install.packages() removes package on Windows

Hi,

Starting with the XML package installed:

"XML" %in% rownames(installed.packages())

[1] TRUE

I ran the following script:

pkgs <- c("XML")

for (i in 1:100)
{
    install.packages(pkgs, repos="http://cran.fhcrc.org")
    if (!all(pkgs %in% rownames(installed.packages())))
    {
        print("failed to install pkgs!")
        print(paste("Iteration", i))
        break
    }
}

And it failed on the third iteration:

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
Content type 'application/zip' length 4287270 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

package 'XML' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\biocbuild\AppData\Local\Temp\3\Rtmps7OWh0\downloaded_packages
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
Content type 'application/zip' length 4287270 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

package 'XML' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
        C:\Users\biocbuild\AppData\Local\Temp\3\Rtmps7OWh0\downloaded_packages
trying URL 'http://cran.fhcrc.org/bin/windows/contrib/3.0/XML_3.98-1.1.zip'
Content type 'application/zip' length 4287270 bytes (4.1 Mb)
opened URL
downloaded 4.1 Mb

package 'XML' successfully unpacked and MD5 sums checked
Warning: cannot remove prior installation of package 'XML'

The downloaded binary packages are in
        C:\Users\biocbuild\AppData\Local\Temp\3\Rtmps7OWh0\downloaded_packages
[1] "failed to install pkgs!"
[1] "Iteration 3"

At this point the XML package is not installed:

"XML" %in% rownames(installed.packages())

[1] FALSE

Any idea what could cause this? There is no virus scanner running. 

I notice the warning about failing to remove prior installation, but it looks like it removed enough of it so that XML is no longer installed.

I realize my script is a little contrived but I'm trying to track down an elusive problem in our build system that is causing a lot of grief....this may or may not be the same problem but it's certainly a problem, so I thought I'd report it. 

Is there a workaround?

I've only ever seen this issue on Windows.

I did try running the same script on a vanilla windows machine and it did not fail. In fact, it does not always fail on the machine where it fails above. But once is enough to mess us up.

sessionInfo()

R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

Thanks,
Dan