[Bioc-devel] Problem with getBioC()

[Robert Gentleman]

Hi Jelle,
   No, please don't do that. We really do appreciate accurate bug 
reports, even if they end up unresolved, it is important that these 
problems get reported, and accurately, as soon as possible. A lot of 
users are unable, or unwilling to file such complete reports, and that 
mkes it pretty hard from this end. So, to you and the many others - 
please don't wait - please do file a report which bears some resemblance 
to the instructions in the posting guide (as you did).



  Best wishes,
    Robert


Goeman, J.J. (MSTAT) wrote:
>  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
>>>
>>
>