[BioC] package affy / biobase problem with function "geneNames"

[James W. MacDonald]

Hi Cherif,

You don't want to upgrade when you have a bunch of packages already 
loaded. Restart R and then perform the upgrade.

In addition, you won't be able to upgrade the base packages noted in the 
second warning. For that you will want to use apt-get, if you have sudo 
privileges. If not, see if your sysadmin will upgrade for you.

Best,

Jim


On 4/4/2014 11:32 AM, BEN HAMDA Cherif wrote:
> 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 at 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 at 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
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>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>>>
>>
> 	[[alternative HTML version deleted]]
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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