[med-svn] r14832 - in trunk/packages/cain/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2013-10-14 19:43:44 +0000 (Mon, 14 Oct 2013)
New Revision: 14832

Added:
   trunk/packages/cain/trunk/debian/patches/eigen3.patch
Removed:
   trunk/packages/cain/trunk/debian/patches/eigen.patch
Modified:
   trunk/packages/cain/trunk/debian/changelog
   trunk/packages/cain/trunk/debian/control
   trunk/packages/cain/trunk/debian/patches/series
Log:
Replace libeigen2-dev by libeigen3-dev.  (Thanks for the patch to Anton Gladky <gladk at debian.org>)


Modified: trunk/packages/cain/trunk/debian/changelog
===================================================================
--- trunk/packages/cain/trunk/debian/changelog	2013-10-14 19:26:32 UTC (rev 14831)
+++ trunk/packages/cain/trunk/debian/changelog	2013-10-14 19:43:44 UTC (rev 14832)
@@ -1,3 +1,11 @@
+cain (1.9-7) UNRELEASED; urgency=low
+
+  * Replace libeigen2-dev by libeigen3-dev.  (Thanks for the patch to
+    Anton Gladky <gladk at debian.org>)
+    Closes: #726200
+
+ -- Andreas Tille <tille at debian.org>  Mon, 14 Oct 2013 21:35:53 +0200
+
 cain (1.9-6) unstable; urgency=low
 
   * Enable arch only builds (thanks for the patch to Adam Conrad

Modified: trunk/packages/cain/trunk/debian/control
===================================================================
--- trunk/packages/cain/trunk/debian/control	2013-10-14 19:26:32 UTC (rev 14831)
+++ trunk/packages/cain/trunk/debian/control	2013-10-14 19:43:44 UTC (rev 14832)
@@ -7,11 +7,10 @@
 Build-Depends: debhelper (>= 9),
  python-all-dev,
  python (<< 3.0),
- libeigen2-dev,
+ libeigen3-dev,
  zip
 Standards-Version: 3.9.3
 Homepage: http://cain.sourceforge.net
-DM-Upload-Allowed: yes
 Vcs-Browser: http://svn.debian.org/viewvc/debian-med/trunk/packages/cain/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/cain/trunk/
 
@@ -51,7 +50,7 @@
 Package: cain-solvers
 Architecture: any
 Depends: ${shlibs:Depends}, ${misc:Depends},
- libeigen2-dev
+ libeigen3-dev
 Description: simulations of chemical reactions
  Cain performs stochastic and deterministic simulations of chemical reactions.
  It can spawn multiple simulation processes to utilize multi-core computers.

Deleted: trunk/packages/cain/trunk/debian/patches/eigen.patch
===================================================================
--- trunk/packages/cain/trunk/debian/patches/eigen.patch	2013-10-14 19:26:32 UTC (rev 14831)
+++ trunk/packages/cain/trunk/debian/patches/eigen.patch	2013-10-14 19:43:44 UTC (rev 14832)
@@ -1,17 +0,0 @@
-Description: Use Debian packaged libeigen
-Author: Ivo Maintz <ivo at maintz.de>
-Date: Wed, 28 Sep 2011 12:02:11 +0200
-
---- cain-1.9.orig/src/stochastic/TauLeapingImplicit.h
-+++ cain-1.9/src/stochastic/TauLeapingImplicit.h
-@@ -13,8 +13,8 @@
- 
- #include "../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h"
- 
--#include "../third-party/Eigen/LU"
--#include "../third-party/Eigen/Array"
-+#include "/usr/include/eigen2/Eigen/LU"
-+#include "/usr/include/eigen2/Eigen/Array"
- 
- namespace stochastic {
- 

Added: trunk/packages/cain/trunk/debian/patches/eigen3.patch
===================================================================
--- trunk/packages/cain/trunk/debian/patches/eigen3.patch	                        (rev 0)
+++ trunk/packages/cain/trunk/debian/patches/eigen3.patch	2013-10-14 19:43:44 UTC (rev 14832)
@@ -0,0 +1,33 @@
+Description: Use Debian packaged libeigen
+Author: Ivo Maintz <ivo at maintz.de>
+Date: Wed, 28 Sep 2011 12:02:11 +0200
+Last-Update: 2013-10-13 (Anton Gladky <gladk at debian.org>, move to Eigen3)
+
+--- a/src/stochastic/TauLeapingImplicit.h
++++ b/src/stochastic/TauLeapingImplicit.h
+@@ -13,8 +13,8 @@
+ 
+ #include "../numerical/random/poisson/PoissonGeneratorInvAcNormSure.h"
+ 
+-#include "../third-party/Eigen/LU"
+-#include "../third-party/Eigen/Array"
++#include "/usr/include/eigen3/Eigen/LU"
++#include "/usr/include/eigen3/Eigen/Core"
+ 
+ namespace stochastic {
+ 
+--- a/src/stochastic/TauLeapingImplicit.ipp
++++ b/src/stochastic/TauLeapingImplicit.ipp
+@@ -153,10 +153,10 @@
+       //std::cout << "Jacobian =\n" << jacobian << '\n'
+       //<< "f = \n" << f << '\n';
+       Eigen::VectorXd delta(N);
+-      jacobian.lu().solve(f, &delta);
++      delta = jacobian.fullPivLu().solve(f);
+       x += delta;
+       //std::cout << "delta =\n" << delta << '\n';
+-      if (delta.cwise().abs().sum() < tolerance) {
++      if (delta.cwiseAbs().sum() < tolerance) {
+          break;
+       }
+    }

Modified: trunk/packages/cain/trunk/debian/patches/series
===================================================================
--- trunk/packages/cain/trunk/debian/patches/series	2013-10-14 19:26:32 UTC (rev 14831)
+++ trunk/packages/cain/trunk/debian/patches/series	2013-10-14 19:43:44 UTC (rev 14832)
@@ -1,5 +1,5 @@
 cain.patch
-eigen.patch
+eigen3.patch
 gcc-4.7.patch
 hardening.patch
 help.patch