Hi Dan,

When i tried all of this, this is what i got:

> source("http://www.bioconductor.org/biocLite.R")
BiocInstaller version 1.2.1, ?biocLite for help
> biocLite("RNAither")
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Installing package(s) 'RNAither'
Installing package(s) into ‘C:/Users/Catherine/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/RNAither_2.2.0.zip
'
Content type 'application/zip' length 1414362 bytes (1.3 Mb)
opened URL
downloaded 1.3 Mb
package ‘RNAither’ successfully unpacked and MD5 sums checked
The downloaded packages are in
        C:\Users\Catherine\AppData\Local\Temp\RtmpETRn43\downloaded_packages
Warning message:
'boot' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'foreign' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'KernSmooth' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'Matrix' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'mgcv' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'nlme' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'rpart' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'survival' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
> biocLite(character(), ask=FALSE)
BioC_mirror: 'http://www.bioconductor.org'
Using R version 2.14, BiocInstaller version 1.2.1.
Warning message:
'boot' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'foreign' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'KernSmooth' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'Matrix' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'mgcv' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'nlme' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'rpart' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
'survival' cannot be updated, installed directory 'C:/Program
  Files/R/R-2.14.0/library' not writeable
>
Any ideas on how to recify this?

On 8 February 2012 19:13, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

> On Wed, Feb 8, 2012 at 10:58 AM, Catherine Garry <cagarry@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.
> >
> >        [[alternative HTML version deleted]]
> >
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>


-- 
*Catherine Garry
*PhD Research Student

*Rm. 0.36/ Lab 1.16
Department of Clinical Medicine
Institute of Molecular Medicine
Trinity Centre for Health Sciences
Trinity College Dublin
St James's Hospital
Dublin 8
Republic of Ireland
*
Tel: +353 1 896 3350
Mob: +353 87 911 4936

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