Unable to retrieve package records for non packages

I am trying to deploy a Shiny app to shinyapps.io. The app works perfectly locally but when I try to deploy it I get the following message

Error: Unable to retrieve package records for the following packages:

• "foo", "testRcppClass", "testRcppModule"
  In addition: Warning messages:
  1: In FUN(X[[i]], ...) :
  Package 'testRcppClass' not available in repository or locally
  2: In FUN(X[[i]], ...) :
  Package 'foo' not available in repository or locally
  3: In FUN(X[[i]], ...) :
  Package 'testRcppModule' not available in repository or locally

After some searching and experimenting I have traced it back to packrat. I get the same message when I run packrat::init().

I have done some reading and I understand I should create a local repository for non CRAN packages but the above are not actually packages, they are folders within other packages (Rcpp and XML).

Any idea how I can fix this? I am not an IT expert so apologies if the answer is obvious...

Start by reproducing the report with packrat::init() and the listed package records. Read the dependency-record handling involved in that command, then verify that folders named foo, testRcppClass, and testRcppModule inside other packages are not treated as standalone packages and that deployment proceeds without these warnings.