There is the issue that I have:

$ CTEST_OUTPUT_ON_FAILURE=1 make test
Running tests...
Test project /home/alex/Downloads/cpd/build
Start 1: affine
1/9 Test #1: affine ........................... Passed 2.35 sec
Start 2: gauss_transform
2/9 Test #2: gauss_transform .................. Passed 0.37 sec
Start 3: nonrigid
3/9 Test #3: nonrigid ......................... Passed 33.65 sec
Start 4: normalization
4/9 Test #4: normalization ....................***Exception: Other 0.09 sec
Running main() from gtest_main.cc
[==========] Running 1 test from 1 test case.
[----------] Global test environment set-up.
[----------] 1 test from FishTest
[ RUN ] FishTest.CanBeRetrieved
fixed mean: -1.0044e-06
1.76923e-07
fixed dimensions: 91 by 2
moving mean: -1.0044e-06
1.76923e-07
moving dimensions: 91 by 2
scale: 1
normalization: /usr/include/eigen3/Eigen/src/Core/CwiseBinaryOp.h:110: Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::CwiseBinaryOp(const Lhs&, const Rhs&, const BinaryOp&) [with BinaryOp = Eigen::internal::scalar_sum_op; LhsType = const Eigen::CwiseUnaryOp<Eigen::internal::scalar_multiple_op, const Eigen::Matrix<double, -1, -1> >; RhsType = const Eigen::Matrix<double, -1, 1>; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Lhs = Eigen::CwiseUnaryOp<Eigen::internal::scalar_multiple_op, const Eigen::Matrix<double, -1, -1> >; Eigen::CwiseBinaryOp<BinaryOp, Lhs, Rhs>::Rhs = Eigen::Matrix<double, -1, 1>]: Assertion `aLhs.rows() == aRhs.rows() && aLhs.cols() == aRhs.cols()' failed.

Start 5: rigid

5/9 Test #5: rigid ............................ Passed 0.26 sec
Start 6: utils
6/9 Test #6: utils ............................ Passed 0.04 sec
Start 7: version
7/9 Test #7: version .......................... Passed 0.00 sec
Start 8: gauss_transform_fgt
8/9 Test #8: gauss_transform_fgt .............. Passed 0.23 sec
Start 9: jsoncpp
9/9 Test #9: jsoncpp .......................... Passed 0.00 sec

89% tests passed, 1 tests failed out of 9

Total Test time (real) = 37.00 sec

The following tests FAILED:
4 - normalization (OTHER_FAULT)
Errors while running CTest
Makefile:105: recipe for target 'test' failed
make: *** [test] Error 8

I think I might have found the bug. It was a combination of two things I often screw up when working with Eigen (forgetting to replicate out vectors, and the fact that isApprox passes ok even if the matrix dimensions don't agree), and I'm glad your version of Eigen caught it.

If you can pull down this latest version of the branch and test, I would appreciate it.

Edit: To be clear, this bug is only in the test suite, not in the code itself, so this won't fix/change any of your original issues.

Thank you Pete!

$ make test
Running tests...
Test project /home/alex/Downloads/cpd/build
Start 1: affine
1/9 Test #1: affine ........................... Passed 2.25 sec
Start 2: gauss_transform
2/9 Test #2: gauss_transform .................. Passed 0.36 sec
Start 3: nonrigid
3/9 Test #3: nonrigid ......................... Passed 31.93 sec
Start 4: normalization
4/9 Test #4: normalization .................... Passed 0.00 sec
Start 5: rigid
5/9 Test #5: rigid ............................ Passed 0.25 sec
Start 6: utils
6/9 Test #6: utils ............................ Passed 0.04 sec
Start 7: version
7/9 Test #7: version .......................... Passed 0.00 sec
Start 8: gauss_transform_fgt
8/9 Test #8: gauss_transform_fgt .............. Passed 0.23 sec
Start 9: jsoncpp
9/9 Test #9: jsoncpp .......................... Passed 0.00 sec

100% tests passed, 0 tests failed out of 9

Total Test time (real) = 35.06 sec