This question was already answered multiple times, e.g. in Code integrity check errors
In short: extract the file .user.ini from your original tarball or zip and overwrite this file in your ownCloud.installation.
Alternatively, if you made changes to .user.ini which are there for a good reason, you may exclude this file from the integrity check, see the sample configuration: https://github.com/owncloud/core/blob/9db442250583d3b71e633cf77fbcf643ed67e994/config/config.sample.php#L1317