[BioC] Problem with affy mas5 on Linux but not Windows...

[Martin Morgan]

<snip>

>>>>>>>>> sessionInfo()
>>>>>>>>
>>>>>>>> R version 2.12.1 (2010-12-16)
>>>>>>>> Platform: x86_64-redhat-linux-gnu (64-bit)
>>>>>>>>
>>>>>>>> locale:
>>>>>>>>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>>>>>>>>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>>>>>>>>   [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>>>>>>>>   [7] LC_PAPER=en_US.utf8       LC_NAME=C
>>>>>>>>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
>>>>>>>> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>>>>>>>>
>>>>>>>> attached base packages:
>>>>>>>> [1] stats     graphics  grDevices utils     datasets  methods  
>>>>>>>> base
>>>>>>>>
>>>>>>>> other attached packages:
>>>>>>>> [1] hgu133a2cdf_2.7.0 affy_1.28.0       Biobase_2.10.0
>>>>>>>>
>>>>>>>> loaded via a namespace (and not attached):
>>>>>>>> [1] affyio_1.16.0         preprocessCore_1.10.0 tools_2.12.1

uh oh! I get

> sessionInfo()
R version 2.12.0 Patched (2010-11-28 r53696)
Platform: x86_64-unknown-linux-gnu (64-bit)

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] affy_1.28.0    Biobase_2.10.0

loaded via a namespace (and not attached):
[1] affyio_1.18.0         preprocessCore_1.12.0 tools_2.12.0

and see, e.g., affyio 1.18.0 on the Bioc web site

http://bioconductor.org/help/bioc-views/release/bioc/html/affyio.html

so the first thing is to update packages as at

http://bioconductor.org/install/index.html#update-bioconductor-packages

Martin

>>>>>>>>
>>>>>>>> Here's my platform:
>>>>>>>>
>>>>>>>>> uname -a
>>>>>>>>
>>>>>>>> Linux carman-op755 2.6.35.10-74.fc14.x86_64 #1 SMP Thu Dec 23
>>>>>>>> 16:04:50
>>>>>>>> UTC 2010 x86_64 x86_64 x86_64 GNU/Linux
>>>>>>>>
>>>>>>>> Here's the version of R that I'm running:
>>>>>>>>
>>>>>>>>> rpm -qa | grep R-
>>>>>>>>
>>>>>>>> R-core-2.12.1-1.fc14.x86_64
>>>>>>>> R-devel-2.12.1-1.fc14.x86_64
>>>>>>>> R-2.12.1-1.fc14.x86_64
>>>>>>>>
>>>>>>>>
>>>>>>>> We have used this process in the past and it has worked fine.  I
>>>>>>>> got a
>>>>>>>> new computer and installed the latest Bioconductor package(s) on it
>>>>>>>> and now I'm getting this failure.  Any ideas?
>>>>>>>>
>>>>>>>> Thank you,
>>>>>>>>
>>>>>>>> James Carman
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioconductor mailing list
>>>>>>>> Bioconductor at r-project.org
>>>>>>>> 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
>>>>>>> **********************************************************
>>>>>>> Electronic Mail is not secure, may not be read every day, and should
>>>>>>> not
>>>>>>> be
>>>>>>> used for urgent or sensitive issues
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor at r-project.org
>>>>>> 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
>>>>> **********************************************************
>>>>> Electronic Mail is not secure, may not be read every day, and
>>>>> should not
>>>>> be
>>>>> used for urgent or sensitive issues
>>>>>
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at r-project.org
>>>> 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
>>> **********************************************************
>>> Electronic Mail is not secure, may not be read every day, and should
>>> not be
>>> used for urgent or sensitive issues
>>>
> 


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