Yes, this time it worked! Seems ^-C caused the problem - since I was first time using GO from BioC/R, I didn't expect it to take that long and wasn't patient enough. Again, thanks for all your help! Best, Yu-An Robert Gentleman wrote: > Jim makes a good point here. With the system we are currently using, > all of the data are stored in files and loaded on demand. That means > that the first query is always going to be slow (and possibly really > slow on some systems with limited RAM), subsequent queries will be > fast. We are working on a new system that will speed things up > substantially. > > Hitting control-C could certainly do odd things (but I would have > expected general odd things), like no calls to [[ to work, not just > this particular one - now maybe that is the case (and if so, could you > let us know Yu-An?) > > best wishes > Robert > > > James W. MacDonald wrote: >> Yu-An, >> >> Could the problem be impatience on your part? On both WinXP and Linux >> this takes a bit of time for me (using either R-2.2.0 or R-2.3.0): >> >> > library(GO) >> > system.time(GOLOCUSID2GO[["4121"]]) >> [1] 30.94 0.57 31.53 NA NA >> >> Note that any further queries of this sort take no time at all: >> >> > system.time(GOLOCUSID2GO[["4121"]]) >> [1] 0 0 0 NA NA >> > system.time(GOLOCUSID2GO[["4122"]]) >> [1] 0 0 0 NA NA >> >> >> Best, >> >> Jim >> >> Robert Gentleman wrote: >> >>> OK, well the next option is to move to the current version of R >>> (which is not 2.2.0) and see if your problems persist. I cannot >>> replicate the bug on any system I have access to. And since [[ takes >>> one argument, it is hard to see how it has a recursive standard >>> argument...someone is confused (maybe overoptimized compiling, but >>> even that is very rare these days). >>> >>> Or you to get more serious about debugging. Which will most likely >>> involve getting gdb or some similar interface to it working so you >>> can probe the internals. >>> >>> sorry >>> Robert >>> >>> Yu-An Dong wrote: >>> >>>> Hi Robert, >>>> I started R in a clean directory and loaded GO: >>>> >>>> > library(GO) >>>> > GOLOCUSID2GO[["4121"]] >>>> >>>> However, R simply hanged there and I had to use ^-C to interrupt. >>>> But when I issued the command >>>> a second time, I immediately got the same error as before: >>>> >>>> > GOLOCUSID2GO[["4121"]] >>>> Fehler: rekursive Standardargument Referenz ("Error: recursive >>>> standard argument reference") >>>> > traceback() >>>> Kein traceback vef?gbar ("No traceback available") >>>> >>>> > sessionInfo() >>>> R version 2.2.0, 2005-10-06, i686-pc-linux-gnu >>>> >>>> attached base packages: >>>> [1] "methods" "stats" "graphics" "grDevices" "utils" >>>> "datasets" >>>> [7] "base" >>>> >>>> other attached packages: >>>> GO >>>> "1.10.0" >>>> >>>> Mm, strange... Again, I appreciate your help! >>>> Best wishes, >>>> Yu-An >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> Robert Gentleman wrote: >>>> >>>> >>>>> Hi, >>>>> start a clean R and make sure it does not load any save workspaces. >>>>> [If you see this message: [Previously saved workspace restored] >>>>> then you need to move to a different directory to start or move >>>>> the saved workspace so it is not automatically loaded] >>>>> >>>>> then go >>>>> >>>>> library(GO) >>>>> GOLOCUSID2GO[["4121"]] >>>>> >>>>> if you get an error report it and the output of traceback(). And >>>>> if not, then it is not GO, it is something else, probably a >>>>> variable you have created (or that someone else has) that is >>>>> interfering with dispatch in some odd way. To find