayOfArrays(SizeForwardIter sizesBeginning, SizeForwardIter sizesEnd,
+                    ValueForwardIter valuesBeginning,
+                    ValueForwardIter valuesEnd) :
+   Base(valuesBeginning, valuesEnd),
+   _delimiters(1) {
+   _delimiters[0] = 0;
+   std::partial_sum(sizesBeginning, sizesEnd, std::back_inserter(_delimiters));
+}
+
+
+template<typename _T>
+template<typename SizeForwardIter>
+inline
+void
+PackedArrayOfArrays<_T>::
+rebuild(SizeForwardIter sizesBeginning, SizeForwardIter sizesEnd) {
+   _delimiters.resize(1);
+   _delimiters[0] = 0;
+   std::partial_sum(sizesBeginning, sizesEnd, std::back_inserter(_delimiters));
+   Base::resize(_delimiters.back());
+}
+
+
+template<typename _T>
+inline
+void
+PackedArrayOfArrays<_T>::
+put(std::ostream& out) const {
+   out << numArrays() << " " << size() << '\n';
+   for (typename Base::size_type n = 0; n != numArrays(); ++n) {
+      out << size(n) << '\n';
+      std::copy(begin(n), end(n),
+                std::ostream_iterator<typename Base::value_type>(out, " "));
+      out << '\n';
+   }
+}
+
+template<typename _T>
+inline
+void
+PackedArrayOfArrays<_T>::
+get(std::istream& in) {
+   std::size_t numberOfArrays, numberOfElements, sz;
+   in >> numberOfArrays >> numberOfElements;
+   Base::resize(numberOfElements);
+   _delimiters.resize(numberOfArrays + 1);
+
+   _delimiters[0] = 0;
+   for (typename Base::size_type n = 0; n != numberOfArrays; ++n) {
+      in >> sz;
+      _delimiters[n + 1] = _delimiters[n] + sz;
+      for (typename Base::size_type m = 0; m != sz; ++m) {
+         in >> operator()(n, m);
+      }
+   }
+}
+
+} // namespace array
diff -Nru cain-1.9/src/array/SimpleMultiArray.ipp cain-1.10+dfsg/src/array/SimpleMultiArray.ipp
--- cain-1.9/src/array/SimpleMultiArray.ipp	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/array/SimpleMultiArray.ipp	2012-07-02 04:07:30.000000000 +0000
@@ -26,7 +26,7 @@
 SimpleMultiArray(const SimpleMultiArrayConstRef<_T2, _Dimension>& other) :
    Base(0, other.extents()) {
    // Allocate the memory.
-   setData(new typename Base::value_type[other.size()]);
+   Base::setData(new typename Base::value_type[other.size()]);
    // Copy the elements.
    std::copy(other.begin(), other.end(), Base::begin());
 }
@@ -38,7 +38,7 @@
 SimpleMultiArray(const SimpleMultiArray& other) :
    Base(0, other.extents()) {
    // Allocate the memory.
-   setData(new typename Base::value_type[other.size()]);
+   Base::setData(new typename Base::value_type[other.size()]);
    // Copy the elements.
    std::copy(other.begin(), other.end(), Base::begin());
 }
@@ -50,7 +50,7 @@
 SimpleMultiArray(const typename Base::IndexList& extents) :
    Base(0, extents) {
    // Allocate the memory.
-   setData(new typename Base::value_type[product(extents)]);
+   Base::setData(new typename Base::value_type[product(extents)]);
 }
 
 
@@ -62,7 +62,7 @@
                  const typename Base::value_type& value) :
    Base(0, extents) {
    // Allocate the memory.
-   setData(new typename Base::value_type[product(extents)]);
+   Base::setData(new typename Base::value_type[product(extents)]);
    // Initialize the data.
    std::fill(Base::begin(), Base::end(), value);
 }
diff -Nru cain-1.9/src/array/SimpleMultiArrayRef.h cain-1.10+dfsg/src/array/SimpleMultiArrayRef.h
--- cain-1.9/src/array/SimpleMultiArrayRef.h	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/array/SimpleMultiArrayRef.h	2012-07-02 04:07:30.000000000 +0000
@@ -222,7 +222,7 @@
          assert(indices[n] < Base::extents()[n]);
       }
 #endif
-      return _data[arrayIndex(indices)];
+      return _data[Base::arrayIndex(indices)];
    }
 
    //! Array indexing.
@@ -232,7 +232,7 @@
 #ifdef DEBUG_stlib
       assert(i0 < Base::extents()[0]);
 #endif
-      return _data[arrayIndex(i0)];
+      return _data[Base::arrayIndex(i0)];
    }
 
