Are any of the files on a separate (read-only) filesystem? NFS, or something like mount -i ro

Can you can have a look at the output of mount and make sure that none of the files you (and spyder is interested in, are somewhere where they shouldn't)

Also, download into a temporary directory in your homedir (not /tmp. Some systems don't let you execute stuff there) and use the bootstrap method to start:
python bootstrap.py


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