Taking CXXFLAGS and LD_LIBRARY_PATH from Scipion

[dmaluenda]

I'm coping an issue derived from a mail at scipion-users@lists.sourceforge.net.

The generated config file overrides any/some preset environment variables, especially problematic when you compile within Scipion and you set something in the Scipion's config.

I couldn't find a way of inheriting CCFLAGS or CXXFLAGS without hacking the code. Allowing additional variables (LD_LIBRARY_PATH, LIBRARY_PATH, C_INCLUDE_PATH) might be a good enhancement for those of us who have multiple versions of core libraries available in a multiuser environment.

[albertmena]

The behavior of the installation is the opposite (scipion Troubleshooting):

You can manually set some variables in the <SCIPION_HOME>/xmipp-bundle/xmipp.conf. However, Scipion will automatically override this config file when recompiling Xmipp. To prevent this, export XMIPP_NOCONFIG=True or include XMIPP_NOCONFIG=True in the <SCIPION_HOME>/config/scipion.conf prior to trigger a new compilation.

You can add next lines in scipion.conf

[BUILD]
CXX = /usr/bin/g++-9

run scipion3 config and scipion3 run ./xmipp config and the xmipp.conf file 'll get that CXX