    //! Array indexing.
@@ -242,7 +242,7 @@
 #ifdef DEBUG_stlib
       assert(i0 < Base::extents()[0] && i1 < Base::extents()[1]);
 #endif
-      return _data[arrayIndex(i0, i1)];
+      return _data[Base::arrayIndex(i0, i1)];
    }
 
    //! Array indexing.
@@ -254,7 +254,7 @@
       assert(i0 < Base::extents()[0] && i1 < Base::extents()[1] &&
              i2 < Base::extents()[2]);
 #endif
-      return _data[arrayIndex(i0, i1, i2)];
+      return _data[Base::arrayIndex(i0, i1, i2)];
    }
 
    //! Return a pointer to the beginning of the data.
diff -Nru cain-1.9/src/array/StaticArrayOfArrays.h cain-1.10+dfsg/src/array/StaticArrayOfArrays.h
--- cain-1.9/src/array/StaticArrayOfArrays.h	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/array/StaticArrayOfArrays.h	2012-07-02 04:07:30.000000000 +0000
@@ -324,7 +324,7 @@
 
    //! Return true if the arrays are equal.
    bool
-   operator==(const StaticArrayOfArrays<value_type>& x) const {
+   operator==(const StaticArrayOfArrays& x) const {
       if (_elements != x._elements) {
          return false;
       }
@@ -338,7 +338,7 @@
 
    //! Return true if the arrays are not equal.
    bool
-   operator!=(const StaticArrayOfArrays<value_type>& x) const {
+   operator!=(const StaticArrayOfArrays& x) const {
       return ! operator==(x);
    }
 
diff -Nru cain-1.9/src/ext/array.h cain-1.10+dfsg/src/ext/array.h
--- cain-1.9/src/ext/array.h	2011-09-27 19:44:55.000000000 +0000
+++ cain-1.10+dfsg/src/ext/array.h	2012-07-02 04:07:30.000000000 +0000
@@ -3,13 +3,7 @@
 #if !defined(__ext_array_h__)
 #define __ext_array_h__
 
-#ifdef __CUDA_ARCH__
-#include "arrayCuda.h"
-#else
 #include "arrayStd.h"
-#endif
-
-#include "../cuda/compatible.h"
 
 namespace ext {
 //-------------------------------------------------------------------------
@@ -43,7 +37,6 @@
 //! Convert to an array with different value type.
 template<typename _Target, typename _Source, std::size_t _N>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_Target, _N>
 convert_array(const std::tr1::array<_Source, _N>& x) {
    std::tr1::array<_Target, _N> result;
@@ -56,7 +49,6 @@
 //! Return an array filled with the specified value.
 template<typename _Array>
 inline
-CUDA_COMPATIBLE
 _Array
 filled_array(const typename _Array::value_type& value) {
    _Array x;
@@ -69,7 +61,6 @@
 //! Copy from the input iterator to make an array.
 template<typename _Array, typename _InputIterator>
 inline
-CUDA_COMPATIBLE
 _Array
 copy_array(_InputIterator input) {
    _Array x;
@@ -82,7 +73,6 @@
 //! Return an array with the specified components.
 template<typename _T>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_T, 1>
 make_array(const _T& x0) {
    std::tr1::array<_T, 1> x = {{x0}};
@@ -92,7 +82,6 @@
 //! Return an array with the specified components.
 template<typename _T>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_T, 2>
 make_array(const _T& x0, const _T& x1) {
    std::tr1::array<_T, 2> x = {{x0, x1}};
@@ -102,7 +91,6 @@
 //! Return an array with the specified components.
 template<typename _T>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_T, 3>
 make_array(const _T& x0, const _T& x1, const _T& x2) {
    std::tr1::array<_T, 3> x = {{x0, x1, x2}};
@@ -112,7 +100,6 @@
 //! Return an array with the specified components.
 template<typename _T>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_T, 4>
 make_array(const _T& x0, const _T& x1, const _T& x2, const _T& x3) {
    std::tr1::array<_T, 4> x = {{x0, x1, x2, x3}};
@@ -122,7 +109,6 @@
 //! Return an array with the specified components.
 template<typename _T>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_T, 5>
 make_array(const _T& x0, const _T& x1, const _T& x2, const _T& x3,
 const _T& x4) {
@@ -133,7 +119,6 @@
 //! Return an array with the specified components.
 template<typename _T>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_T, 6>
 make_array(const _T& x0, const _T& x1, const _T& x2, const _T& x3,
 const _T& x4, const _T& x5) {
@@ -144,7 +129,6 @@
 //! Return an array with the specified components.
 template<typename _T>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_T, 7>
 make_array(const _T& x0, const _T& x1, const _T& x2, const _T& x3,
 const _T& x4, const _T& x5, const _T& x6) {
@@ -155,7 +139,6 @@
 //! Return an array with the specified components.
 template<typename _T>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_T, 8>
 make_array(const _T& x0, const _T& x1, const _T& x2, const _T& x3,
 const _T& x4, const _T& x5, const _T& x6, const _T& x7) {
@@ -166,7 +149,6 @@
 //! Return an array with the specified components.
 template<typename _T>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_T, 9>
 make_array(const _T& x0, const _T& x1, const _T& x2, const _T& x3,
 const _T& x4, const _T& x5, const _T& x6, const _T& x7,
@@ -178,7 +160,6 @@
 //! Return an array with the specified components.
 template<typename _T>
 inline
-CUDA_COMPATIBLE
 std::tr1::array<_T, 10>
 make_array(const _T& x0, const _T& x1, const _T& x2, const _T& x3,
 const _T& x4, const _T& x5, const _T& x6, const _T& x7,
@@ -188,6 +169,50 @@
 }
 
