Two quick comments:
1. You do not need to reset the timeout limits yourself; it's already
taken care of, cf. help("evalWithTimeout").
2. Have you tried example(evalWithTimeout)? It should illustrate how
it works/is used. It's also a good example to verify that it also
works on your machine (I'd be really surprised if it doesn't). When
you have confirmed that example code works, then extend it.
Hope this helps. Unfortunately, that's all we can help you with
(unless you send a minimal reproducible example that we can also test
on our end).
/Henrik
On Wed, May 14, 2014 at 1:05 AM, n omranian <n_omran...@yahoo.com> wrote:
> Here is my code... I tried to remove many parts and keep the part which is
> related to evalWithTimeout.
> I have two similar while(1) loop in my original code. I only include one here.
> tnx a lot
> NO
>
>
> while (perm <= 1000)
> {
> setTimeLimit(cpu = Inf, elapsed = Inf)
> while (1)
> {
> data <- main_data[,sample(1:ncol(main_data),size=10,replace=F)]
> dd <- ....
> while(i<= dd)
> {
> y <- time[i,]
>
> fit <- NULL
>
> tryCatch(fit <-
> {evalWithTimeout({penalized(y,x,lambda1=lambda1[i],lambda2=lambda2[i],fusedl=a,standardize=T,trace=F);},
> timeout=360)},
> TimeoutException = function(ex) cat("Timeout. Skipping.\n"))
> setTimeLimit(cpu = Inf, elapsed = Inf)
> if (is.null(fit)==T)
> break
> i<-i+1
> }
> if (i>dd)
> break
> }
>
> perm<-perm+1
> }
>
> On Wednesday, May 14, 2014 9:50 AM, "ONKELINX, Thierry"
> <thierry.onkel...@inbo.be> wrote:
>
> Yes.
>
> Give us a minimal and reproducible example of your code and don't post in
> HTML.
>
> See fortunes::fortune(244)
>
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
> Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> thierry.onkel...@inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more than
> asking him to perform a post-mortem examination: he may be able to say what
> the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> Van: n omranian [mailto:n_omran...@yahoo.com]
> Verzonden: dinsdag 13 mei 2014 22:13
> Aan: ONKELINX, Thierry; r-packages-ow...@r-project.org; r-help@r-project.org;
> r-help-requ...@r-project.org
> Onderwerp: Re: [R] stop a function
>
> Hi,
> Another problem arised now. I got this error:
> Error in match(x, table, nomatch = 0L) : reached CPU time limit
>
> I googled it but nothing could help me to get rid of this error. Any
> comments, help or hints?
>
> Thanks a lot,
> NO
> On Tuesday, May 13, 2014 2:36 PM, "ONKELINX, Thierry"
> <thierry.onkel...@inbo.be> wrote:
> Have a look at evalWithTimeout() from the R.utils package
>
> Best regards,
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
> Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> thierry.onkel...@inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more than
> asking him to perform a post-mortem examination: he may be able to say what
> the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
> -----Oorspronkelijk bericht-----
> Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org]
> Namens n omranian
> Verzonden: dinsdag 13 mei 2014 14:15
> Aan: r-packages-ow...@r-project.org; r-help@r-project.org;
> r-help-requ...@r-project.org
> Onderwerp: [R] stop a function
>
> Hi all,
>
> If I use a function in R which takes some parameters as an input, how can I
> stop this function in the while loop and try another parameter in case the
> function takes long time or could not converge.
>
> Actually, I'm using "penalized" function in a loop for some fixed lambdas
> (pre-calculated), for some of them the function converged, but for some not.
> Now I decide to proceed in this way that if it takes longer than 3 mins, stop
> the "penalized" function and try the other lambdas.
>
> I need to do it in the loop since the loop is in the big program and I can't
> manually stop and begin again.
>
> Looking forward to your reply.
> NO
>
>
> [[alternative HTML version deleted]]
>
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> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
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> The views expressed in this message and any annex are purely those of the
> writer and may not be regarded as stating an official position of INBO, as
> long as the message is not confirmed by a duly signed document.
>
> * * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
> Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer
> en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd
> is door een geldig ondertekend document.
> The views expressed in this message and any annex are purely those of the
> writer and may not be regarded as stating an official position of INBO, as
> long as the message is not confirmed by a duly signed document.
> [[alternative HTML version deleted]]
>
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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