
Le 04/08/2011 16:03, Vincent Carey a écrit :
> there's a clue there:
>
> look at your data input and see if there is something distinguishing 
> list(goAnnotation)[6797] from list(goAnnotation)[6796]
Within that input file, the highlighted GO term is GO:0030165.**If I run 
the program on the last 4000 lines, the error show the "same line".*

3: FUN(X[[6797]], ...)*
6796 GO:0005515
*6797 GO:0030165*
6798 GO:0097016

*3: FUN(X[[3797]], ...)*
3796 GO:0005515
*3797 GO:0030165*
3798 GO:0097016

You could think it's related to that GO term but it's more complicated...
- I run the program without any problem on the first 1000 lines where 
the GO:0030165 is present...
- the GO:0030165 term appears many times in the input file and it 
doesn't fail at the first occurrence.

> also see if the program succeeds with a shorter input list, say 
> list(goAnnotation)[1:10] ... if it does, it suggests that there is a 
> problem with the input data relative to the software expectations.  it 
> could be a volume issue or some discrepancy among list elements
I tested on shorter lists with success... (see my previous post).

I made a test on a list composed of Cellular Component GO terms and it 
doesn't like the "GO:0060053" term.
>
> you should also consider engaging the package authors, or looking for 
> a piece of software, perhaps in Bioconductor, that is maintained and 
> that addresses the same testing problem.
I'll try to contact the maintainers to say that between BioConductor 
2.0.8 (goTools 1.8) and 2.5 (goTools 1.26), several problems appears:
- negative performance changes (is this due to the goTools package 
himself or to other required packages as suggested in 2009)
- the same input list (GO terms) worked with the old version and now 
crashes.

Thanks again for the time you spent helping.

