So right now the tutorial errors out in the last step with:
install.packages("sashimi", type = "source")
Installing package into ‘E:/Dave/Analysis/packratDemo/packrat/lib/x86_64-w64-mingw32/3.4.1’
(as ‘lib’ is unspecified)
Warning in install.packages :
cannot open compressed file '//C:/Users/dparr/Documents/local-cran/src/contrib/PACKAGES', probable reason 'Invalid argument'
Error in install.packages : scheme not supported in URL '/no/such/path/here/i/hope//PACKAGES'
I'm not sure why the "no such path here I hope" thing is returned by the Error, that's not my joke 
My actual repos list is:
getOption("repos")
BioCsoft BioCann
"https://bioconductor.org/packages/3.4/bioc" "https://bioconductor.org/packages/3.4/data/annotation"
BioCexp BioCextra
"https://bioconductor.org/packages/3.4/data/experiment" "https://bioconductor.org/packages/3.4/extra"
CRAN CRANextra
"https://cran.rstudio.com/" "https://www.stats.ox.ac.uk/pub/RWin"
sushi
"file://C:/Users/dparr/Documents/local-cran"
Copying the three files named in the documented tutorials still gives the same error, as does deleting those contents to make the files 'empty'.
Oddly, I initially thought that the issue was because the write_PAKAGES() wasn't filling out the bin folders while the tutorial said it would. However I've just noticed the error is actually from reading the src folder, which should be correctly populated. Any other suggestions?
Update:
I just did this on a macbook running Sierra 10.12.4 (16E195), and it worked. The issue is on a windows machine running Windows Server 2012 R2.
The error seems to be in the creation of the cranUI variable. Removing the file:\\ prefix changes the output to:
Installing package into ‘E:/Dave/Analysis/packratDemo/packrat/lib/x86_64-w64-mingw32/3.4.1’
(as ‘lib’ is unspecified)
Warning in install.packages :
unable to access index for repository C:/Users/dparr/Documents/local-cran/src/contrib:
scheme not supported in URL 'C:/Users/dparr/Documents/local-cran/src/contrib/PACKAGES'
Warning in install.packages :
package ‘sashimi’ is not available (for R version 3.4.1)