[BioC] Error message with RNAither

[Martin Morgan]

On 02/09/2012 02:54 AM, Catherine Garry wrote:
> 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?

These are warnings, and can be ignored; you could update your R 
installation to R-2.14.1 but that is not strictly necessary. The good 
news is

 > package ‘RNAither’ successfully unpacked and MD5 sums checked

do you still have the problems

>>> 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

? Martin

>
> 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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>>
>>
>
>
>
>
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