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
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