'recursive default argument' error in GOENTREZID2GO
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Oleg Sklyar ▴ 260
@oleg-sklyar-1882
Last seen 10.2 years ago
Hi, anybody has an idea as for the following error, the example is actually from the GO package examples. Thanks, Oleg > library(GO) > egId <- "10043" > egIdGoData <- GOENTREZID2GO[[egId]] Error: recursive default argument reference > sessionInfo() R version 2.5.0 (2007-04-23) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB .UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: Category Matrix lattice genefilter survival annotate "2.2.1" "0.9975-11" "0.15-4" "1.14.1" "2.31" "1.14.1" KEGG graph Biobase GO biomaRt RCurl "1.16.0" "1.14.0" "1.14.0" "1.16.0" "1.10.0" "0.8-0" XML "1.9-0" -- Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
GO Biobase genefilter graph Category GO Biobase genefilter graph Category • 2.0k views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.2 years ago
"James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > Hi Oleg, > > Oleg Sklyar wrote: >> Hi, >> >> anybody has an idea as for the following error, the example is actually >> from the GO package examples. Thanks, Oleg >> >> > library(GO) >> > egId <- "10043" >> > egIdGoData <- GOENTREZID2GO[[egId]] >> Error: recursive default argument reference > > I sometimes see that error as well. I have no idea what causes it, as it > doesn't seem repeatable. Anyway, quitting R and starting over has always > fixed the problem for me. Oleg, is this reproducible for you? I wasn't able to get the error. Have you tried updating to R patched? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
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It was reproducible *within* one session -- maybe other package's interference. Regarding the updates, I know I should test on R devel, but this is our release installation, which would be pity if it reproducibly occurs there. Oleg Seth Falcon wrote: > "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > >> Hi Oleg, >> >> Oleg Sklyar wrote: >>> Hi, >>> >>> anybody has an idea as for the following error, the example is actually >>> from the GO package examples. Thanks, Oleg >>> >>> > library(GO) >>> > egId <- "10043" >>> > egIdGoData <- GOENTREZID2GO[[egId]] >>> Error: recursive default argument reference >> I sometimes see that error as well. I have no idea what causes it, as it >> doesn't seem repeatable. Anyway, quitting R and starting over has always >> fixed the problem for me. > > Oleg, is this reproducible for you? I wasn't able to get the error. > Have you tried updating to R patched? > > + seth > -- Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
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Hi Oleg, James and Seth. I also found the same problem (or very close) and used the same approach mentioned by James to solve it, which works fine but still it too annoying. After reading the post I've tried to reproduce the steps that use to reach me to that point. It happens with any environment, or at least annotation packages stored as environments. I can't think of any reason why this happens but let me show you the code: > library(rae230a) > xx <- as.list(rae230aENTREZID) ^C > xx <- as.list(rae230aENTREZID) Error in as.list(rae230aENTREZID) : recursive default argument reference now, while the as.list() is working, cancel the process with control- C, and after that, the mentioned error happens whenever you try to repeat the process of transforming the environment to a list. The cancel must be done soon after hitting return, I found one case when delaying a little made me unable to reproduce the error. Other environments found in the package are not affected (i.e. rae230aSYMBOL, rae230aGENENAME, etc). Going deeper to the problem, I found that canceling the environment "loading" with any function reproduces the problem: > is(rae230aSYMBOL) ^C > is(rae230aSYMBOL) Error in .class1(object) : recursive default argument reference > rae230aSYMBOL Error: recursive default argument reference By "loading" a mean that the first time I execute as.list (rae230aSYMBOL) or is(rae230aSYMBOL) there is a delay which I assume is the environment being loaded into memory. Any further execution of the same commands will occur almost immediately. So, why should I cancel an environment loading soon after trying to load it? It happens that I was loading an environment inside a function, ran the function and wanted to cancel the execution, thus, the error appeared and the environemnt was unusable. Anyway, this seems to me more an R related issue. HTH, Diego. > sessionInfo() R version 2.5.0 (2007-04-23) powerpc-apple-darwin8.9.1 locale: C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" other attached packages: rae230a "1.16.0" > On Jun 11, 2007, at 11:27 PM, Seth Falcon wrote: > "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: > >> Hi Oleg, >> >> Oleg Sklyar wrote: >>> Hi, >>> >>> anybody has an idea as for the following error, the example is >>> actually >>> from the GO package examples. Thanks, Oleg >>> >>>> library(GO) >>>> egId <- "10043" >>>> egIdGoData <- GOENTREZID2GO[[egId]] >>> Error: recursive default argument reference >> >> I sometimes see that error as well. I have no idea what causes it, >> as it >> doesn't seem repeatable. Anyway, quitting R and starting over has >> always >> fixed the problem for me. > > Oleg, is this reproducible for you? I wasn't able to get the error. > Have you tried updating to R patched? > > + seth > > -- > Seth Falcon | Computational Biology | Fred Hutchinson Cancer > Research Center > http://bioconductor.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
