and right now when i try to upgrade one more

i have this message
* DONE (BiocInstaller)

The downloaded source packages are in
'/tmp/Rtmp9PxG1j/downloaded_packages'
BiocInstaller version 1.4.9, ?biocLite for help
A newer version of Bioconductor is available for this version of R,
  ?BiocUpgrade for help
'BiocInstaller' changed to version 1.4.9
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.4.9.
Warning messages:
1: 'BiocInstaller' namespace cannot be unloaded:
  namespace 'BiocInstaller' is imported by 'gcrma', 'affy' so cannot be
unloaded
2: installed directory not writable, cannot update packages 'bit',
'mvtnorm',
  'xtable', 'cluster', 'KernSmooth', 'lattice', 'mgcv', 'nnet', 'rpart',
  'survival


thanks


2014-04-04 16:27 GMT+01:00 BEN HAMDA Cherif <cherifbenhamda@gmail.com>:

> Hi,
> Thank you Martin and Jim for all your response.
> R 3.0.3 and bioconductor 2.13 it's for windows !
> I work with debian and the latest version for this distribution its  mine .
>
> it works very well but after the update for bioconductor packages (today)
> he released this kind of error .
>
> so there is other solution ?
> thank you
>
>
> 2014-04-04 16:18 GMT+01:00 Martin Morgan <mtmorgan@fhcrc.org>:
>
> On 04/04/2014 08:08 AM, BEN HAMDA Cherif wrote:
>>
>>> Hello,
>>>
>>> after updating all packages. I have a problem when i want normalize my
>>> data
>>> !
>>>
>>
>> This is a package version mismatch. Biobase is from Bioconductor version
>> 2.11, affy and BiocInstaller from version 2.10. I think
>>
>>   library(BiocInstaller)
>>   biocLite("BiocUpgrade")
>>
>> will update all packages to version 2.11.
>>
>> Really you should update to the current R (3.0.3) and Bioconductor (2.13)
>> or wait until after April 15 and update to R 3.1.0 and Bioconductor 2.14.
>>
>> Martin
>>
>>
>>> and the error message is  :
>>>
>>>  eset <- rma(rawdata)
>>>>
>>> Error in rma(rawdata) : could not find function "geneNames"
>>>
>>> Someone can help me Please , Thank you very much
>>>
>>> Best
>>> Cherif
>>>
>>>  sessionInfo()
>>>>
>>> R version 2.15.1 (2012-06-22)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> locale:
>>>   [1] LC_CTYPE=en_US.UTF-8    LC_NUMERIC=C            LC_TIME=C
>>>   [4] LC_COLLATE=en_US.UTF-8  LC_MONETARY=C
>>> LC_MESSAGES=en_US.UTF-8
>>>   [7] LC_PAPER=C              LC_NAME=C               LC_ADDRESS=C
>>> [10] LC_TELEPHONE=C          LC_MEASUREMENT=C        LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] hgu133plus2cdf_2.11.0 AnnotationDbi_1.18.4  simpleaffy_2.34.0
>>> [4] gcrma_2.30.0          genefilter_1.38.0     affy_1.34.0
>>> [7] Biobase_2.18.0        BiocGenerics_0.4.0    limma_3.12.3
>>>
>>> loaded via a namespace (and not attached):
>>>   [1] affyio_1.24.0         annotate_1.34.1       BiocInstaller_1.4.9
>>>   [4] Biostrings_2.24.1     DBI_0.2-7             IRanges_1.14.4
>>>   [7] preprocessCore_1.18.0 RSQLite_0.11.4        splines_2.15.1
>>> [10] stats4_2.15.1         survival_2.37-7       tools_2.15.1
>>> [13] XML_3.98-1.1          xtable_1.7-1          zlibbioc_1.2.0
>>>
>>>         [[alternative HTML version deleted]]
>>>
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>>>
>>>
>>
>> --
>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
>> Location: Arnold Building M1 B861
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>
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