[BioC] Error message with RNAither

[Dan Tenenbaum]

On Wed, Feb 8, 2012 at 10:58 AM, Catherine Garry <cagarry at tcd.ie> wrote:
> Hi,
>
> I keep getting an error message when i try to generate the dataset file in
> RNAither. This is the error i keep getting.
>
>> generateDatasetFile("DGS", "DGScreen in cells",
> + NA_character_, "RNAither_output_Rep1.txt", plateLayout1, plateLayout2,
> + 8, 12, 1, emptyWells, poorWells, controlCoordsOutput,
> backgroundValOutput, cellnumOutput)
>
> Error: could not find function "generateDatasetFile"
> Can anyone help explain why this is happening?
> At the beginning, as usual, i add in:
>
> library("RNAither"). but i also get an error here:
>
> Loading required package: robustbase
> Error: package ‘robustbase’ could not be loaded
> In addition: Warning messages:
> 1: package ‘AnnotationDbi’ was built under R version 2.14.1
> 2: package ‘SparseM’ was built under R version 2.14.1
> 3: In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
> lib.loc) :
>  there is no package called ‘robustbase’
>
> I also used:
>
> source("http://www.bioconductor.org/biocLite.R")
> biocLite("RNAither")
>
> , to install all the files etc.
>
> Can anyone help me rectify whatever is happening?

It would be helpful to see the output of sessionInfo() so we can see
exactly what packages you have, and a little bit about your system
configuration.

Without seeing it, I can guess that you have some out of date
packages, and you can fix this as follows:

biocLite(character(), ask=FALSE)
That will update ALL Bioconductor and CRAN packages on your system
which are outdated.

It would also be good to see the complete output of
biocLite("RNAither").

Thanks,
Dan


>
> Thank you.
>
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>
>
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