Installing sources: curl fails with 404 Not Found many times for old packages

I have a repo with packrat. When I clone it and install sources again, libraries that have newer versions on Cran return a curl error many times before installing. I'm not sure if this is intentional, or whether this has more to do with http://cran.rstudio.com. Up-to-date libraries do not return an error.

After initializing, all the unit tests pass, so it seems to be installing the dependencies. The main inconvenience with the errors, is that initializing takes a fair amount of time.

Error message

After starting R, I see..

Packrat is not installed in the local library -- attempting to bootstrap an installation...
> No source tarball of packrat available locally
> Using user-library packrat (0.4.6.4) to bootstrap this project
Installing GlobalOptions (0.0.8) ... 
    OK (downloaded binary)
Installing R6 (2.1.1) ... 
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
    OK (built source)

packrat.lock (truncated)

PackratFormat: 1.4
PackratVersion: 0.4.6.4
RVersion: 3.1.3
Repos: BioCsoft=http://bioconductor.org/packages/3.0/bioc,
    BioCann=http://bioconductor.org/packages/3.0/data/annotation,
    BioCexp=http://bioconductor.org/packages/3.0/data/experiment,
    BioCextra=http://bioconductor.org/packages/3.0/extra,
    CRAN=http://cran.rstudio.com

Package: GetoptLong
Source: CRAN
Version: 0.1.1
Hash: 9f608e3c8362ced890dfdbe5440333a9
Requires: GlobalOptions, rjson

Package: GlobalOptions
Source: CRAN
Version: 0.0.8
Hash: 0d1ccb74fae610880703b251d25ed3be

Package: R6
Source: CRAN
Version: 2.1.1
Hash: 20a88b2c9c84aecff2702789a4d102f5

Start by reproducing initialization with the reported packrat.lock, especially the R6 2.1.1 source installation, and inspect the source-installation path responsible for repeated downloads. Use the existing unit-test suite as the regression check; done means obsolete package URLs no longer produce repeated 404 errors while the dependency installation still completes.