[BioC] ontoCompare (goTools) : goidvect error

[Robert Gentleman]

Hi Oana,
  I was making no claims other than that your R and BIoC were out of
date and that
no one (even the primary developer) would be able to help with out of date
packages.

  Vince Carey has subsequently pointed out that since you are using private data
no one else can run your code to see what the issue is.  A
reproducible example that anyone
can run is essential to detect the real issues.  As you report others have
seen performance issues as well with this package and the developer
seems not to have modified their
code, so you now have the choice of running as is, or switching to
another tool which
is more performant or where the developer is more active.

  best wishes
    Robert


On Wed, Aug 3, 2011 at 11:49 PM, Oana VIGY <oana.vigy at igf.cnrs.fr> wrote:
> 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    Your R and bioconductor are still very out of date.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 at 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]]
>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>>
>
> --
>
>
> ------------------------------------------------------------------------
> *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]]
>
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
Robert Gentleman
rgentlem at gmail.com