, I had
occasionallz wanted an easy way to revert the byte compilation
before debugging or another way to get rid of this
drawback..
Martin
>>
>> Best regards
>> Petr
>>
>>> -Original Message-
>>> From: Duncan Murdoch
To: PIKAL Petr ; r-help@r-project.org
Subject: Re: [R] debug only top level function
On 06/06/2019 4:55 a.m., PIKAL Petr wrote:
Dear all
I have a question about debug function. I did not use it for long time but my
vague memory tell me, that when I used debug(myfunction) in past, only
d be worth considering to add something about it
to debug help page.
Best regards
Petr
> -Original Message-
> From: Duncan Murdoch
> Sent: Thursday, June 6, 2019 11:11 AM
> To: PIKAL Petr ; r-help@r-project.org
> Subject: Re: [R] debug only top level function
>
> On 0
On 06/06/2019 4:55 a.m., PIKAL Petr wrote:
Dear all
I have a question about debug function. I did not use it for long time but my
vague memory tell me, that when I used debug(myfunction) in past, only
myfunction was debugged and browser ignored any embedded function.
example (simple)
fff
Dear all
I have a question about debug function. I did not use it for long time but my
vague memory tell me, that when I used debug(myfunction) in past, only
myfunction was debugged and browser ignored any embedded function.
example (simple)
fff <- function(x) mean(x, na.rm=T)
when I issue
Duncan,
Thanks for the help.
Since I am the only person using this machine and I couldn’t figure out where
to put the option statement aside from:
C:\Program Files\R\R-3.1.2\etc
In the file Rprofile.site
The option that I wanted was:
options(debug.font = Consolas 12”)
Which allowed me to
On 30/03/2015 1:50 PM, Keith S Weintraub wrote:
Folks,
I would like change some of the options for the Tk window that pops up when
using the debug package.
I know how to change the options: e.g. options(debug.font = Courier 12
italic”).
Is there a way to “preset” these in my
Folks,
I would like change some of the options for the Tk window that pops up when
using the debug package.
I know how to change the options: e.g. options(debug.font = Courier 12
italic”).
Is there a way to “preset” these in my environment so when debug starts up I
have all the options set
Dear R experts,
recently I tried to debug a R function with an internal lapply call.
When debugging I seem not to be able to use the n command to debug the
inner function called by lapply.
How could I achieve this?
*For example:*
test - function( ) {
lapply( 1:3, function( x ) x + 1 )
}
debug(
Typically when I am debugging an 'lapply', I put a browser call inside
the lapply function that is being called and then make sure I 'source'
in the code instead of copy/paste -- the copy/paste will use any
trailing statements after the lapply call as commands to the browser
function.
Here is the
On 11/12/2012 1:17 PM, Asis Hallab wrote:
Dear R experts,
recently I tried to debug a R function with an internal lapply call.
When debugging I seem not to be able to use the n command to debug the
inner function called by lapply.
How could I achieve this?
Jim gave you one solution. Another
Hi! I'm trying to debug the cosmo R package because I'm trying to find out
where all the motifs are.
I display some of them printing the motif variable but I don't know how
to show all of the found motifs in one run.
http://www.bioconductor.org/packages/2.10/bioc/html/cosmo.html
I think that
On 2012-08-10 06:10, Zhang, Peng wrote:
Thanks to both for your reply.
library(glmulti)
testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol = 50)))
glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16, data
= testdata, level = 2)
This is reproducible to get a
You are right. I am running Arch Linux. However, I obtained a
segmentation directly, so didn't know where to find the bug??
library(glmulti)
Loading required package: rJava
testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol
= 50)))
On 2012-08-10 15:42, Zhang, Peng wrote:
You are right. I am running Arch Linux. However, I obtained a
segmentation directly, so didn't know where to find the bug??
library(glmulti)
Loading required package: rJava
testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol
=
Thanks! It is interesting that Windows has pointed the problem to Java.
So it is probable that how I did my debug led me to the wrong direction.
Since I was unsure how to debug S4 class, I copied the source implement
R function from glmulti package into my testing program.
The segmentation
Not to spoil your fun, but this is getting a bit off-topic for R-help. If you
wish to continue the debugging process in public, I think you should move to
R-devel.
Also, it sounds like the problem is in the glmulti package, so you might want
to involve its maintainer at some point.
-pd
On
On Aug 10, 2012, at 21:23 , Zhang, Peng wrote:
Ok. I will stop here. I have just created a bug report.
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15013
...which is exactly what you should NOT do, if the bug is likely to live in a
contributed package!!
-pd
If anyone is
Ok. I will stop here. I have just created a bug report.
https://bugs.r-project.org/bugzilla3/show_bug.cgi?id=15013
If anyone is interested, please see if you can reproduce it.