 //@}
+//-------------------------------------------------------------------------
+/*! \defgroup extArraySimd SIMD Functions
+  I provide these functions because in some implementation std::tr1::array
+  is 16-byte aligned, while in others it is not. Note that these functions are
+  defined in the ext namespace so that they are not confused with the SSE 
+  intrinsics.
+*/
+//@{
+
+#if 0
+//! Store for 3-D points.
+inline
+void
+_mm_store_ps(std::tr1::array<float, 3>* p, __m128 a) {
+   // CONTINUE: Implement specialization for 16-byte aligned structure.
+#if 0
+   // If the structure is aligned, we can use the aligned store.
+   ::_mm_store_ps(&(*p)[0], a);
+#endif
+   else {
+      // Otherwise, use the slower method. Note that we can't just use the
+      // unaligned store because it would write the fourth element.
+      (*p)[0] = reinterpret_cast<const float*>(&a)[0];
+      (*p)[1] = reinterpret_cast<const float*>(&a)[1];
+      (*p)[2] = reinterpret_cast<const float*>(&a)[2];
+   }
+}
+
+//! Load for 3-D points.
+inline
+__m128
+_mm_load_ps(const std::tr1::array<float, 3>* p) {
+   if (sizeof(std::tr1::array<float, 3>) == 4 * sizeof(float)) {
+      // If the structure is aligned, we can use the aligned load.
+      return ::_mm_load_ps(&(*p)[0]);
+   }
+   else {
+      // Otherwise, use the slower set.
+      return _mm_set_ps(0, (*p)[2], (*p)[1], (*p)[0]);
+   }
+}
+#endif
+
+//@}
 
