Upgrading your R libraries after OS upgrade

I recently posted about how to do an upgrade to Fedora 26 while maintaining the Nvidia drivers. So, what are you supposed to do with your R libraries you downloaded? If you try to use audit-explorer in RStudio, you'll get an error because system library versions have changed.

There are instructions on the web about how to do this. They basically say to run:

update.packages(ask=FALSE, checkBuilt = TRUE)

This basically works fine in some cases, but in our case the OS was upgraded and R can't tell that anything needs to be done because our R libraries were up to date before upgrading the OS.

We can run a script to remove and re-install the old libraries. The script works because the R libraries on the system were upgraded when you went to F26. All we need to do is rebuild the ones kept in your home dir.

The following script should be self explanatory.

# Ask R where it keeps its libraries
all <- .libPaths()

# Ask R where its system libraries are
site <- .Library.site

# Now subtract one from the other to get your home dir libraries
loc <- setdiff(all, site)

# Take a look at loc to ensure it only point to the R directory in your home dir
loc

# Ask R for the list of packages in your home dir
plist <- installed.packages(lib.loc = loc)
df <- as.data.frame(plist)
# Take a look at the packages to ensure this looks about right
#View(df)

# Get rid of the old ones
for (p in df$Package) { remove.packages(p) }

# Reinstall the packages
for (p in df$Package) { install.packages(p) }

When you run this, single step one line at a time. Do not run the whole thing. Single step it to the point where it outputs 'loc'. Does it look like a directory in your home dir? I get

"/home/sgrubb/R/x86_64-redhat-linux-gnu-library/3.4"

OK. Now single step down to the View(df) call. Uncomment that if you want. It shows a real nice table of all the package info.

Now its time for the scary part...deleting all the packages. Step over the first for loop. You will see a whole bunch of red text scroll in the Console pane. This is normal.

Now to put it all back, step over the last for loop. RStudio  will ask you if you want to restart R prior to installing. Tell it yes. It will ask again. This time cancel it by clicking on the X in the corner of the dialog. The dialog will pop up again and again. Click the X to close it. At some point it thinks it finished your for loop and it didn't. You can tell because you see an empty cursor ready to use in the console pane.

Fear not. Run the last for loop again. This time it will be unimpeded and will proceed to download and install all of your packages.

Whatever you do, do not exit RStudio until it after the second run of the for loop finishes. This can take 10 or 20 minutes depending on how many libraries you have. Exiting before the building finishes will surely lose the list of packages. You can tell its done because the Console pane is ready to use again.


Conclusion
When you upgrade the OS, sometimes R libraries won't work and upgrading doesn't work because you are on the latest version. The solution is running a script. It is not without danger, but it does the trick.