Did you check SELinux options ??

I have a similar problem. For some unknown reason scan_dir() is not
able to read /home/user when run as Apache module. but the CLI is
giving expected results. I did not find any work around, but had to
read /var/www which is the home directory of 'apache' (this is the
user under which apache runs by default. hence you script needs 777 to

So if every thing else fails I'll recommend you to move the script to
/var/ww (usually your server root) instead of /home/user

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