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
"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
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
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
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
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
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.
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
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.
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
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
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