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I have downloaded and unpacked Bluez 5.45. I successfully ran

./configure
make
make install

And I restarted my machine.

bluetoothctl
[bluetooth]#version

Gives me Version 5.45, however

bluetoothd -v 

Gives me 5.37.

Why the discrepancy?

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If you look at the contents of the bluez package you'll note that bluetoothd and bluetoothctl are seperate programs, not to be confused with the version of the package. It's not uncommon for a collection for programs in a package to have their own separate versions. In order to insure that you aren't using an out pf date version of one of the aforementioned programs you could use which to insure that you are launching the one that you installed by checking the location against the file list shown in the first link that I provided. You'll see that which bluetoothd should respond with /usr/sbin and which bluetoothctl should respond with /usr/bin/ if you get those results odds are good that nothing is wrong. Unless you've used a PPA or installed bluez by compiling it yourself, in which case your question requires further detail.

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