[Bioc-devel] Problem with getBioC()

[Robert Gentleman]

Hi,
  I am wondering if this is related to the locale settings (are you 
using a non-English locale?) and some of the recent changes in R to 
support other character sets. Which would explain why we have not seen 
it - since we don't use non-English settings (anyone else out there with 
non-English settings willing to give this a try).


  You might also try and set options(error=recover), to see if that pops 
you into a debugger at some useful point (did you try traceback()?) 
Also, debug(install.packages), and then running this, would help to 
narrow down just what we are looking for.

   Or another experiment - try just downloading the zip file, to the 
desktop and then loading it...

HTH,
   Robert


Goeman, J.J. (MSTAT) wrote:
>  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
>>
>>_______________________________________________
>>Bioc-devel at stat.math.ethz.ch mailing list
>>https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 
> 
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