 } // namespace ext
 
diff -Nru cain-1.9/src/ext/arrayStd.h cain-1.10+dfsg/src/ext/arrayStd.h
--- cain-1.9/src/ext/arrayStd.h	2011-09-27 19:44:56.000000000 +0000
+++ cain-1.10+dfsg/src/ext/arrayStd.h	2012-07-02 04:07:30.000000000 +0000
@@ -286,9 +286,9 @@
 inline
 array<_T, _N>
 operator-(const array<_T, _N>& x) {
-   array<_T, _N> y(x);
+   array<_T, _N> y;
    for (size_t n = 0; n != _N; ++n) {
-      y[n] = -y[n];
+      y[n] = -x[n];
    }
    return y;
 }
@@ -353,8 +353,9 @@
 template<typename _X, typename _Y>
 struct ArithmeticResult {
    //! An ordered list of numeric types.
-   typedef LOKI_TYPELIST_10(double, float, unsigned long, long, unsigned, int,
-                            unsigned short, short, unsigned char, signed char)
+   typedef LOKI_TYPELIST_11(double, float, unsigned long, long, unsigned, int,
+                            unsigned short, short, unsigned char, signed char,
+                            bool)
    OrderedTypes;
    //! The result type.
    typedef typename Loki::Select < int(Loki::TL::IndexOf<OrderedTypes, _X>::value)
@@ -1168,9 +1169,14 @@
 inline
 float
 dot(const array<float, 3>& x, const array<float, 3>& y) {
+   // CONTINUE: Implementent specialization for 16-byte aligned structure.
+#if 0
    // Note: Using load is OK because I don't access the fourth element,
    // which might be NaN.
    __m128 d = _mm_dp_ps(_mm_load_ps(&x[0]), _mm_load_ps(&y[0]), 0x71);
+#endif
+   __m128 d = _mm_dp_ps(_mm_set_ps(0, x[2], x[1], x[0]),
+                        _mm_set_ps(0, y[2], y[1], y[0]), 0x71);
    return *reinterpret_cast<const float*>(&d);
 }
 #endif
@@ -1182,7 +1188,11 @@
 inline
 float
 dot(const array<float, 4>& x, const array<float, 4>& y) {
+   // CONTINUE: Implementent specialization for 16-byte aligned structure.
+#if 0
    __m128 d = _mm_dp_ps(_mm_load_ps(&x[0]), _mm_load_ps(&y[0]), 0xF1);
+#endif
+   __m128 d = _mm_dp_ps(_mm_loadu_ps(&x[0]), _mm_loadu_ps(&y[0]), 0xF1);
    return *reinterpret_cast<const float*>(&d);
 }
 #endif
@@ -1194,10 +1204,17 @@
 inline
 double
 dot(const array<double, 4>& x, const array<double, 4>& y) {
+   // CONTINUE: Implementent specialization for 16-byte aligned structure.
+#if 0
    __m128d a = _mm_add_sd(_mm_dp_pd(_mm_load_pd(&x[0]), _mm_load_pd(&y[0]),
                                     0x31),
                           _mm_dp_pd(_mm_load_pd(&x[2]), _mm_load_pd(&y[2]),
                                     0x31));
+#endif
+   __m128d a = _mm_add_sd(_mm_dp_pd(_mm_loadu_pd(&x[0]), _mm_loadu_pd(&y[0]),
+                                    0x31),
+                          _mm_dp_pd(_mm_loadu_pd(&x[2]), _mm_loadu_pd(&y[2]),
+                                    0x31));
    return *reinterpret_cast<const double*>(&a);
 }
 #endif
@@ -1376,7 +1393,12 @@
 float
 squaredDistance(const array<float, 3>& x, const array<float, 3>& y) {
    // Take the difference of the two vectors.
-   __m128 d = _mm_sub_ps(_mm_load_ps(&x[0]), _mm_load_ps(&y[0]));
+   // CONTINUE: Implementent specialization for 16-byte aligned structure.
+#if 0
+    __m128 d = _mm_load_ps(&x[0]) - _mm_load_ps(&y[0]);
+#endif
+    __m128 d = _mm_set_ps(0, x[2], x[1], x[0]) -
+       _mm_set_ps(0, y[2], y[1], y[0]);
    // Perform the dot product.
    d = _mm_dp_ps(d, d, 0x71);
    return *reinterpret_cast<const float*>(&d);
@@ -1391,7 +1413,11 @@
 float
 squaredDistance(const array<float, 4>& x, const array<float, 4>& y) {
    // Take the difference of the two vectors.
-   __m128 d = _mm_sub_ps(_mm_load_ps(&x[0]), _mm_load_ps(&y[0]));
+   // CONTINUE: Implementent specialization for 16-byte aligned structure.
+#if 0
+   __m128 d = _mm_load_ps(&x[0]) - _mm_load_ps(&y[0]);
+#endif
+   __m128 d = _mm_loadu_ps(&x[0]) - _mm_loadu_ps(&y[0]);
    // Perform the dot product.
    d = _mm_dp_ps(d, d, 0xF1);
    return *reinterpret_cast<const float*>(&d);
@@ -1406,8 +1432,13 @@
 double
 squaredDistance(const array<double, 4>& x, const array<double, 4>& y) {
    // Take the difference of the two vectors.
-   __m128d a = _mm_sub_pd(_mm_load_pd(&x[0]), _mm_load_pd(&y[0]));
-   __m128d b = _mm_sub_pd(_mm_load_pd(&x[2]), _mm_load_pd(&y[2]));
+   // CONTINUE: Implementent specialization for 16-byte aligned structure.
+#if 0
+   __m128d a = _mm_load_pd(&x[0]) - _mm_load_pd(&y[0]);
+   __m128d b = _mm_load_pd(&x[2]) - _mm_load_pd(&y[2]);
+#endif
+   __m128d a = _mm_loadu_pd(&x[0]) - _mm_loadu_pd(&y[0]);
+   __m128d b = _mm_loadu_pd(&x[2]) - _mm_loadu_pd(&y[2]);
    // Perform the dot product.
    a = _mm_add_pd(_mm_dp_pd(a, a, 0x31), _mm_dp_pd(b, b, 0x31));
    return *reinterpret_cast<const double*>(&a);
@@ -1446,7 +1477,11 @@
 float
 euclideanDistance(const array<float, 4>& x, const array<float, 4>& y) {
    // Take the difference of the two vectors.
-   __m128 d = _mm_sub_ps(_mm_load_ps(&x[0]), _mm_load_ps(&y[0]));
+   // CONTINUE: Implementent specialization for 16-byte aligned structure.
+#if 0
+   __m128 d = _mm_load_ps(&x[0]) - _mm_load_ps(&y[0]);
+#endif
+   __m128 d = _mm_loadu_ps(&x[0]) - _mm_loadu_ps(&y[0]);
    // Perform the dot product and then take the square root.
    d = _mm_sqrt_ss(_mm_dp_ps(d, d, 0xF1));
    return *reinterpret_cast<const float*>(&d);
diff -Nru cain-1.9/src/numerical/random/discrete/DiscreteGeneratorBinned.h cain-1.10+dfsg/src/numerical/random/discrete/DiscreteGeneratorBinned.h
--- cain-1.9/src/numerical/random/discrete/DiscreteGeneratorBinned.h	2011-09-27 19:44:56.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/discrete/DiscreteGeneratorBinned.h	2012-07-02 04:07:31.000000000 +0000
@@ -8,6 +8,8 @@
 #if !defined(__numerical_DiscreteGeneratorBinned_h__)
 #define __numerical_DiscreteGeneratorBinned_h__
 