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Does not it look like a bug in R, Should not it be reported as such, Diego could you maybe do that? I did hit many ^C before getting my error as I had large objects and often used ^C to terminate printing. And well, quitting R is *not* a solution, such things run in scripts and need to be stable. Best, Oleg Diego Diez wrote: > Hi Oleg, James and Seth. > > I also found the same problem (or very close) and used the same approach > mentioned by James to solve it, which works fine but still it too > annoying. After reading the post I've tried to reproduce the steps that > use to reach me to that point. It happens with any environment, or at > least annotation packages stored as environments. I can't think of any > reason why this happens but let me show you the code: > > > library(rae230a) > > xx <- as.list(rae230aENTREZID) > ^C > > xx <- as.list(rae230aENTREZID) > Error in as.list(rae230aENTREZID) : recursive default argument reference > > now, while the as.list() is working, cancel the process with control-C, > and after that, the mentioned error happens whenever you try to repeat > the process of transforming the environment to a list. The cancel must > be done soon after hitting return, I found one case when delaying a > little made me unable to reproduce the error. Other environments found > in the package are not affected (i.e. rae230aSYMBOL, rae230aGENENAME, etc). > > Going deeper to the problem, I found that canceling the environment > "loading" with any function reproduces the problem: > > > is(rae230aSYMBOL) > ^C > > is(rae230aSYMBOL) > Error in .class1(object) : recursive default argument reference > > rae230aSYMBOL > Error: recursive default argument reference > > By "loading" a mean that the first time I execute as.list(rae230aSYMBOL) > or is(rae230aSYMBOL) there is a delay which I assume is the environment > being loaded into memory. Any further execution of the same commands > will occur almost immediately. > > So, why should I cancel an environment loading soon after trying to load > it? It happens that I was loading an environment inside a function, ran > the function and wanted to cancel the execution, thus, the error > appeared and the environemnt was unusable. Anyway, this seems to me more > an R related issue. > > HTH, > > Diego. > > > > sessionInfo() > R version 2.5.0 (2007-04-23) > powerpc-apple-darwin8.9.1 > > locale: > C > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" > [7] "base" > > other attached packages: > rae230a > "1.16.0" > > > > > > On Jun 11, 2007, at 11:27 PM, Seth Falcon wrote: > >> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: >> >>> Hi Oleg, >>> >>> Oleg Sklyar wrote: >>>> Hi, >>>> >>>> anybody has an idea as for the following error, the example is actually >>>> from the GO package examples. Thanks, Oleg >>>> >>>>> library(GO) >>>>> egId <- "10043" >>>>> egIdGoData <- GOENTREZID2GO[[egId]] >>>> Error: recursive default argument reference >>> >>> I sometimes see that error as well. I have no idea what causes it, as it >>> doesn't seem repeatable. Anyway, quitting R and starting over has always >>> fixed the problem for me. >> >> Oleg, is this reproducible for you? I wasn't able to get the error. >> Have you tried updating to R patched? >> >> + seth >> >> --Seth Falcon | Computational Biology | Fred Hutchinson Cancer >> Research Center >> http://bioconductor.org >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
