[Bioc-devel] Problem with getBioC()

 Hi Robert and Seth,

I succeeded in installing affy without problems by downloading the zip file. Since that moment I failed to reproduce the problem, even by starting again from installation of R. So I could not try the debugging tools.

So probably it was just my computer who consistenty went berserk for a few hours... It running on Windows after all. Next time I'll wait with emailing you all until the problem persists for at least 24 hours.

Best,

Jelle

-----Original Message-----
From: Robert Gentleman [mailto:rgentlem@fhcrc.org]
Sent: 24 May 2005 16:48
To: Goeman, J.J. (MSTAT)
Cc: Seth Falcon; bioc-devel@stat.math.ethz.ch
Subject: Re: [Bioc-devel] Problem with getBioC()


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@stat.math.ethz.ch
[mailto:bioc-devel-bounces@stat.math.ethz.ch]On Behalf Of 

Seth Falcon

Sent: 24 May 2005 15:54
To: bioc-devel@stat.math.ethz.ch
Subject: Re: [Bioc-devel] Problem with getBioC()


Hi Jelle,

"Goeman, J.J. \(MSTAT\)" <J.J.Goeman@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