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Maybe the difference is that Sage has Fortran installed but your basic installation on your computer does not, and PyNIO detects it with the Sage version, tries to install the Fortran code, and runs into problems. If this is the case, maybe the problems can be avoided by setting environment variables correctly: see http://www.pyngl.ucar.edu/Download/build_pynio_from_src.shtml#SetEnvVars. For example, maybe

export F2CLIBS=gfortran
export F2CLIBS_PREFIX=.../path/to/sage/local/lib


will fix it.

Maybe the difference is that in the Fortran installations in Sage has Fortran installed but your basic installation vs. on your computer does not, and PyNIO detects it with the Sage version, tries to install the Fortran code, and runs into problems. computer. If this is the case, maybe the problems can be avoided by setting environment variables correctly: see http://www.pyngl.ucar.edu/Download/build_pynio_from_src.shtml#SetEnvVars. For example, maybe

export F2CLIBS=gfortran
export F2CLIBS_PREFIX=.../path/to/sage/local/lib


will fix it.