[Rd] update.packages fails with directory not found

[Duncan Murdoch]

On 12/05/2010 12:42 PM, Mike Prager wrote:
> Shortened a bit further. Answers to queries are at the end.  MHP
>
> Duncan Murdoch wrote on 5/11/2010 7:03 PM:
> > On 11/05/2010 6:21 PM, Mike Prager wrote:
> >> On Tue, 11 May 2010 11:05:45 -0400, Duncan Murdoch
> >> <murdoch.duncan at gmail.com> wrote:
> >>> I'd appreciate it if you could check whether the problems remain in 
> >>> R-devel, revision 51980 or later.
> >> Thanks for trying to fix this. Here is a cut-and-paste [...edited]
> >> from Rgui.exe.  Hope it helps.  MHP
> >>
> >> R version 2.12.0 Under development (unstable) (2010-05-11 r51980)
> >> Copyright (C) 2010 The R Foundation for Statistical Computing
> >> ISBN 3-900051-07-0  [...]
> > Was rJava among the packages loaded at the time you tried this?
> >>> update.packages(ask='graphics')
> >> trying URL [...]
> >> downloaded 1.0 Mb
> >>
> >> package 'rJava' successfully unpacked and MD5 sums checked
> >> Warning: unable to move temporary installation 'c:\Program
> >> Files\R\Library\file390c7e87\rJava' to 'c:\Program
> >> Files\R\Library\rJava'
> > After the install was complete, was rJava present in Library?  Was it 
> > updated?  Was the temporary directory file390c7e87 still present?
> [...]
> > The downloaded packages are in
> >>         C:\Documents and Settings\mike.prager\Local
> >> Settings\Temp\RtmpyrBgXD\downloaded_packages
> >> Warning message:
> >> In normalizePath(path) :
> >>   path[1]="c:\Program Files\R\Library/rJava": The system cannot find
> >> the file specified
> >
> Answers:
>
> rJava was not loaded when the update started.
> After the install, rJava was no longer present in the library.
> The temporary directory file390c7e87 was not present.  Checking my 
> undelete program, the temp directory had existed and had contained the 
> rJava package but was (and is) deleted.
>
>   

I don't know what the problem is.  My current guesses:

  - Antivirus bugs.  Are you running some AV program?  Sometimes they 
interfere with other programs.
  - Permissions problems.  I don't know why rJava would have had 
different permissions than the other packages you successfully updated, 
but if it did, that could be a cause.
  - Windows bug.  R uses Windows services to move the temporary 
directory into place, and that's failing for no apparent reason. 

If you can follow Bill Dunlap's advice and monitor the process as it's 
taking place, you might be able to diagnose this, but I don't see a way 
to make any progress otherwise.

Duncan Murdoch