+#include "DiscreteGeneratorBinsSplittingStacking.h"
+
 #include "../uniform/Default.h"
 
 #include "../../../ads/algorithm/sort.h"
diff -Nru cain-1.9/src/numerical/random/discrete/DiscreteGeneratorBinned.ipp cain-1.10+dfsg/src/numerical/random/discrete/DiscreteGeneratorBinned.ipp
--- cain-1.9/src/numerical/random/discrete/DiscreteGeneratorBinned.ipp	2011-09-27 19:44:56.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/discrete/DiscreteGeneratorBinned.ipp	2012-07-02 04:07:31.000000000 +0000
@@ -196,70 +196,6 @@
 }
 
 
-
-
-// Count the number of required bins for the given maximum height.
-template<typename T, typename ForwardIterator>
-inline
-std::size_t
-countBins(ForwardIterator begin, ForwardIterator end, const T height) {
-   const T inverse = 1.0 / height;
-   std::size_t count = 0;
-   // Count the splitting bins.
-   while (begin != end && *begin > height) {
-      count += std::size_t(*begin * inverse) + 1;
-      ++begin;
-   }
-   // Count the stacking bins.
-   // The following loop is a little complicated because I must allow for the
-   // possibility of blocks with zero height.
-   T currentHeight = -1;
-   while (begin != end) {
-      // If we are starting a new bin.
-      if (currentHeight == -1) {
-         // Add the first block to the bin.
-         currentHeight = *begin;
-         // We are using a new bin.
-         ++count;
-         // Move to the next block.
-         ++begin;
-      }
-      else {
-         // Try adding a block to the current bin.
-         currentHeight += *begin;
-         // If we can fit it in the current bin.
-         if (currentHeight <= height) {
-            // Move to the next block.
-            ++begin;
-         }
-         else {
-            // Start a new bin.
-            currentHeight = -1;
-         }
-      }
-   }
-   return count;
-}
-
-
-// Compute a bin height such that all the blocks will fit in the bins.
-template<typename T, typename ForwardIterator>
-inline
-T
-computeBinHeight(ForwardIterator begin, ForwardIterator end,
-                 const std::size_t NumberOfBins) {
-   const T content = std::accumulate(begin, end, T(0));
-   T factor = 1;
-   T height;
-   do {
-      factor += 0.1;
-      height = factor * content / NumberOfBins;
-   }
-   while (countBins(begin, end, height) > NumberOfBins);
-   return height;
-}
-
-
 // Pack the block into bins.
 template<class Generator>
 inline
diff -Nru cain-1.9/src/numerical/random/discrete/DiscreteGeneratorCompositionRejectionStatic.h cain-1.10+dfsg/src/numerical/random/discrete/DiscreteGeneratorCompositionRejectionStatic.h
--- cain-1.9/src/numerical/random/discrete/DiscreteGeneratorCompositionRejectionStatic.h	2011-09-27 19:44:56.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/discrete/DiscreteGeneratorCompositionRejectionStatic.h	2012-07-02 04:07:31.000000000 +0000
@@ -216,6 +216,7 @@
    DiscreteGeneratorCompositionRejectionStatic
    (DiscreteUniformGenerator* generator,
     ForwardIterator begin, ForwardIterator end) :
+      _discreteUniformGenerator(generator),
       // Make a continuous uniform generator using the discrete uniform generator.
       _continuousUniformGenerator(generator),
       // Empty.
diff -Nru cain-1.9/src/numerical/random/discrete.h cain-1.10+dfsg/src/numerical/random/discrete.h
--- cain-1.9/src/numerical/random/discrete.h	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/discrete.h	2012-07-02 04:07:31.000000000 +0000
@@ -12,8 +12,6 @@
 #include "discrete/DiscreteGeneratorBinned.h"
 #include "discrete/DiscreteGeneratorBinsSplitting.h"
 #include "discrete/DiscreteGeneratorBinsSplittingStacking.h"
-#include "discrete/DiscreteGeneratorCdfInversionUsingPartialPmfSums.h"
-#include "discrete/DiscreteGeneratorCdfInversionUsingPartialRecursiveCdf.h"
 #include "discrete/DiscreteGeneratorLinearSearch.h"
 #include "discrete/DiscreteGeneratorLinearSearchInteger.h"
 #include "discrete/DiscreteGeneratorRejectionBinsSplitting.h"
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionBuildUp.h cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionBuildUp.h
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionBuildUp.h	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionBuildUp.h	2012-07-02 04:07:32.000000000 +0000
@@ -8,6 +8,8 @@
 #if !defined(__numerical_PoissonGeneratorInversionBuildUp_h__)
 #define __numerical_PoissonGeneratorInversionBuildUp_h__
 
