[BioC] Error message with RNAither

[Dan Tenenbaum]

On Wed, Feb 8, 2012 at 11:44 AM, Catherine Garry <cagarry at tcd.ie> wrote:
> This is the output from sessionInfo()
>
>> sessionInfo()
> R version 2.14.0 (2011-10-31)
> Platform: i386-pc-mingw32/i386 (32-bit)
> locale:
> [1] LC_COLLATE=English_Ireland.1252  LC_CTYPE=English_Ireland.1252
> [3] LC_MONETARY=English_Ireland.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Ireland.1252
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
> other attached packages:
>  [1] RColorBrewer_1.0-5    RankProd_2.26.0       topGO_2.6.0
>  [4] SparseM_0.91          GO.db_2.6.1           RSQLite_0.11.1
>  [7] DBI_0.2-5             AnnotationDbi_1.16.11 Biobase_2.14.0
> [10] graph_1.32.0
> loaded via a namespace (and not attached):
> [1] IRanges_1.12.6 lattice_0.20-0 tools_2.14.0
>

Thanks.


> When i put in biocLite("RNAither"), i am also getting the error message
> (Error: could not find function "biocLite")

Do this first:
source("http://bioconductor.org/biocLite.R")

Also please CC the list because others may also be able to help.
Thanks,
Dan


>
> On 8 February 2012 19:13, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> 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.
>> >
>> >        [[alternative HTML version deleted]]
>> >
>> >
>> > _______________________________________________
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>>
>
>
>
> --
> 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
>