I have several responses, not necessarily consistent with each other.

1. An appendix should be a user manual with screen shots.

2. The archival version of the package should be Yourpackage_x.y-z.tar.gz
stored
at your university's archival web location.  The actual usable version of
your package
will be the Yourpackage_a.b-c.tar.gz on CRAN and the version number will
keep
moving upward every few months.

3. A printed dissertation is a collection of paper pages.  Why do you feel
the need to
reformat the Yourpackage.pdf that is created by the
    R CMD build Yourpackage
command?  The pdf file is already something that can be printed.
Reformating it will almost
certainly introduce errors.

Rich

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