+#include "PoissonGeneratorInversionMaximumMean.h"
+
 #include "../uniform/ContinuousUniformGenerator.h"
 
 #include <cmath>
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionBuildUp.ipp cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionBuildUp.ipp
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionBuildUp.ipp	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionBuildUp.ipp	2012-07-02 04:07:32.000000000 +0000
@@ -4,10 +4,6 @@
 #error This file is an implementation detail of PoissonGeneratorInversionBuildUp.
 #endif
 
-#define __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-#include "PoissonGeneratorInversionMaximumMean.ipp"
-#undef __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-
 namespace numerical {
 
 template<class _Uniform, typename _Result>
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionBuildUpSimple.h cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionBuildUpSimple.h
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionBuildUpSimple.h	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionBuildUpSimple.h	2012-07-02 04:07:32.000000000 +0000
@@ -8,6 +8,8 @@
 #if !defined(__numerical_PoissonGeneratorInversionBuildUpSimple_h__)
 #define __numerical_PoissonGeneratorInversionBuildUpSimple_h__
 
+#include "PoissonGeneratorInversionMaximumMean.h"
+
 #include "../uniform/ContinuousUniformGenerator.h"
 
 #include <cmath>
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionBuildUpSimple.ipp cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionBuildUpSimple.ipp
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionBuildUpSimple.ipp	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionBuildUpSimple.ipp	2012-07-02 04:07:32.000000000 +0000
@@ -4,10 +4,6 @@
 #error This file is an implementation detail of PoissonGeneratorInversionBuildUpSimple.
 #endif
 
-#define __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-#include "PoissonGeneratorInversionMaximumMean.ipp"
-#undef __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-
 namespace numerical {
 
 template<class _Uniform, typename _Result>
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionCheckPdf.h cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionCheckPdf.h
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionCheckPdf.h	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionCheckPdf.h	2012-07-02 04:07:32.000000000 +0000
@@ -8,6 +8,8 @@
 #if !defined(__numerical_PoissonGeneratorInversionCheckPdf_h__)
 #define __numerical_PoissonGeneratorInversionCheckPdf_h__
 
+#include "PoissonGeneratorInversionMaximumMean.h"
+
 #include "../uniform/ContinuousUniformGenerator.h"
 
 #include <limits>
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionCheckPdf.ipp cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionCheckPdf.ipp
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionCheckPdf.ipp	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionCheckPdf.ipp	2012-07-02 04:07:32.000000000 +0000
@@ -4,10 +4,6 @@
 #error This file is an implementation detail of PoissonGeneratorInversionCheckPdf.
 #endif
 
-#define __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-#include "PoissonGeneratorInversionMaximumMean.ipp"
-#undef __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-
 namespace numerical {
 
 template<class _Uniform, typename _Result>
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionChopDown.h cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionChopDown.h
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionChopDown.h	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionChopDown.h	2012-07-02 04:07:32.000000000 +0000
@@ -8,6 +8,8 @@
 #if !defined(__numerical_PoissonGeneratorInversionChopDown_h__)
 #define __numerical_PoissonGeneratorInversionChopDown_h__
 
+#include "PoissonGeneratorInversionMaximumMean.h"
+
 #include "../uniform/ContinuousUniformGenerator.h"
 
 #ifdef NUMERICAL_POISSON_HERMITE_APPROXIMATION
@@ -24,10 +26,6 @@
 #include <cmath>
 #include <cstddef>
 
