You are using a rather old guide, you should always use the latest guides on http://geonetwork-opensource.org/
I am not familiar with this installation of geonetwork, but there are some things you can check. It is complaining because the database (h2 database) which should be created on ~/.geonetwork/geonetwork is not correctly configured.
If you really followed the steps on the guide, you should be using postgreSQL and not h2. Check the config.xml file on WEB-INF to disable the h2 database and use the postgreSQL one.
For simplicity, if you don't want to use postgreSQL yet and just want to test the installation:
- If you really followed the steps on the guide, you should be using postgreSQL and not h2. Check the config.xml file on WEB-INF to disable the h2 database and use the postgreSQL one.
- Can you check ~/.geonetwork/geonetwork to see if there is something there? If there is, just remove it and restart geoNetwork. ~ represents your home folder, like /home/gabriel
- The log also talks about some configuration on the svn. Can you check the property geonet:dburl on /var/lib/tomcat7/webapps/geonetwork/WEB-INF/data/data/metadata_subversion? Try to change it with 'jdbc:h2:~/.geonetwork/geonetwork;LOCK_TIMEOUT=20000;DB_CLOSE_ON_EXIT=FALSE;MVCC=TRUE' and see if it works.
- If nothing of the above works, you can try to just remove the data folder so it can be recreated after a restart. Can you remove the folder /var/lib/tomcat7/webapps/geonetwork/WEB-INF/data/ and restart?
Anyway, I always recommend to deploy geoNetwork just dropping the war on any webapps folder of any tomcat without modifying anything else. It is the simplest way to do it and it works 99% of the time.