Packrat doesn't install packages in local repository

I am migrating my project from Mac to Windows 10. When loading the project via RStudio and R 3.3.3, packrat loads a large number of packages but does not subsequently install them. After downloading when it restarts the session it writes:

Error in ensurePackageSymlink(source, target) : 
  Target 'C:/Users/jdv22/MarkdownProj/packrat/lib-R/base' already exists and is not a symlink
Loading required package: rugarch
Error in .requirePackage(package) : 
  unable to find required package ‘rugarch’
In addition: Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rugarch’
Error in loadNamespace(name) : there is no package called ‘rmarkdown’

If I run packrat::status(), packrat returns

Error in packageVersion("knitr") : package ‘knitr’ not found

Both packages are in the lib folder in packrat, together with a large number of other packages that aren't installed. If I try to install a package, for example ggplot2, I get the following:

> packrat::install_local("ggplot2")
Installing package from '/Users/jdv22/Dropbox/Algo/Rapportering/PQI.DK/Markdown/packrat/lib/x86_64-w64-mingw32/3.3.3/ggplot2'
Installing ggplot2
"C:/PROGRA~1/R/R-33~1.3/bin/x64/R" --vanilla CMD INSTALL  \
  "C:\Users\jdv22\Dropbox\Algo\Rapportering\PQI.DK\Markdown\packrat\lib\x86_64-w64-mingw32\3.3.3\ggplot2"  \
  --library="\\cued-fs/users/divf/jdv22/windows-home/Documents/R/win-library/3.3" --install-tests 
* installing *binary* package 'ggplot2' ...
cp: unknown option -- )
Try '/usr/bin/cp --help' for more information.
Warning: running command 'cp -R . "\\cued-fs/users/divf/jdv22/windows-home/Documents/R/win-library/3.3/ggplot2" || ( internal cd - .| (cd "\\cued-fs/users/divf/jdv22/windows-home/Documents/R/win-library/3.3/ggplot2" && internal -xf -))' had status 1
ERROR: installing binary package failed
* removing '\\cued-fs/users/divf/jdv22/windows-home/Documents/R/win-library/3.3/ggplot2'

I feel like I am missing something obvious. I just expected packrat to install all packages that I already had loaded.

Start by reproducing the Windows R 3.3.3 workflow with packrat::status() and packrat::install_local("ggplot2"), focusing on the existing packrat/lib packages and the ensurePackageSymlink error. Done means the local packages are installed successfully and required packages such as rugarch, rmarkdown, knitr, and ggplot2 load without errors.