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Hi Oleg, 1. as Seth pointed out, if there is a patched versions of the latest release of R (as there is now), then it would be helpful to test and report bugs on that, rather than on the release. There is not so much point in spending time on problems that may already have been fixed. See http://cran.at.r-project.org/sources.html 2. AfaIu, it is not safe to assure that R behaves well after an interrupt (Ctrl-C). It may well do so in most cases, and it probably does for Ctrl-C encountered during running most of the code in R itself, but I would be surprised if all contributed packages allowed Ctrl-C only then when it is safe. (I would be happy to be proven wrong.) Best wishes Wolfgang > Does not it look like a bug in R, Should not it be reported as such, > Diego could you maybe do that? I did hit many ^C before getting my error > as I had large objects and often used ^C to terminate printing. And > well, quitting R is *not* a solution, such things run in scripts and > need to be stable. > > Best, > Oleg > > Diego Diez wrote: >> Hi Oleg, James and Seth. >> >> I also found the same problem (or very close) and used the same approach >> mentioned by James to solve it, which works fine but still it too >> annoying. After reading the post I've tried to reproduce the steps that >> use to reach me to that point. It happens with any environment, or at >> least annotation packages stored as environments. I can't think of any >> reason why this happens but let me show you the code: >> >> > library(rae230a) >> > xx <- as.list(rae230aENTREZID) >> ^C >> > xx <- as.list(rae230aENTREZID) >> Error in as.list(rae230aENTREZID) : recursive default argument reference >> >> now, while the as.list() is working, cancel the process with control-C, >> and after that, the mentioned error happens whenever you try to repeat >> the process of transforming the environment to a list. The cancel must >> be done soon after hitting return, I found one case when delaying a >> little made me unable to reproduce the error. Other environments found >> in the package are not affected (i.e. rae230aSYMBOL, rae230aGENENAME, etc). >> >> Going deeper to the problem, I found that canceling the environment >> "loading" with any function reproduces the problem: >> >> > is(rae230aSYMBOL) >> ^C >> > is(rae230aSYMBOL) >> Error in .class1(object) : recursive default argument reference >> > rae230aSYMBOL >> Error: recursive default argument reference >> >> By "loading" a mean that the first time I execute as.list(rae230aSYMBOL) >> or is(rae230aSYMBOL) there is a delay which I assume is the environment >> being loaded into memory. Any further execution of the same commands >> will occur almost immediately. >> >> So, why should I cancel an environment loading soon after trying to load >> it? It happens that I was loading an environment inside a function, ran >> the function and wanted to cancel the execution, thus, the error >> appeared and the environemnt was unusable. Anyway, this seems to me more >> an R related issue. >> >> HTH, >> >> Diego. >> >> >> > sessionInfo() >> R version 2.5.0 (2007-04-23) >> powerpc-apple-darwin8.9.1 >> >> locale: >> C >> >> attached base packages: >> [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" >> [7] "base" >> >> other attached packages: >> rae230a >> "1.16.0" >> > >> >> >> >> On Jun 11, 2007, at 11:27 PM, Seth Falcon wrote: >> >>> "James W. MacDonald" <jmacdon at="" med.umich.edu=""> writes: >>> >>>> Hi Oleg, >>>> >>>> Oleg Sklyar wrote: >>>>> Hi, >>>>> >>>>> anybody has an idea as for the following error, the example is actually >>>>> from the GO package examples. Thanks, Oleg >>>>> >>>>>> library(GO) >>>>>> egId <- "10043" >>>>>> egIdGoData <- GOENTREZID2GO[[egId]] >>>>> Error: recursive default argument reference >>>> I sometimes see that error as well. I have no idea what causes it, as it >>>> doesn't seem repeatable. Anyway, quitting R and starting over has always >>>> fixed the problem for me. >>> Oleg, is this reproducible for you? I wasn't able to get the error. >>> Have you tried updating to R patched? >>> >>> + seth >>> >>> --Seth Falcon | Computational Biology | Fred Hutchinson Cancer >>> Research Center >>> http://bioconductor.org >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
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@james-w-macdonald-5106
Last seen 1 day ago
United States
Hi Oleg, Oleg Sklyar wrote: > Hi, > > anybody has an idea as for the following error, the example is actually > from the GO package examples. Thanks, Oleg > > > library(GO) > > egId <- "10043" > > egIdGoData <- GOENTREZID2GO[[egId]] > Error: recursive default argument reference I sometimes see that error as well. I have no idea what causes it, as it doesn't seem repeatable. Anyway, quitting R and starting over has always fixed the problem for me. Best, Jim > > sessionInfo() > R version 2.5.0 (2007-04-23) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_ GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_G B.