out who/what, >>>>> start adding the libraries you have listed, one at a time until >>>>> the culprit is found. >>>>> >>>>> >>>>> best wishes >>>>> Robert >>>>> >>>>> >>>>> Yu-An Dong wrote: >>>>> >>>>> >>>>>> Hi Ting-Yuan, >>>>>> >>>>>> I still get the same problem, e.g. >>>>>> >>>>>> > GOLOCUSID2GO[["4121"]] >>>>>> Fehler: rekursive Standardargument Referenz >>>>>> >>>>>> The error message says: "Error: recursive standard argument >>>>>> reference". Here's my >>>>>> session info: >>>>>> >>>>>> > sessionInfo() >>>>>> R version 2.2.0, 2005-10-06, i686-pc-linux-gnu >>>>>> >>>>>> attached base packages: >>>>>> [1] "splines" "tools" "methods" "stats" "graphics" >>>>>> "grDevices" >>>>>> [7] "utils" "datasets" "base" >>>>>> >>>>>> other attached packages: >>>>>> hgu95av2 GOstats multtest genefilter survival >>>>>> xtable RBGL >>>>>> "1.10.0" "1.4.0" "1.8.0" "1.8.0" "2.20" >>>>>> "1.3-0" "1.6.0" >>>>>> annotate Biobase GO graph Ruuid cluster >>>>>> "1.8.0" "1.8.0" "1.10.0" "1.8.0" "1.8.0" "1.10.2" >>>>>> >>>>>> Any suggestions? Thanks! >>>>>> >>>>>> Yu-An >>>>>> >>>>>> >>>>>> >>>>>> Ting-Yuan Liu wrote: >>>>>> >>>>>> >>>>>>> Hi Yu-An, >>>>>>> >>>>>>> I think the error message is not written in English, right? >>>>>>> Could you translate it to English so that it will be more helpful. >>>>>>> >>>>>>> I cannot reproduce the same error in my machine, and here is the >>>>>>> result: >>>>>>> >>>>>>> >>>>>>> >>>>>>>> GOLOCUSID2GO[["4121"]] >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> $"GO:0005975" >>>>>>> $"GO:0005975"$GOID >>>>>>> IEA >>>>>>> "GO:0005975" >>>>>>> >>>>>>> $"GO:0005975"$Evidence >>>>>>> [1] "IEA" >>>>>>> >>>>>>> $"GO:0005975"$Ontology >>>>>>> [1] "BP" >>>>>>> >>>>>>> >>>>>>> $"GO:0006487" >>>>>>> $"GO:0006487"$GOID >>>>>>> IEA >>>>>>> "GO:0006487" >>>>>>> >>>>>>> $"GO:0006487"$Evidence >>>>>>> [1] "IEA" >>>>>>> >>>>>>> $"GO:0006487"$Ontology >>>>>>> [1] "BP" >>>>>>> >>>>>>> .... skip ... >>>>>>> >>>>>>> Here is the result of my sessionInfo(): >>>>>>> >>>>>>> >>>>>>> >>>>>>>> sessionInfo() >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> R version 2.2.1, 2006-01-04, x86_64-unknown-linux-gnu >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] "methods" "stats" "graphics" "grDevices" "utils" >>>>>>> "datasets" >>>>>>> [7] "base" >>>>>>> >>>>>>> other attached packages: >>>>>>> GO >>>>>>> "1.10.0" >>>>>>> >>>>>>> >>>>>>> Could you also provide the sessionInfo() output for more >>>>>>> information please? Thanks. >>>>>>> >>>>>>> Ting-Yuan >>>>>>> ______________________________________ >>>>>>> Ting-Yuan Liu >>>>>>> Program in Computational Biology >>>>>>> Division of Public Health Sciences >>>>>>> Fred Hutchinson Cancer Research Center >>>>>>> Seattle, WA, USA >>>>>>> ______________________________________ >>>>>>> >>>>>>> On Wed, 25 Jan 2006, Yu-An Dong wrote: >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>>> Hello, I've installed BioC 1.7 (with R 2.2.0) without problem. >>>>>>>> The GO package was installed but I can't >>>>>>>> access the data: >>>>>>>> >>>>>>>> >>>>>>>>> GOLOCUSID2GO[["4121"]] >>>>>>>> >>>>>>>> >>>>>>>> Fehler: rekursive Standardargument Referenz >>>>>>>> >>>>>>>> And I get similar error messages with the other functions in >>>>>>>> the GO package. Any suggestions? Thanks! >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Bioconductor mailing list >>>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>> >>>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at stat.math.ethz.ch >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> >>>>> >>>> >>> >> >> >