You are missing the default Ivritex fonts. You can try installing them from http://ivritex.sourceforge.net, but it's considered deprecated.
Preferably, you should install culmus-latex which provides a Hebrew support based on the Culmus fonts.
The TeX systems relies on a cache for finding files, in order to reduce search time in its huge directories.
The main trees all have at their top level a file named ls-R that contains a tree representation of the subdirectories and their contents.
When a new file is installed in a directory in the main tree, the cache needs to be updated by
sudo texhash
However, it's not a good idea to modify the directories in the main tree because they might be restored during an update and you'd end up with an unstable TeX system.
All TeX distributions maintain a "local" tree, which you can find the location of with the shell command
kpsewhich -var-value TEXMFLOCAL
On my machine it is
/usr/local/texlive/texmf-local
You can create the relevant subtree with
sudo mkdir -p $(kpsewhich -var-value TEXMFLOCAL)/tex/latex/microtype
and then copy the files belonging to the microtype package in the created directory by
sudo cp * $(kpsewhich -var-value TEXMFLOCAL)/tex/latex/microtype
assuming you are in a work directory containing the downloaded file. A new
sudo texhash
will enable you to work with microtype version 2.5 without touching the original, since the "local" tree is looked at before the main tree.
Best Answer
Try removing TeX Live's
expl3. It seems thatexpl3is now known asl3kernelbut jnovy's repository still includes both and causes some confusion.