[BioC] impute package

[Martin Morgan]

On 02/12/2012 05:01 PM, Wendy Yim wrote:
> Hi everyone,
>
> I am new to R and I had a question in regards to the impute library. This
> library is no longer supported by CRAN, so I am posting this question to
> the Bioconductor users.
>
> My question is whether I had installed this library correctly.
>
> Two observations:
>
>     1. When I installed the impute library, there were a list of warnings. I
>     followed the instructions from here -
>     http://www.bioconductor.org/packages/release/bioc/html/impute.html . I
>     also tried to change the permission for the folder manually, but the old
>     permission reverted back to the original status.

The warning messages likely result because your R was installed with an 
'administrator' account, but is being run as a 'user' who doesn't have 
permission to update the full installation. The warnings are saying that 
newer versions of the listed packages are available, but cannot be 
installed, so that you are using slightly out-of-date pacakgs; likely 
the warnings can be ignored. Martin

>     2. When I call the impute.knn() function, the error message is "Error:
>     could not find function "impute.knn""
>
>
> Thank you in advance,
>
> Wendy Yim
> M.S. Candidate at Johns Hopkins University.
>
>
> _____________________________________________________
>
>> source("http://www.bioconductor.org/biocLite.R")
> BiocInstaller version 1.2.1, ?biocLite for help
>
>> biocLite("impute")
> BioC_mirror: 'http://www.bioconductor.org'
> Using R version 2.14, BiocInstaller version 1.2.1.
> Installing package(s) 'impute'
> Installing package(s) into ‘C:/Users/W/Documents/R/win-library/2.14’
> (as ‘lib’ is unspecified)
> trying URL '
> http://www.bioconductor.org/packages/2.9/bioc/bin/windows/contrib/2.14/impute_1.28.0.zip
> '
> Content type 'application/zip' length 1216377 bytes (1.2 Mb)
> opened URL
> downloaded 1.2 Mb
>
> package ‘impute’ successfully unpacked and MD5 sums checked
>
> The downloaded packages are in
>          C:\Users\W\AppData\Local\Temp\RtmpKMcIoN\downloaded_packages
> Warning message:
> 'boot' cannot be updated, installed directory 'C:/Program
>    Files/R/R-2.14.1/library' not writeable
> 'cluster' cannot be updated, installed directory 'C:/Program
>    Files/R/R-2.14.1/library' not writeable
> 'foreign' cannot be updated, installed directory 'C:/Program
>    Files/R/R-2.14.1/library' not writeable
> 'MASS' cannot be updated, installed directory 'C:/Program
>    Files/R/R-2.14.1/library' not writeable
> 'Matrix' cannot be updated, installed directory 'C:/Program
>    Files/R/R-2.14.1/library' not writeable
> 'mgcv' cannot be updated, installed directory 'C:/Program
>    Files/R/R-2.14.1/library' not writeable
> 'nlme' cannot be updated, installed directory 'C:/Program
>    Files/R/R-2.14.1/library' not writeable
> 'rpart' cannot be updated, installed directory 'C:/Program
>    Files/R/R-2.14.1/library' not writeable
> 'survival' cannot be updated, installed directory 'C:/Program
>    Files/R/R-2.14.1/library' not writeable
>
>> impute.knn(data=cdc28,k=6)
> Error: could not find function "impute.knn"
>> impute.knn
> Error: object 'impute.knn' not found
>> knn
> Error: object 'knn' not found
>> imputeknn
> Error: object 'imputeknn' not found
>
> 	[[alternative HTML version deleted]]
>
>
>
>
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