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

[James Carman]

Ding, dong, the witch is dead!  Thank you Martin!  I just did:

source("http://bioconductor.org/biocLite.R")
biocLite("affyio")

and it updated the "affyio" package.  Then I tried again and all seems
to be working.  So, I don't have to do debugging after all! WHEW! :)
Thank you guys for all your help.  Now, if anyone has any R book
suggestions, I'm all ears!

On Fri, Jan 28, 2011 at 2:50 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> <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
>>>>
>>
>
>
> --
> Computational Biology
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
>
> Location: M1-B861
> Telephone: 206 667-2793
>