i get the next compile error

checking for Eigen 3 library:
ERROR: compiler error!

Use the EIGEN_CFLAGS environment variable to set the path to
the Eigen3 include files and to set any required flags
For example:
EIGEN_CFLAGS="-isystem /usr/include/eigen3" ./configure

I tried to fix it but I can’t. Any help? tanks!


Hi Inaki,
Looks like you will need to install the Eigen library dependency. Check out the ‘Install dependency’ instructions for your OS here: http://mrtrix.readthedocs.org/en/latest/


I am having the same issue (on a Mac). Homebrew installed Eigen into /usr/local/Cellar/eigen/3.2.8/include/eigen3/Eigen. I have set EIGEN_CFLAGS as an environment variable (in tcsh: setenv EIGEN_CFLAGS /usr/local/Cellar/eigen/3.2.8/include/eigen3/Eigen). printenv shows that it points to the right directory. However, I can’t get ./configure to see it. Any help appreciated.


Hello Anthony,

I don’t need to set this flag on my mac with Eigen installed via homebrew. It appears that you forgot the isystem part of the CFLAG. Have you tried
setenv EIGEN_CFLAGS "-isystem /usr/local/Cellar/eigen/3.2.8/include/eigen3/Eigen" ./configure?
Also it might be worth running brew doctor to check whether there are any issues with your eigen installation.


setenv EIGEN_CFLAGS “-isystem /usr/local/Cellar/eigen/3.2.8/include/eigen3/Eigen” returns the same error, but it proceeds fine if I put this in my .cshrc file:

setenv EIGEN_CFLAGS “-isystem /usr/local/Cellar/eigen/3.2.8/include/eigen3”

Sorry–wasn’t familiar with the -isystem flag, but to be fair it is right in the error!

Now I have a qmake error to deal with, but thanks for the help on this one!