I'm working to install the Bioconductor packages for MSGF+ and MSGFgui on a new windows box. The problem I'm seeing is one that has been reported before. Namely complaints by the installer that the directory is unavailable.
Installation path not writeable, unable to update packages: boot, foreign,
lattice, MASS, nlme, nnet
Old packages: 'plyr', 'rlang'
Previous responses have indicated that this is due to installation of packages without admin access and concerns about changing permissions. However, my user account does have admin rights under which I installed R 3.6.2
The suggestions in the following post did not resolve the issue
Even though your account has Admin rights, on Windows, you may still have to run R as Admin by right-clicking on the R icon and then selecting 'Run as Administrator' (I think). After you do that, please try again.
When posting R code or output, you need to either highlight the code and click the 101010 box, or surround with triple backticks. I have done that for you, and the code now shows something different. What it is saying is that you cannot update the recommended packages that come with R, which is pretty much always true for a Windows installation, unless you force the installation to be somewhere other than C:\Program Files. That you can't update those packages is usually irrelevant, as they have been around since the early days and aren't likely to be updated within release cycles.
You are also being told that plyr and rlang which are not recommended packages, and are almost surely not being installed in a library dir that requires admin privileges are in need of update, and you have cut off the part where you are asked if you want to update.
Long story short, this isn't an issue and you can ignore the part about Installation path not writeable
Thanks - I appreciate the comments. I've been able to make some progress now.