Yes, PHP up to and including 5.4 (the patch hasn't been ported to 5.5
yet) is using system implementation of available ciphers.
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https://bugs.launchpad.net/bugs/1183338
Tit
Debian/Ubuntu may use a different implementation perhaps, such as the
system one. But what you have is a question rather than a bug - perhaps
try askubuntu.com?
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My question is then, why does this behaviour only show itself on Ubuntu
(debian?) based systems? None of the other OS'es I have tried seem to
have this issue. In fact it seems they fill the 'missing' salt with '$'.
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I have reproduced the behaviour you describe on 5.4.9-4ubuntu2.
According to the documentation, the salt provided for Blowfish must be:
22 characters from the alphabet "./0-9A-Za-z"
See: http://php.net/manua