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You can upgrade the cPanel from the command line of the server, But before that you need to check some things on your server,
1. Check the current cPanel version.
2. Change the file /etc/cpupdate.conf to,
3. Also you need to backup some important files and folders used by the mail server,
cp /etc/exim.conf /etc/exim.conf-`date +%F` cp /etc/exim.conf.local /etc/exim.conf-`date +%F` cp -arf /etc/exim /etc/exim-`date +%F` cp /etc/exim.pl /etc/exim.pl-`date +%F` cp -arf /etc/mail/spamassassin /etc/mail/spamassassin-`date +%F` cp -arf /usr/local/cpanel/etc/exim /usr/local/cpanel/etc/exim-`date +%F`
4. Now you can run the scricpt for upgrading cPanel,
5. Wait for the upgrading process to complete.
6. After the completion of the process, check the current cPanel version and confirm it have been successfully upgraded.
7. Now copy the mailserver conf(exim.conf) from backup to /etc/exim.conf.local
8. Run the following script to rebuild the exim configuration,
9. Make sure the rebuild process completed successfully.
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