Ok, I'm starting to think the problem is not related to paperconf, but to 
the next step (gfortran).

This is in R's config.log, at the bottom, when run by Sage as part of the 
Sage build process:

configure:35349: result: yes
configure:35369: checking for lpr
configure:35385: found /usr/bin/lpr
configure:35396: result: lpr
configure:35417: checking for paperconf
configure:35435: found /home/svanzwam/local/bin/paperconf
configure:35448: result: /home/svanzwam/local/bin/paperconf
autodetect~

Note the auto detectline, which has no newline at the end.

When I run "./configure" from the Sage shell, I get the following after 
paperconf:

checking for lpr... lpr
checking for paperconf... /home/svanzwam/local/bin/paperconf
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking whether we are using the GNU Fortran compiler... (cached) yes
checking whether gfortran accepts -g... (cached) yes
checking if libtool supports shared libraries... yes

Note no autodetect line at all. What's going on? What's different when the 
Sage installation runs configure?

--Stefan.

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