When trying to upgrade Magento from 2.0.2 to 2.0.4 I got a windows saying Update in progress and the last line from the system log says “./composer.json has been updated” then nothing more happens for quite a long time. Finally an error screen displays “Error in Update!”.
To restart the update process while trying to figure out the error i had to manually delete the files var/.maintenance.flag and var/.update_in_progress.flag.
To make Magento run in Apache we had set php.ini for the web user to memory_limit=1024M and according to instructions, the cron jobs should be called with the -c pointing to the php.ini used by the web server, in our case /etc/php5/fpm/php.ini.
No error message revealed why the update failed but I found out that the php.ini we used for cron (/etc/php5/fpm/php.ini) had a memory_limit=128M. By editing this file and increasing it to 1024M the update worked.