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Course preparation - troubleshooting

December 20 2022

install_troubleshooting.Rmd

If a package installation didn’t work or a library(xxx) call didn’t work, then you have probably got an installation issue. The installation details should be printed in your RStudio Console and can help you troubleshoot the error. We’ll use the example here of errors while calling install_github("SBOHVM/RPiR"), but it could equally apply to installing another package, such as install.packages("vegan").

Restarting R

Quite often restarting R (Session > Restart R) can solve your problem. Just remember that once you’ve restarted R, you’ll need to call library(devtools) again to load it back into RStudio.

Also, if you find you’re stuck in a loop (perhaps after installing fansi), and R is asking if you’d like to restart over and over again (because the package is already loaded):

then just say no to restarting it the second time.

Non-zero exit status 

Warning in install.packages :
  installation of package ‘rlang’ had non-zero exit status

Try restarting R (Session > Restart R) and reinstalling whatever package had non-zero exit status (zero is success, so non-zero is a failed install), in this case rlang:

Assuming this worked, restart R again(!), and re-run install_github("SBOHVM/RPiR").

Rtools is required to build R packages but is not currently installed… 

WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

Go here to download and install Rtools.

This might also be associated with a package install error, such as:

namespace ‘rlang’ 0.4.0 is already loaded, but >= 0.4.1 is required

In which case you should reinstall whatever package had the problem, in this case the rlang package:

Assuming this worked, restart R again(!), and re-run install_github("SBOHVM/RPiR").

Cannot remove prior installation… 

"Error in install.packages : cannot remove prior installation of package ‘rlang’ "

For any cannot remove prior installation error, try restarting R (Session > Restart R) and reinstalling whatever package Windows couldn’t remove, in this case rlang:

Assuming this worked, restart R again(!), and re-run install_github("SBOHVM/RPiR").

Try removing ‘C:.../00LOCK’ 

package ‘rlang’ successfully unpacked and MD5 sums checked
Error in install.packages : ERROR: failed to lock directory ‘C:\Users\User\Documents\R\win-library\3.6’ for modifying
Try removing ‘C:\Users\User\Documents\R\win-library\3.6/00LOCK’

For this one, you need to find the 00LOCK file and delete it. Then try installing whatever package was being unpacked, in this case rlang:

Assuming this worked, restart R again(!), and re-run install_github("SBOHVM/RPiR").

If that doesn’t work after a couple of attempts, then you can try installing the package while ignoring the lock files:

install.packages("Rcpp", dependencies = TRUE, INSTALL_opts = '--no-lock')

Fortran on Mac

If you have trouble getting a package (e.g. vegan) to install with inscrutable errors that mention fortran, then this is normal! If you’re on a Mac, then you should go to this site and download the correct version of gfortran depending on your computer and install it. Then restart R and try again!

If you’re on Windows or some other platform and find this error, ask for help!

libgit2 on Mac / Linux

If you are on a Mac, it’s very likely you got an error because you need to have libgit2 installed. If so, then you probably also need to install Homebrew - follow the instructions on https://brew.sh to do this. Once Homebrew is installed, you can install libgit2 using Homebrew by opening the Terminal app and then typing:

brew install libgit2

The same may happen on Linux, and you will need to use the distribution’s package manager to install either libgit2-dev or libgit2-devel, depending on whether you are on Debian/Ubuntu or Fedora/CentOS/RHEL, respectively.