Why R packages are removed after updating them? - r

Question

I was trying to update some R packages since RStudio showed they could be updated. After updating, two packages are simply removed. (rgdal and spatstat). The same thing has happened several times recently. What is happening here?
> install.packages(c("data.table", "rgdal", "spatstat"))
Installing packages into ‘C:/Users/Patrick/Documents/R/win-library/3.4’
(as ‘lib’ is unspecified)
also installing the dependency ‘spatstat.data’
There is a binary version available but the source version is later:
binary source needs_compilation
spatstat.data 1.1-0 1.1-1 FALSE
trying URL 'https://mirror.las.iastate.edu/CRAN/bin/windows/contrib/3.4/data.table_1.10.4-1.zip'
Content type 'application/zip' length 1577319 bytes (1.5 MB)
downloaded 1.5 MB
trying URL 'https://mirror.las.iastate.edu/CRAN/bin/windows/contrib/3.4/rgdal_1.2-13.zip'
Content type 'application/zip' length 30475771 bytes (29.1 MB)
downloaded 29.1 MB
trying URL 'https://mirror.las.iastate.edu/CRAN/bin/windows/contrib/3.4/spatstat_1.53-2.zip'
Content type 'application/zip' length 14521163 bytes (13.8 MB)
downloaded 13.8 MB
package ‘data.table’ successfully unpacked and MD5 sums checked
package ‘rgdal’ successfully unpacked and MD5 sums checked
Warning in install.packages :
cannot remove prior installation of package ‘rgdal’
package ‘spatstat’ successfully unpacked and MD5 sums checked
Warning in install.packages :
cannot remove prior installation of package ‘spatstat’
The downloaded binary packages are in
C:\Users\Patrick\AppData\Local\Temp\RtmpeaKi0Y\downloaded_packages
installing the source package ‘spatstat.data’
trying URL 'https://mirror.las.iastate.edu/CRAN/src/contrib/spatstat.data_1.1-1.tar.gz'
Content type 'application/x-gzip' length 2837063 bytes (2.7 MB)
downloaded 2.7 MB
* installing *source* package 'spatstat.data' ...
** package 'spatstat.data' successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (spatstat.data)
The downloaded source packages are in
‘C:\Users\Patrick\AppData\Local\Temp\RtmpeaKi0Y\downloaded_packages’
> library(rgdal)
Error in library(rgdal) : there is no package called ‘rgdal’
> library(spatstat)
Error in library(spatstat) : there is no package called ‘spatstat’

Answer 1

You can find the directory that contains your installed packages with
.libPaths()
Which should give you something like:
"/Library/Frameworks/R.framework/Versions/3.3/Resources/library"
If you see rgdal or spatstat there I would delete them and then try installing again.