-#define __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-#include "PoissonGeneratorInversionMaximumMean.ipp"
-#undef __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-
 namespace numerical {
 
 //! Generator for Poisson deviates using the inversion (chop-down) method.
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionChopDownSimple.h cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionChopDownSimple.h
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionChopDownSimple.h	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionChopDownSimple.h	2012-07-02 04:07:32.000000000 +0000
@@ -8,6 +8,8 @@
 #if !defined(__numerical_PoissonGeneratorInversionChopDownSimple_h__)
 #define __numerical_PoissonGeneratorInversionChopDownSimple_h__
 
+#include "PoissonGeneratorInversionMaximumMean.h"
+
 #include "../uniform/ContinuousUniformGenerator.h"
 
 #include <cmath>
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionChopDownSimple.ipp cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionChopDownSimple.ipp
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionChopDownSimple.ipp	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionChopDownSimple.ipp	2012-07-02 04:07:32.000000000 +0000
@@ -4,10 +4,6 @@
 #error This file is an implementation detail of PoissonGeneratorInversionChopDownSimple.
 #endif
 
-#define __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-#include "PoissonGeneratorInversionMaximumMean.ipp"
-#undef __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-
 namespace numerical {
 
 template<class _Uniform, typename _Result>
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionChopDownUnrolled.h cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionChopDownUnrolled.h
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionChopDownUnrolled.h	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionChopDownUnrolled.h	2012-07-02 04:07:32.000000000 +0000
@@ -8,6 +8,8 @@
 #if !defined(__numerical_PoissonGeneratorInversionChopDownUnrolled_h__)
 #define __numerical_PoissonGeneratorInversionChopDownUnrolled_h__
 
+#include "PoissonGeneratorInversionMaximumMean.h"
+
 #include "../uniform/ContinuousUniformGenerator.h"
 
 #include "../../interpolation/hermite.h"
@@ -19,10 +21,6 @@
 #include <cmath>
 #include <cassert>
 
-#define __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-#include "PoissonGeneratorInversionMaximumMean.ipp"
-#undef __numerical_random_PoissonGeneratorInversionMaximumMean_ipp__
-
 namespace numerical {
 
 //! Generator for Poisson deviates using the inversion (chop-down) method.
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h	1970-01-01 00:00:00.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionMaximumMean.h	2012-07-02 04:07:32.000000000 +0000
@@ -0,0 +1,45 @@
+// -*- C++ -*-
+
+/*!
+  \file numerical/random/poisson.h
+  \brief Constants for the inversion method.
+*/
+
+#if !defined(__numerical_random_poisson_PoissonGeneratorInversionMaximumMean_h__)
+#define __numerical_random_poisson_PoissonGeneratorInversionMaximumMean_h__
+
+namespace numerical {
+
+//! Maximum allowed mean for using the PoissonGeneratorInversion class.
+/*!
+  If the mean is too large, we will get underflow in computing the
+  probability density function.
+*/
+template<typename T>
+class PoissonGeneratorInversionMaximumMean {
+public:
+   //! Invalid value for an unknown number type.
+   enum {Value = -1};
+};
+
+template<>
+class PoissonGeneratorInversionMaximumMean<double> {
+public:
+   //! - std::log(std::numeric_limits<double>::min()) == 708.396
+   enum {Value = 708};
+};
+
+template<>
+class PoissonGeneratorInversionMaximumMean<float> {
+public:
+   //! - std::log(std::numeric_limits<float>::min()) == 87.3365
+   /*!
+     Here I assume that the arithmetic is actually done in single precision.
+     However, floats are typically converted to double's.
+   */
+   enum {Value = 87};
+};
+
+} // namespace numerical
+
+#endif
diff -Nru cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionRatioOfUniformsWinrand.ipp cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionRatioOfUniformsWinrand.ipp
--- cain-1.9/src/numerical/random/poisson/PoissonGeneratorInversionRatioOfUniformsWinrand.ipp	2011-09-27 19:44:57.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random/poisson/PoissonGeneratorInversionRatioOfUniformsWinrand.ipp	2012-07-02 04:07:32.000000000 +0000
@@ -12,11 +12,11 @@
 typename PoissonGeneratorInversionRatioOfUniformsWinrand<_Uniform, _Result>::result_type
 PoissonGeneratorInversionRatioOfUniformsWinrand<_Uniform, _Result>::
 operator()(const argument_type my) {
-#define       C0      9.18938533204672742e-01       /* constants for */
-#define       C1      8.33333333333333333e-02       /* Stirling's    */
-#define       C3     -2.77777777777777778e-03       /* approximation */
-#define       C5      7.93650793650793651e-04       /* of ln(k!)     */
-#define       C7     -5.95238095238095238e-04
+   const Number C0 = 9.18938533204672742e-01;       /* constants for */
+   const Number C1 = 8.33333333333333333e-02;       /* Stirling's    */
+   const Number C3 = -2.77777777777777778e-03;       /* approximation */
+   const Number C5 = 7.93650793650793651e-04;       /* of ln(k!)     */
+   const Number C7 = -5.95238095238095238e-04;
 
