[Bioc-devel] Problem with getBioC()

[Goeman, J.J. (MSTAT)]

 Hi Seth,

This was a really fresh new install of R 2.1.0 on this machine and 

> source("http://www.bioconductor.org/getBioC.R")
> getBioC()

were the very first commands I typed on this installation of R. There is of course a version of affy in the library of a previous version of R, but that should not interfere.

Doing 

> source("http://www.bioconductor.org/getBioC.R")
> getBioC("affy")

reproduces the error in a new R session. See below. 

Jelle


Running getBioC version 0.7  with R version  2.1.0 

Running biocinstall version 1.0  with R version  2.1.0 
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/windows/contrib/2.1/affy_1.6.7.zip'
Content type 'application/zip' length 1438528 bytes
opened URL
downloaded 1404Kb

package 'affy' successfully unpacked and MD5 sums checked
Error in sprintf(gettext("unable to move temp installation '%d' to '%s'"),  : 
        use format %s for character objects





> -----Original Message-----
> From: bioc-devel-bounces at stat.math.ethz.ch
> [mailto:bioc-devel-bounces at stat.math.ethz.ch]On Behalf Of Seth Falcon
> Sent: 24 May 2005 15:54
> To: bioc-devel at stat.math.ethz.ch
> Subject: Re: [Bioc-devel] Problem with getBioC()
> 
> 
> Hi Jelle,
> 
> "Goeman, J.J. \(MSTAT\)" <J.J.Goeman at lumc.nl> writes:
> > I'm running getBioC() on a newly installed R 2.1.0 on windows.
> > All works fine, until I come to the following error message:
> >
> > Error in sprintf(gettext("unable to move temp installation 
> '%d' to '%s'"),  : 
> >         use format %s for character objects
> >
> > This terminates the installation. It did not install all packages. 
> 
> Any chance you had some Bioc packages already loaded via library()
> before you ran getBioC?  In particular, if you happened to have an old
> version of affy loaded, this would, I believe, be the expected failure
> mode.
> 
> We have not seen this issue in our testing on Windows.  
> 
> One thing you could try from a fresh R session:
> 
> source("http://www.bioconductor.org/getBioC.R")
> getBioC("affy")
> 
> This should just download and install affy and its direct
> dependencies.  Since that seemed to be the package that caused the
> error, this would be a faster way of trying to reproduce.
> 
> Best,
> 
> + seth
> 
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