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > Category Matrix lattice genefilter survival annotate > "2.2.1" "0.9975-11" "0.15-4" "1.14.1" "2.31" "1.14.1" > KEGG graph Biobase GO biomaRt RCurl > "1.16.0" "1.14.0" "1.14.0" "1.16.0" "1.10.0" "0.8-0" > XML > "1.9-0" > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Well, I had a several GB data set in memory... James W. MacDonald wrote: > Hi Oleg, > > Oleg Sklyar wrote: >> Hi, >> >> anybody has an idea as for the following error, the example is >> actually from the GO package examples. Thanks, Oleg >> >> > library(GO) >> > egId <- "10043" >> > egIdGoData <- GOENTREZID2GO[[egId]] >> Error: recursive default argument reference > > I sometimes see that error as well. I have no idea what causes it, as it > doesn't seem repeatable. Anyway, quitting R and starting over has always > fixed the problem for me. > > Best, > > Jim > > >> > sessionInfo() >> R version 2.5.0 (2007-04-23) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en _GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_ GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UT F-8;LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >> [7] "datasets" "methods" "base" >> >> other attached packages: >> Category Matrix lattice genefilter survival annotate >> "2.2.1" "0.9975-11" "0.15-4" "1.14.1" "2.31" "1.14.1" >> KEGG graph Biobase GO biomaRt RCurl >> "1.16.0" "1.14.0" "1.14.0" "1.16.0" "1.10.0" "0.8-0" >> XML >> "1.9-0" >> > > -- Dr Oleg Sklyar | EBI-EMBL, Cambridge CB10 1SD, UK | +44-1223-494466
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Oleg Sklyar wrote: > Well, I had a several GB data set in memory... Of course you did. I think the probability that you need to restart R is in exact inverse to your desire to do so. ;-D I _have_ tried to detach() the offending package in the past rather than doing a clean restart, but of course that doesn't work. Seth - I have seen this problem intermittently (usually when using annaffy, but it's just when trying to pull data out of an env so I don't think it is annaffy specific) for years now. I have yet to figure out why it happens, mainly because a clean restart of R _always_ clears the problem up. Best, Jim > > James W. MacDonald wrote: > >> Hi Oleg, >> >> Oleg Sklyar wrote: >> >>> Hi, >>> >>> anybody has an idea as for the following error, the example is >>> actually from the GO package examples. Thanks, Oleg >>> >>> > library(GO) >>> > egId <- "10043" >>> > egIdGoData <- GOENTREZID2GO[[egId]] >>> Error: recursive default argument reference >> >> >> I sometimes see that error as well. I have no idea what causes it, as >> it doesn't seem repeatable. Anyway, quitting R and starting over has >> always fixed the problem for me. >> >> Best, >> >> Jim >> >> >>> > sessionInfo() >>> R version 2.5.0 (2007-04-23) >>> x86_64-unknown-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=e n_GB.UTF-8;LC_MONETARY=en_GB.UTF-8;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en _GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.U TF-8;LC_IDENTIFICATION=C >>> >>> >>> attached base packages: >>> [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" >>> [7] "datasets" "methods" "base" >>> >>> other attached packages: >>> Category Matrix lattice genefilter survival annotate >>> "2.2.1" "0.9975-11" "0.15-4" "1.14.1" "2.31" "1.14.1" >>> KEGG graph Biobase GO biomaRt RCurl >>> "1.16.0" "1.14.0" "1.14.0" "1.16.0" "1.10.0" "0.8-0" >>> XML >>> "1.9-0" >>> >> >> > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.2 years ago
Hi Diego, Thanks for looking into this and coming up with something that is reproducible. It does look to be a defficiency in R, but it may not be one that is easy to resolve. At least understanding the likely culprit should help to avoid having to restart R during a long session; be careful not to interrupt when loading annotation data environments. :-\ The SQLite-based annotation data packages, which we expect to be in the next release won't have this problem. [Although honestly, there may be other issues to be discovered in terms of how RSQLite interacts with ^C, however, we are more likely to be able to produce fixes in this case] Best, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
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Nianhua Li ▴ 70
@nianhua-li-2181
Last seen 10.2 years ago
Maybe it is not a R problem but an AnnBuilder problem. When AnnBuilder creates annotation packages, the last step is to call the function "makeLLDB" in AnnBuilder and re-index all the annotation (rda) files. So the lazy loading mechanisms used in annoation packages are slightly different from the lazy loading in R. best nianhua
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 10.2 years ago
Nianhua Li <nialicn at="" yahoo.com=""> writes: > Maybe it is not a R problem but an AnnBuilder problem. When AnnBuilder creates > annotation packages, the last step is to call the function "makeLLDB" in > AnnBuilder and re-index all the annotation (rda) files. So the lazy loading > mechanisms used in annoation packages are slightly different from the lazy > loading in R. While it is true that we build the lazy loading DB "by hand", we use the same code as the package tools do. See the recent thread on R-devel. This situation arises when the lazyload loading code is interrupted. The current solution is: don't do that. The long term solution is that annotation packages won't be environment based :-) + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
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