Hi Robert,

it's the contrary : the script still works with the old R and 
BioConductor but not with the current release versions... that's why I 
keep the old ones.
So, if I could upgrade with a working script, that would be great.

Best regards,

Oana


Le 03/08/2011 21:57, Robert Gentleman a écrit :
> Hi Oana,
>    Your R and bioconductor are still very out of date.  Unfortunately
> there is no support
> for such old versions, you really should be using the current release versions.
>
>    best wishes
>      Robert
>
>
> On Wed, Aug 3, 2011 at 8:30 AM, Oana VIGY<oana.vigy@igf.cnrs.fr>  wrote:
>> Dear All,
>>
>> I'm using the "goTools" package in a script which is working fine for
>> few years with the given system : R 2.5.1 and BioConductor 2.0.8.
>>
>> In 2009, I tried to upgrade BioConductor and R but I encountered
>> time-consuming problems as others on the list (1st message by Scott
>> Markel, 11/06/2009).
>> So I keep the "old" versions.
>>
>> This time, I try again both upgrades as new versions of goTools have
>> been released meantime but... I have the following errors :
>>
>> /Starting ontoCompare...
>> Error in goidvect[test] : invalid subscript type 'list'/
>>
>> As input of the ontoCompare function is given a list of GO terms
>> concerning the Molecular Function for the given test.
>> Please find below the whole script and the sessionInfo.
>>
>> Thanks for any help.
>>
>> Best regards,
>> Oana
>>
>>
>> ##################
>> ##### Script #######
>>   >  library(goTools)
>> Loading required package: GO.db
>> Loading required package: AnnotationDbi
>> Loading required package: Biobase
>>
>> Welcome to Bioconductor
>>
>>    Vignettes contain introductory material. To view, type
>>    'openVignette()'. To cite Bioconductor, see
>>    'citation("Biobase")' and for packages 'citation(pkgname)'.
>>
>> Loading required package: DBI
>>   >  rankgo = as.numeric(2)
>>   >  root = "GO:0003674"
>>   >  listRank = CustomEndNodeList(root, rank=rankgo)
>> rank= 1
>> rank= 2
>>   >  pathData =
>> paste("/var/www/html/tmp/YpFrh3eu/","AnnotationFile","MF",".txt",sep="");
>>   >  goAnnotation<- read.table(pathData, sep="\t", header=TRUE,
>> colClasses="character")
>>   >  goAnnotation = as.vector(unlist(goAnnotation))
>>   >  Count = ontoCompare(list(goAnnotation), probeType="GO",
>> method="TIDS", goType="MF")
>> Starting ontoCompare...
>> Error in goidvect[test] : invalid subscript type 'list'
>>
>> ###########
>>   >sessionInfo()
>> R version 2.10.0 (2009-10-26)
>> x86_64-redhat-linux-gnu
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> --
>>
>>
>> ------------------------------------------------------------------------
>> *Oana VIGY*
>> Plate-forme de Protéomique Fonctionnelle (FPP)
>> IGF, UMR 5203 CNRS - INSERM U661 - UM1 - UM2
>> 141 rue de la Cardonille
>> 34 094 Montpellier Cedex 5, France
>> ------------------------------------------------------------------------
>> Tel: +33 (0)4 34 35 92 39
>> www.fpp.cnrs.fr<http://www.fpp.cnrs.fr>
>> ------------------------------------------------------------------------
>>
>> --
>> Passerelle antivirus IGF.
>>
>>
>>         [[alternative HTML version deleted]]
>>
>>
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>>
>
>

-- 


------------------------------------------------------------------------
*Oana VIGY*
Plate-forme de Protéomique Fonctionnelle (FPP)
IGF, UMR 5203 CNRS - INSERM U661 - UM1 - UM2
141 rue de la Cardonille
34 094 Montpellier Cedex 5, France
------------------------------------------------------------------------
Tel: +33 (0)4 34 35 92 39
www.fpp.cnrs.fr <http://www.fpp.cnrs.fr>
------------------------------------------------------------------------

-- 
Passerelle antivirus IGF.


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