[Bioc-devel] Problem with getBioC()

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

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Bioc-devel@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

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
 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

_______________________________________________
Bioc-devel@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel

_______________________________________________
Bioc-devel@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel