I had a similar problem earlier this week. The cause was the MikTeX mirror
I was using was reporting that versions of LaTeX elements were present, but
when the updater would run from LyX to install missing things, it would
fail. The errors show in LyX message console, but they aren't fatal. I
discovered this by running the update/package manager myself outside of
LyX.

The short term solution was to choose another LaTeX distribution mirror in
MikTeX updater by running it outside LyX.

On Thu, Dec 8, 2016, 23:35 Scott Kostyshak <skost...@lyx.org> wrote:

> On Sun, Nov 27, 2016 at 04:20:22PM +0000, Guillermo Cruces wrote:
> > Hi everyone, I have been a Lyx user for years. Awesome program! Every
> version change has been a bit bumpy, but a reconfigure used to work. Not
> now. Here are my issues, just posted on stackexchange too:
> >
> > I have issues with packages with Lyx 2.2 on Windows 10. I have updated
> packages on MikTex as admin, I have changed the option to ask me first
> instead of update packages on the fly (even though I selected ask me first
> during install, it still got set at on the fly), I have updated directories
> on miktex options (admin), I have reconfigured lyx, and nothing. When I
> open a beamer file, it says the beamer.cls (and set space and many others
> are available) and while it asks for downloading them within lyx, they
> don't seem to "stick".
> >
> > I have managed to compile my file by going to the Miktex package manager
> (as admin) and installing manually every package that lyx complained was
> not available. I get a PDF (although it complains the PDF viewer is
> missing...). While it compiles, it still complains that the beamer class,
> xcolor, etc., are not available when opening the file.
> > It seems to me something in the settings/update/confir of Lyx+Miktex is
> not working. Anyone can confirm this? Any solutions? I'll try running Lyx
> as admin just in case...
>
> Hi Guillermo,
>
> I'm CC'ing Uwe, who is our only developer on Windows. Hopefully he has
> an idea of what's going on.
>
> Sorry for the frustration.
>
> Scott
>

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