The case of the not-so-missing library file
I hit the first of what will no doubt be several adventures when I reinstalled RStudio desktop and discovered it would not run. Despite the installer saying that all dependencies were satisfied, when I tried to run it from a command line I was told that a library file (libGL.so.1) could not be found.
I'll skip over another hour or so of pointless flailing and cut to the chase scene. It turns out that libGL.so.1 actually was installed on my laptop, as part of the libgl1-mesa-glx package. It was hiding in plain sight in /usr/lib/x86_64-linux-gnu/mesa/. Somehow, that folder had not made it onto the system library path. (I have no idea why.) So I ran the command
sudo ldconfig /usr/lib/x86_64-linux-gnu/mesa
and that fixed the problem.
Editor? We don't need no stinkin' editor
Next up, I couldn't find a text editor! Note that LibreOffice was installed, and was the default program to open text (.txt) files. Huh?? Poking around, I found nano, but xed (the default text editor in Mint 18) and gedit (the previous default editor) were not installed (even though xed was present before the upgrade).
Fixing this was at least (to quote a math prof I had in grad school) "tedious but brutally straightforward". In the software manager, I installed xed ... and xreader, also MIA. For whatever reason, the other X-Apps (xviewer, xplayer and pix) were already installed (as they all should have been).
The mystery of the launcher that wouldn't launch
Mint has a utility (mintsources) that lets you manage the sources (repositories, PPAs etc.) that you use. There is an entry for it in the main menu, but clicking that entry failed to launch the source manager. On the other hand, running the command ("pkexec mintsources") from a terminal worked just fine.
I found the original desktop file at /usr/share/applications/mintsources.desktop (owned by root, with read and write permissions but not execute permission). After a bunch of messing around, I edited the menu entry through the menu editor (by right-clicking the menu entry and selecting "Edit properties"), changing "pkexec mintsources" to "gksudo mintsources". That creating another version at ~/.local/share/applications/mintsources.desktop. After right-clicking the main menu button and clicking "Reload plugins", the modified entry worked. I have no idea why that works but "pkexec mintsources" does not, even though it does from a terminal. I tried editing back to "pkexec", just in case the mere act of editing was what did the trick, but no joy there. So I edited back to "gksudo", which seems to be working ... for now ... until the gremlins return from their dinner break.
Update: No sooner did I publish this than I found another instance of the same problem. The driver manager would not launch from the main menu. I edited "pkexec" to "gksudo" for that one, and again it worked. I guess "pkexec" is somehow incompatible with the Mint menu (at least on my laptop).
I'll close for now with a link to "Solutions for 24 bugs in Linux Mint 19".