    static int m, b;
 
diff -Nru cain-1.9/src/numerical/random.h cain-1.10+dfsg/src/numerical/random.h
--- cain-1.9/src/numerical/random.h	2011-09-27 19:44:58.000000000 +0000
+++ cain-1.10+dfsg/src/numerical/random.h	2012-07-02 04:07:33.000000000 +0000
@@ -9,19 +9,19 @@
 #define __numerical_random_h__
 
 // Discrete deviates.
-#include "discrete.h"
+#include "random/discrete.h"
 // Exponential
-#include "exponential.h"
+#include "random/exponential.h"
 // Gamma
-#include "gamma.h"
+#include "random/gamma.h"
 // Hypoexponential
-#include "hypoexponential.h"
+#include "random/hypoexponential.h"
 // Normal (Gaussian) deviates.
-#include "normal.h"
+#include "random/normal.h"
 // Poisson deviates.
-#include "poisson.h"
+#include "random/poisson.h"
 // Uniform random deviates.
-#include "uniform.h"
+#include "random/uniform.h"
 
 namespace numerical {
 
diff -Nru cain-1.9/src/solvers/env.py cain-1.10+dfsg/src/solvers/env.py
--- cain-1.9/src/solvers/env.py	2011-09-27 19:44:58.000000000 +0000
+++ cain-1.10+dfsg/src/solvers/env.py	2012-07-02 04:07:33.000000000 +0000
@@ -35,6 +35,9 @@
     # uses long long.
     serial.AppendUnique(CCFLAGS=['-ansi', '-Wall', '-Wextra',
                                  '-Wstrict-aliasing=2', '-Wno-unknown-pragmas'])
+    # Use the rt library on linux, but not on darwin or windows.
+    if serial['PLATFORM'] == 'posix':
+        serial.AppendUnique(LIBS=['rt'])
     # We need this to compile the implicit tau-leaping solvers for PPC
     # architectures.
     serial.AppendUnique(CCFLAGS=['-DEIGEN_DONT_VECTORIZE'])
Binary files /tmp/tmpowQPTK/Alr96NWhxb/cain-1.9/src/solvers/env.pyc and /tmp/tmpowQPTK/MhUGwm3H4P/cain-1.10+dfsg/src/solvers/env.pyc differ
diff -Nru cain-1.9/src/solvers/Makefile cain-1.10+dfsg/src/solvers/Makefile
--- cain-1.9/src/solvers/Makefile	2011-09-27 19:44:58.000000000 +0000
+++ cain-1.10+dfsg/src/solvers/Makefile	2012-07-02 04:07:34.000000000 +0000
@@ -21,6 +21,10 @@
 # Commented out for Eigen.
 #CXXFLAGS += -pedantic
 
+ifeq ($(shell uname),Linux)
+  LOADLIBES += -lrt
+endif
+
 ifndef SOURCES
 # The homogeneous sources have mass action solvers that can be pre-compiled.
 SOURCES = $(wildcard Homogeneous*.cc)
diff -Nru cain-1.9/state/State.py cain-1.10+dfsg/state/State.py
--- cain-1.9/state/State.py	2011-09-27 19:44:46.000000000 +0000
+++ cain-1.10+dfsg/state/State.py	2012-07-02 04:07:16.000000000 +0000
@@ -299,7 +299,7 @@
         self.seed = 2**31
         self.listOfMt19937States = []
         self.customSolversDirectory = tempfile.mkdtemp()
-        self.version = '1.9'
+        self.version = '1.10'
 
     def __del__(self):
         if os.access(self.customSolversDirectory, os.F_OK):
@@ -844,6 +844,9 @@
                 ' -I' + os.path.join(rp, 'src') +\
                 ' -I' + self.customSolversDirectory + ' '
             command = cxx + cxxFlags + source
+            # For linux, we need the rt library.
+            if re.match('linux', sys.platform):
+                command += ' -lrt'
         process = subprocess.Popen(command, bufsize=-1,
                                    universal_newlines=True, shell=True,
                                    stdin=subprocess.PIPE,