The following steps should help to fix the problem:
Another possible cause is an issue with the protections on the files: Please run
- Remove any related v3.5.CR(x).done file under /opt/Deployment/lrs folder. This allows Portal to re-run the patch using the upgrade script.
- Edit /etc/httpd/conf/httpd.conf and change default Timeout value from 60 to 300 seconds.
- Enable new settings by executing at command prompt: service httpd reload
- Reinstall the patch.
chown -R l7portal:portalusers /opt/Deployments/lrs/repository
on the portal to ensure, that all files have the right owner and group.