Confusion with .libPaths during package install - r

Question

This will probably be answered by someone directing me to a help file but I'm clearly missing it thus far. My quandry is that when I install a package (sometimes), it does not appear to default to the contents of my .libPaths - instead it appears to want to install to a network path to which it does not have permission.
Here is my library path
>.libPaths()
[1] "C:/Program Files/R/R-3.3.0/library"
If I try to install this package without specifying the lib argument it seems like it is trying to save to a network folder (I have changed the name of the network drive in the error message but you get the idea):
> install.packages("rmarkdown")
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/rmarkdown_0.9.6.zip'
Content type 'application/zip' length 2182803 bytes (2.1 MB)
downloaded 2.1 MB
package ‘rmarkdown’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\my.name\AppData\Local\Temp\RtmpkFVHnn\downloaded_packages
Warning message:
In dir.create(configDir, recursive = TRUE) :
cannot create dir '\\server.name\server_directory', reason 'Permission denied'
However, if I specify .libpaths() in the "lib" argument, then it works. But isn't this the default to the lib argument?
> install.packages("rmarkdown",lib=.libPaths())
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.3/rmarkdown_0.9.6.zip'
Content type 'application/zip' length 2182803 bytes (2.1 MB)
downloaded 2.1 MB
package ‘rmarkdown’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\jordan.watson\AppData\Local\Temp\RtmpkFVHnn\downloaded_packages
This does not happen every time however. For example, I just loaded the "forecast" library no problem by simply writing install.packages("forecast").
I'd just like to understand this behavior better. Can someone explain why this is happening? I am on Windows 7 without full admin privileges - but I do have admin privileges to my R folder on the C drive.
Apologies in advance that I can not make a reproducible example - it's not really that type of question.

Answer 1

Jordan,
My feeling is your setup is incorrect.
Proposed Solution
Try running the following command and see if this fixes the situation.
Note: I have replaced my userid with <user> in the examples below.
.libPaths( c( "C:/Users/<user>/Documents/R/win-library/3.3", .libPaths()) )
Explanation
I would expect .libPaths() to return two directories not one by default.
> .libPaths()
[1] "C:/Users/<user>/Documents/R/win-library/3.3" "C:/Program Files/R/R-3.3.0/library"
When you install R it installs the base libraries under
C:/Program Files/R/R-3.3.0/library
any new libraries are normally added to:
"C:/Users/<user>/Documents/R/win-library/3.3"
if you type View(installed.packages()) you will be able to see where the packages are installed.
The packages that come with the R install (base, stats, and nearly 30 others) are stored in the library subdirectory of wherever you installed R. You can retrieve the location of this with:
> R.home("library")
[1] "C:/PROGRA~1/R/R-33~1.1/library"
> .Library
[1] "C:/PROGRA~1/R/R-33~1.1/library
You also get a user library for installing packages that will only be accessible by you. The location under Windows, for R version x.y.z, it is in the R/win-library/x.y subfolder of the home directory, where the home directory can be found via:
> path.expand("~")
[1] "C:/Users/<user>/Documents"
> Sys.getenv("HOME")
[1] "C:/Users/<user>/Documents"
Issue
Thus, I would expect .libPaths() to return two paths not one which implies that you have somehow misconfigured the R installation libpath.
I hope the above helps.
Refs:
https://stat.ethz.ch/R-manual/R-devel/library/base/html/libPaths.html
Learning R By: Richard Cotton