Best regards,

Oana

>
> On Thu, Aug 4, 2011 at 9:57 AM, Oana VIGY <oana.vigy@igf.cnrs.fr 
> <mailto:oana.vigy@igf.cnrs.fr>> wrote:
>
>     I set the option and I obtain the following after half hour:
>
>
>     Starting ontoCompare...
>     Error in goidvect[test] : invalid subscript type 'list'
>
>     Enter a frame number, or 0 to exit
>
>     1: ontoCompare(list(goAnnotation), probeType = "GO", method =
>     "TIDS", goType =
>     2: lapply(tmp, parentsVectWraper, endnode)
>     3: FUN(X[[6797]], ...)
>
>     I tried few values but I'm not able to debug.
>     If someone wants to try, I can send my test file with pleasure.
>
>     Thanks again Vincent.
>
>     Best regards,
>
>     Oana
>
>
>     Le 04/08/2011 14:45, Vincent Carey a écrit :
>>     to move further, please set
>>
>>     options(error=recover)
>>
>>     and rerun your example.  you will see a traceback that will show
>>     where in the code the error emerges.  this may help to
>>     patch the code or alter your call to avoid the error.
>>
>>     On Thu, Aug 4, 2011 at 8:13 AM, Oana VIGY <oana.vigy@igf.cnrs.fr
>>     <mailto:oana.vigy@igf.cnrs.fr>> wrote:
>>
>>         Hi All,
>>
>>         thanks for your replies.
>>
>>         I've just finished few more tests on an up-to-date R and
>>         BioConductor as
>>         Robert suggested (R 2.13 and goTools 1.26.0).
>>         My original test file contains 7000 GO terms (can be sent)
>>         and it fails
>>         after 25 minutes.
>>
>>         /Starting ontoCompare...
>>         Error in goidvect[test] : invalid subscript type 'list'/
>>
>>         In comparison, the same file is processed in around 5s on my
>>         old system
>>         (R 2.5.1 and goTools 1.8.0).
>>
>>         I tested the "ontoCompare" function with a smaller set : the
>>         process
>>         goes through for the 1000 first lines, etc until the 6000
>>         first lines
>>         (1000 lines in 5min, 3000lines in 12min, 6000 lines in 24 min).
>>
>>         To resume :
>>         - the performance has increased between goTools 1.8.0 and
>>         goTools 1.26 ;
>>         it was already mentioned in 2009 on that list. I hoped the
>>         versions
>>         meantime were patched but it doesn't seem to be... : I'll try
>>         to contact
>>         directly the maintainers as you suggest.
>>         - I don't understand why smaller sets succeed and not the
>>         whole one...
>>
>>         Thanks.
>>
>>         Best regards,
>>
>>         Oana
>>
>>
>>         #### Script
>>         ###############
>>         library(goTools)
>>         rankgo = as.numeric(2)
>>         root = "GO:0003674"
>>         goAnnotation <- read.table("/home/AnnotationFileMF.txt",
>>         sep="\t",
>>         header=TRUE, colClasses="character")
>>         goAnnotation = as.vector(unlist(goAnnotation))
>>         Count = ontoCompare(list(goAnnotation), probeType="GO",
>>         method="TIDS",
>>         goType="MF")
>>
>>         #### Extract of the "AnnotationFileMF.txt" data file
>>         ###############
>>         GOTerm
>>         GO:0003674
>>         GO:0005488
>>         GO:0030234
>>         GO:0005488
>>         GO:0008494
>>         GO:0003755
>>         GO:0005515
>>         GO:0016853
>>         GO:0042277
>>         GO:0003723
>>         GO:0003743
>>         GO:0005488
>>         GO:0008190
>>
>>         #### sessionInfo()
>>         ###############
>>         > sessionInfo()
>>         R version 2.13.1 (2011-07-08)
>>         Platform: x86_64-redhat-linux-gnu (64-bit)
>>
>>         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
>>
>>
>>         Le 04/08/2011 13:00, Vincent Carey a écrit :
>>         > your example code involves private directories and data, so
>>         is not
>>         > reproducible by others, so does not give a basis for diagnosis.
>>         >
>>         > i did try to run the code in ontoCompare example section --
>>         this is
>>         > marked \dontrun{}, so R check would not identify that it
>>         takes hours
>>         > to run on an 8GB laptop.  I'd suggest you contact the
>>         authors directly
>>         > for guidance.  there may be a role for profiling the
>>         example and
>>         > finding out what takes so long -- might give rise to a patch.
>>         >
>>         > On Thu, Aug 4, 2011 at 2:49 AM, Oana VIGY
>>         <oana.vigy@igf.cnrs.fr <mailto:oana.vigy@igf.cnrs.fr>
>>         > <mailto:oana.vigy@igf.cnrs.fr
>>         <mailto:oana.vigy@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@igf.cnrs.fr <mailto:oana.vigy@igf.cnrs.fr>
>>         > <mailto:oana.vigy@igf.cnrs.fr
>>         <mailto: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
>>         > >>
>>         >    
>>         ------------------------------------------------------------------------
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>>         <tel:%2B33%20%280%294%2034%2035%2092%2039>
>>         > <tel:%2B33%20%280%294%2034%2035%2092%2039>
>>         > >> www.fpp.cnrs.fr <http://www.fpp.cnrs.fr>
>>         <http://www.fpp.cnrs.fr><http://www.fpp.cnrs.fr>
>>         > >>
>>         >    
>>         ------------------------------------------------------------------------
>>         > >>
>>         > >> --
>>         > >> Passerelle antivirus IGF.
>>         > >>
>>         > >>
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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
>>         >    
>>         ------------------------------------------------------------------------
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>>         <tel:%2B33%20%280%294%2034%2035%2092%2039>
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>>         <http://www.fpp.cnrs.fr> <http://www.fpp.cnrs.fr>
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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
>>         ------------------------------------------------------------------------
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>>         <tel:%2B33%20%280%294%2034%2035%2092%2039>
>>         www.fpp.cnrs.fr <http://www.fpp.cnrs.fr> <http://www.fpp.cnrs.fr>
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>>         --
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>>
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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.
>
>
>
> -- 
> Passerelle antivirus IGF. 

-- 


------------------------------------------------------------------------
*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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