Thanks to alecmascot which explained to us how to configure to build from source.
In the Makefile in the line CONFIGURE_ARGS at the end we add --enable-embedded-cryptopp.
The procedure is as follows:
#In urbackup-server jail
iocase console urbackup
portsnap auto
cd /usr/ports/archivers/urbackup-server
pkg install `make build-depends-list | sed s%/usr/ports/%%g | sed '/sqlite3/d'`
sed -i '.bak' -e 's/CONFIGURE_ARGS.*/& --enable-embedded-cryptopp/' Makefile
make
make deinstall
make reinstall
service urbackup_server start