> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] gcrma_2.18.0  affy_1.24.1   Biobase_2.6.0

loaded via a namespace (and not attached):
[1] affyio_1.14.0        Biostrings_2.14.2    IRanges_1.4.4
[4] preprocessCore_1.8.0 splines_2.10.0       tools_2

The only difference I see is we don't have the patched R 2.10.0.  Is that
the dev version?

Thanks,
Joe


On Mon, Nov 9, 2009 at 9:25 AM, James W. MacDonald <jmacdon@med.umich.edu>wrote:

> Hi Joseph,
>
>
> Joseph Dougherty wrote:
>
>> Hello,
>>
>> Has this bug been resolved?  I am working in R 2.10 for the first time
>> (also
>> a on a new linux server) and I am getting a strange error with ReadAffy().
>> I don't have this error on my Windows machine, or our old server, which
>> are
>> still on earlier versions of R.
>>
>
> The bug in justRMA() didn't affect ReadAffy().
>
>
>  dat<-ReadAffy()
>>>
>> Error in value[[3L]](cond) :
>>  row names supplied are of the wrong length
>>  AnnotatedDataFrame 'initialize' could not update varMetadata:
>>  perhaps pData and varMetadata are inconsistent?
>>
>> I am just trying to load all of the Cel files in a directory.  I get the
>> same message without a phenoData file (the way I usually run it), or if I
>> make a simple one, which suggests to me this error message is probably not
>> germane.     This could also be some other problem with the new server or
>> the R install, but since Frasier had a similar error message, I thought I
>> would check with you all first, before trying to make guess on what else
>> could be going on.  I first got the error on Thursday.  I deleted and
>> re-installed by bioconductor libraries tonight and stil get the error.
>>
>
> You always need to supply us with your sessionInfo(). I get this to work
> with a new version of R, so it is likely you have mis-matched packages.
>
> > dat <- ReadAffy()
> > sessionInfo()
> R version 2.10.0 Patched (2009-11-05 r50317)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] affy_1.24.1   Biobase_2.6.0
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.0
>
> Best,
>
> Jim
>
>
>
>> Thanks,
>>
>> Joe Dougherty
>>
>>        [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
>

	[[alternative HTML version deleted]]

