[Bioc-devel] Problem with getBioC()

[Goeman, J.J. (MSTAT)]

 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 at fhcrc.org]
> Sent: 24 May 2005 16:48
> To: Goeman, J.J. (MSTAT)
> Cc: Seth Falcon; bioc-devel at 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 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
> >>
> > 
> > 
> > _______________________________________________
> > Bioc-devel at stat.math.ethz.ch mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
>