I'm posting in case others have this issue.

warning: opendir(sites/all/libraries) [function.opendir]: failed to open dir: Permission denied in /modules/contrib/libraries/libraries.module on line 100.

my setup
sites/all/libraries -> /var/aegir/platforms/libraries
I created a symbolic link to the directory
I had to :
chmod 775 /var/aegir/platforms/libraries and it all went away

the line in question is

 if (is_dir($dir) && $handle = opendir($dir)) {

while this error shows up all libraries are included in admin/reports/status