similar to: withTimeout bug, it does not work properly with nlme anymore

Hello, I was relying on withTimeout (from R.utils) to help me stop nlme when it ?hangs?. However, recently this stopped working. I am pasting a reproducible example below: withTimeout should stop nlme after 10 seconds but in this example it does not. I tried this both on a linux (64 bit, CentOS 7, R 3.4.1, nlme 3.1-131 R.util 2.6) and mac (Sierra 10.13.1, R 3.4.2, same versions or nlme and

>>>>> Ramiro Barrantes <ramiro at precisionbioassay.com> >>>>> on Mon, 27 Nov 2017 21:02:52 +0000 writes: > Hello, I was relying on withTimeout (from R.utils) to help > me stop nlme when it ?hangs?. However, recently this > stopped working. I am pasting a reproducible example > below: withTimeout should stop nlme after 10

Hello, I am working on a web system (php) that uses R in the backend, and we need some basic fast encryption/decryption for the underlying mysql database that can be used by both R AND php. It does not need to be top-of-the-line, but just provide some basic level of fast encryption/decryption. Any suggestions? Thank you, Ramiro [[alternative HTML version deleted]]

Hello, I am working on tests to compare figures. I have been using ImageMagick, which creates a figure signature, and I can compare a "test" figure signature against a saved "reference" figure signature. It seems to work pretty well. However, it is slow as it requires reading from the file system. Are there any options to compare figures on memory? For example, if I

I suggest perceptual diff. You could write a wrapper around it. http://pdiff.sourceforge.net On Mon, 7 May 2018 16:49 Ramiro Barrantes, <ramiro at precisionbioassay.com> wrote: > Hello, > > I am working on tests to compare figures. I have been using ImageMagick, > which creates a figure signature, and I can compare a "test" figure > signature against a saved

Hello, In my code I found something that looks like an anomaly, I found a reproducible example in which I am just trying to compare each row in a data frame against the first row: a<-data.frame(row=c("B","C","B"),column=c(2,2,10),assay=c("Assay1","Assay1","Assay1"),plate=c(1,1,1),stringsAsFactors=FALSE) apply(a[1:2,],1,function(x) {

Hello, I am using CentOS Linux 6.0, R 2.14.1 and nlme 3.1-103 I am trying to fit some models using nlme, and what was happening was that it would get to some datasets and just "stall", the memory usage would grow and grow and eventually crash. I looked carefully into one of the datasets and ran it separately. It worked. After narrowing down on all possibilities, I found that the main

Hello, I have a program that consists of a loop fitting a function over many models. Sometimes the fitting on a particular model takes minutes to converge. Is there a way that I can limit the amount of time that R spends on a given model: say if my line is: fittingFunction( func, model.1) can I have some function: stopIfUnderTime( fittingFunction( func, model.1) , 5 ) where

Hello, I come from using different programming languages (C++, Mathematica, Perl) but have been using R extensively for several months. I see the data frame as a key piece of the language and wanted to inquire people's experience regarding its use. Say you have a data frame D D <- data.frame(some columns) and you define a function that needs the information from this data frame and is

Hello, I tried looking for a Sweave-specific list but didn't find one, nor did I find an answer via google, so will send this question to the general R list. Please feel free to point me in the right direction. I am using Sweave and would like to have a single .Rnw document that generates 1) a summary report, 2) a full report, 3) slides for a talk. I think my material lends itself to have

Dear list, I am trying to reclaim what I think is lost memory in R, I have been using gc(), rm() and also using Rprof to figure out where all the memory is going but I might be missing something. I have the following situation basic loop which calls memoryHogFunction: for i in (1:N) { dataset <- generateDataset(i) fit <- try( memoryHogFunction(dataset, otherParameters)) } and

Hi, Is there currently any way to guarantee that on.exit does not fail to execute the recorded expression because of a user interrupt arriving during function exit? Consider: f <- function() { suspendInterrupts({ on.exit(suspendInterrupts(cntr_on.exit <<- cntr_on.exit + 1L)) cntr_f <<- cntr_f + 1L }) TRUE } It is possible to interrupt this function such that cntr_f

Hello, I have a general question on the possibility of how to "catch and stop" a function when it uses too much memory. The problem is that some datasets, when applied to nlme (a relatively older version), cause the nlme function to just hang forever and start taking over memory (this afternoon one of those calls was about 40GB!) and not returning an answer. Other datasets work fine.

Hello, I am developing some packages. Package1 requires Package2, both of which I developed: Right now Package2 is installed properly here: /myHome/libraries/Package2 Package1 needs Package2. Package1 refers to Package2 both in the Roxygen @import field for one of the functions, and also in the Imports section in the DESCRIPTION However, when I do ?R CMD check Package1? I get: * checking

I am looking for R code to be able to fit a linear-linear piecewise model with person-specific changepoint. I have searched the web, but have not been able to locate any code. Below is my attempt at some code: chgpt = function(a1,a2,a3,gam,wave){ yht=numeric(10) y1=(wave <= gam)*(a1+(a2*wave)) y2=(wave > gam)*((a1+(a2-a3)*gam)+a3*wave) yhat=y1+y2 return(yht) } nl.dat <- nlme(y ~

Hello, I want to have the x-axis title of my plot in 2 lines, centered: experiment 1: log2(Ratio H/L) I know that in principle that works with '\n'. However, I am also using the 'substitute' command for my axis title. However, it does not make a new line. What I have so far: logbase <- 2 test <- "bait" cellline <- "cellline" plot(

Hello, I am trying to convert BY to a data frame, consider the following example: exampleDF<-data.frame(a=c(1,2),b=c(10,20),name=c("first","second")) exampleBY<-by(exampleDF,with(exampleDF,paste(a,b,sep="_")),               function(x) {                 data.frame(                     name=as.character(x$name),                     a=x$a,                    

Hello, I have been trying since long to send a mail thorough rails.. Previously when I had rails version 1.2.5 the sending mails worked fine. But now when i try to send a mail in rails 2.0.2 I always get timeout error Execution expired. Though i am able to catch the error I cannot understand why the error is generated in rails 2.0.2 and not in rails 1.2.5. Please advice me how can i fix the

I am trying to find methods for testing and visualizing calibration to Cox models with time-depended coefficients. I have read this nice article <http://journals.sagepub.com/doi/10.1177/0962280213497434>. In this paper, we can fit three models: fit0 <- coxph(Surv(futime, status) ~ x1 + x2 + x3, data = data0) p <- log(predict(fit0, newdata = data1, type = "expected")) lp

Dear All, Since upgrading to 3.6.0, I've been getting a strange error messages from the child process when using mcparallel/mccollect. Before filing a report in the Bugzilla, I want to figure out whether I had been doing something wrong all this time and R 3.6.0 has exposed it, or whether something else is going on. # Background # Ultimately, what I want to do is to be able to set a time