ontoCompare (goTools) : goidvect error
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Oana VIGY ▴ 80
@oana-vigy-3597
Last seen 9.6 years ago
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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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 9.0 years ago
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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 Prot?omique 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
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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",se p=""); >> > 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@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]]
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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> 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> 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@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@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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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 ?crit : >> 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",s ep=""); >>> ? > ?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 Prot?omique 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 Prot?omique 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
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Oana VIGY ▴ 80
@oana-vigy-3597
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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>> 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>> 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 > <tel:%2b33%20%280%294%2034%2035%2092%2039> > >> www.fpp.cnrs.fr <http: www.fpp.cnrs.fr=""><http: www.fpp.cnrs.fr=""> > >> > ---------------------------------------------------------------- -------- > >> > >> -- > >> Passerelle antivirus IGF. > >> > >> > >> [[alternative HTML version deleted]] > >> > >> > >> _______________________________________________ > >> Bioconductor mailing list > >> Bioconductor@r-project.org <mailto:bioconductor@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 <tel:%2b33%20%280%294%2034%2035%2092%2039> > www.fpp.cnrs.fr <http: www.fpp.cnrs.fr=""> <http: www.fpp.cnrs.fr=""> > ---------------------------------------------------------------- -------- > > -- > Passerelle antivirus IGF. > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > 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. [[alternative HTML version deleted]]
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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> 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>> 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>> 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 > > <tel:%2b33%20%280%294%2034%2035%2092%2039> > > >> www.fpp.cnrs.fr <http: www.fpp.cnrs.fr=""><http: www.fpp.cnrs.fr=""> > > >> > > > -------------------------------------------------------------------- ---- > > >> > > >> -- > > >> Passerelle antivirus IGF. > > >> > > >> > > >> [[alternative HTML version deleted]] > > >> > > >> > > >> _______________________________________________ > > >> Bioconductor mailing list > > >> Bioconductor@r-project.org <mailto:bioconductor@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 <tel:%2b33%20%280%294%2034%2035%2092%2039> > > www.fpp.cnrs.fr <http: www.fpp.cnrs.fr=""> <http: www.fpp.cnrs.fr=""> > > > -------------------------------------------------------------------- ---- > > > > -- > > Passerelle antivirus IGF. > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > -- > > 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. > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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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 > > >> > > > ---------------------------------------------------------------- -------- > > >> Tel: +33 (0)4 34 35 92 39 > <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. > > >> > > >> > > >> [[alternative HTML version deleted]] > > >> > > >> > > >> _______________________________________________ > > >> Bioconductor mailing list > > >> Bioconductor@r-project.org > <mailto:bioconductor@r-project.org> > <mailto:bioconductor@r-project.org> <mailto:bioconductor@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 > <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. > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > <mailto:bioconductor@r-project.org> <mailto:bioconductor@r-project.org>> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > > > -- > > 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 <tel:%2b33%20%280%294%2034%2035%2092%2039> > www.fpp.cnrs.fr <http: www.fpp.cnrs.fr=""> <http: www.fpp.cnrs.fr=""> > ---------------------------------------------------------------- -------- > > -- > Passerelle antivirus IGF. > > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -- > 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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there's a clue there: look at your data input and see if there is something distinguishing list(goAnnotation)[6797] from list(goAnnotation)[6796] 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 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. On Thu, Aug 4, 2011 at 9:57 AM, Oana VIGY <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> 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>> 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>> 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",se p=""); >> > >> > 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 >> > <tel:%2b33%20%280%294%2034%2035%2092%2039> >> > >> www.fpp.cnrs.fr <http: www.fpp.cnrs.fr=""><http: www.fpp.cnrs.fr=""> >> > >> >> > >> ------------------------------------------------------------------- ----- >> > >> >> > >> -- >> > >> Passerelle antivirus IGF. >> > >> >> > >> >> > >> [[alternative HTML version deleted]] >> > >> >> > >> >> > >> _______________________________________________ >> > >> Bioconductor mailing list >> > >> Bioconductor@r-project.org <mailto:bioconductor@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<tel:%2b33%20%280%294%2034%2035%2092%2039> >> > www.fpp.cnrs.fr <http: www.fpp.cnrs.fr=""> <http: www.fpp.cnrs.fr=""> >> > >> ------------------------------------------------------------------- ----- >> > >> > -- >> > Passerelle antivirus IGF. >> > >> > >> > [[alternative HTML version deleted]] >> > >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > >> > >> > -- >> > 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. >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- > 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 > ------------------------------ > > -- > Passerelle antivirus IGF. > [[alternative HTML version deleted]]
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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 >> > >> >> > >> ----------------------------------------------------------- ------------- >> > >> Tel: +33 (0)4 34 35 92 39 >> <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. >> > >> >> > >> >> > >> [[alternative HTML version deleted]] >> > >> >> > >> >> > >> _______________________________________________ >> > >> Bioconductor mailing list >> > >> Bioconductor@r-project.org >> <mailto:bioconductor@r-project.org> >> <mailto:bioconductor@r-project.org>> <mailto:bioconductor@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 >> <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. >> > >> > >> > [[alternative HTML version deleted]] >> > >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor@r-project.org >> <mailto:bioconductor@r-project.org> >> <mailto:bioconductor@r-project.org>> <mailto:bioconductor@r-project.org>> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> > >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> > >> > >> > -- >> > 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 >> <tel:%2b33%20%280%294%2034%2035%2092%2039> >> www.fpp.cnrs.fr <http: www.fpp.cnrs.fr=""> <http: www.fpp.cnrs.fr=""> >> ----------------------------------------------------------- ------------- >> >> -- >> Passerelle antivirus IGF. >> >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org <mailto:bioconductor@r-project.org> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> -- >> 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. > > > > -- > 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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