On 01/28/2011 11:54 AM, James Carman wrote:
> Ding, dong, the witch is dead! Thank you Martin! I just did:
>
> source("http://bioconductor.org/biocLite.R")
> biocLite("affyio")
You want to follow the instructions for updating packages, not
installing a particular one; likely you have a Frankenstein system at
the moment. In a new R
source('http://bioconductor.org/biocLite.R')
update.packages(repos=biocinstallRepos(), ask=FALSE)
or a recently learned (for me) and probably better approach
options(repos=c(CRAN="http://cran.fhrcr.org"))
setRepositories() ## select CRAN and all BioC
old.packages() ## to see what you are saving yourself from...
update.packages(ask=FALSE)
In terms of books from a developer perspective (rather than 'using R' or
'bioinformatic analysis') I'm partial to Chambers' Software for Data
Analysis and Gentleman's R Programming for Bioinformatics.
Martin
>
> 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
>>
--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109
Location: M1-B861
Telephone: 206 667-2793