The patch is attached. Anton
diff -Nru cain-1.9/debian/changelog cain-1.9/debian/changelog --- cain-1.9/debian/changelog 2012-08-16 12:55:22.000000000 +0200 +++ cain-1.9/debian/changelog 2013-10-13 15:30:35.000000000 +0200 @@ -1,3 +1,10 @@ +cain (1.9-6.1) unstable; urgency=low + + * Non-maintainer upload. + * Replace libeigen2-dev by libeigen3-dev. (Closes: #726200) + + -- Anton Gladky <gl...@debian.org> Sun, 13 Oct 2013 15:25:39 +0200 + cain (1.9-6) unstable; urgency=low * Enable arch only builds (thanks for the patch to Adam Conrad diff -Nru cain-1.9/debian/control cain-1.9/debian/control --- cain-1.9/debian/control 2012-08-10 13:49:26.000000000 +0200 +++ cain-1.9/debian/control 2013-10-13 10:08:27.000000000 +0200 @@ -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. diff -Nru cain-1.9/debian/patches/eigen3.patch cain-1.9/debian/patches/eigen3.patch --- cain-1.9/debian/patches/eigen3.patch 1970-01-01 01:00:00.000000000 +0100 +++ cain-1.9/debian/patches/eigen3.patch 2013-10-13 15:10:31.000000000 +0200 @@ -0,0 +1,33 @@ +Description: Use Debian packaged libeigen +Author: Ivo Maintz <i...@maintz.de> +Date: Wed, 28 Sep 2011 12:02:11 +0200 +Last-Update: 2013-10-13 (Anton Gladky <gl...@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; + } + } diff -Nru cain-1.9/debian/patches/eigen.patch cain-1.9/debian/patches/eigen.patch --- cain-1.9/debian/patches/eigen.patch 2012-05-22 08:20:43.000000000 +0200 +++ cain-1.9/debian/patches/eigen.patch 1970-01-01 01:00:00.000000000 +0100 @@ -1,17 +0,0 @@ -Description: Use Debian packaged libeigen -Author: Ivo Maintz <i...@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 { - diff -Nru cain-1.9/debian/patches/series cain-1.9/debian/patches/series --- cain-1.9/debian/patches/series 2012-08-10 13:28:41.000000000 +0200 +++ cain-1.9/debian/patches/series 2013-10-13 15:09:38.000000000 +0200 @@ -1,5 +1,5 @@ cain.patch -eigen.patch +eigen3.patch gcc-4.7.patch hardening.patch help.patch
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