Thanks,
Peng
On 08/10/2012 03:04 PM, peter dalgaard wrote:
Not to spoil your fun, but this is getting a bit off-topic
If you read my bug report, I just ran the same thing on both regular
mode and debug mode. That is why I think it is related with R base,
though there might be some other bugs related with glmulti or rJava.
Peng
On 08/10/2012 04:03 PM, peter dalgaard wrote:
On Aug 10, 2012, at 21:23 , Zhang,
Dear all,
I had a R segmentation fault, and then invoked debug mode and ran step
by step.
When I reached terms(Y~X1*X2*...*X16), I would then have
segmentation fault. However, if I just ran this under regular R
interactive mode, it would be fine though taking long time.
My questions are:
1.
On Aug 9, 2012, at 4:56 PM, Zhang, Peng wrote:
Dear all,
I had a R segmentation fault, and then invoked debug mode and ran step
by step.
When I reached terms(Y~X1*X2*...*X16), I would then have
segmentation fault. However, if I just ran this under regular R
interactive mode, it would be fine
On Aug 9, 2012, at 9:14 PM, David Winsemius dwinsem...@comcast.net wrote:
On Aug 9, 2012, at 4:56 PM, Zhang, Peng wrote:
Dear all,
I had a R segmentation fault, and then invoked debug mode and ran step
by step.
2. Why does the same function behave differently under debug and
Thanks to both for your reply.
library(glmulti)
testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol = 50)))
glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16, data
= testdata, level = 2)
This is reproducible to get a segmentation fault. But I have troubles to
On 12-02-10 12:48 PM, Justin Haynes wrote:
You can add
if(is.na(tab[i])) browser()
or
if(is.na(tab[i])) break
see inline
You can also do this temporarily. Supposing that you used
source(foo.R) to enter a function with that code in it, and you want
the check on line 10, you'd enter
Hi,
I'd like to debug in a loop (using debug() and browser() etc but not print()
). I'am looking for the first occurence of NA.
For instance:
tab = c(1:300)
tab[250] = NA
len = length(tab)
for (i in 1:len){
if(i != len){
tab[i] = tab[i]+tab[i+1]
}
}
I do not want to do Browse[2] n
You can add
if(is.na(tab[i])) browser()
or
if(is.na(tab[i])) break
see inline
On Fri, Feb 10, 2012 at 7:22 AM, ikuzar raz...@hotmail.fr wrote:
Hi,
I'd like to debug in a loop (using debug() and browser() etc but not
print()
). I'am looking for the first occurence of NA.
For instance:
Hi all,
Since three month ago I started working with R professionally, I never did
it before, so I am such a newbie.
I am having some problems using the 'debug' package. I love this package,
but most of the times I wanna use it it just fails :P
When typing at prompt 'mtrace(myfunct)' most of
Hi Deivit,
Can you offer a self contained example of r code when the function fails
for you?
Contact
Details:---
Contact me: tal.gal...@gmail.com | 972-52-7275845
Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il
I'll try,
Here is a piece of code it fails for me, the error I get is always the same,
and it happens in most of my functions. The problem is always the same
trying to execute 'mtrace'.
Thanks!
--- execution --
mtrace(index_remap)
Error in x[[i]] : subscript out of
Hi List,
I have a question regarding debug R code. I know I can use
debug(fuction_name) and when code runs to that point, it will go to debugger.
My question is inside debugger, how to stop a code at a specified line. For
example, in C (gdb or dbx debugger) I can run stop at 123
On 11-06-03 4:49 PM, Hui Du wrote:
Hi List,
I have a question regarding debug R code. I know I can use
debug(fuction_name) and when code runs to that point, it will go to debugger. My question
is inside debugger, how to stop a code at a specified line. For example, in C (gdb
Not sure if you ever figured this out, but I was just directed to this post.
You need to look for a file (it may not be in your project directory) that
contains ___LOCK in its file name and delete it. filehash creates this to
prevent multiple writes to the same file at the same time and somehow
cameron.bracken wrote:
You need to look for a file (it may not be in your project directory) that
contains ___LOCK in its file name and delete it.
Specifically, the rogue lockfile should be in the same directory as
options('tikzMetricsDictionary'). Or, if you haven't set a permanent
Hi there,
I was doing great with R, ggplot and tikzDevice, when suddenly it stopped
working.
I can do a plot just fine on the R online graphics device. I can also open a
tikzdevice via tikz(). However, the plot (both ggplot and R graphics plot)
call leads to the error:
createLockFile(lockname):
Center
Intermountain Healthcare
greg.s...@imail.org
801.408.8111
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
project.org] On Behalf Of Mike Harwood
Sent: Monday, January 10, 2011 6:29 AM
To: r-h...@r-project.org
Subject: [R] debug biglm
G'morning
What does the error message Error in x %*% coef(object) : non-
conformable arguments indicate when calculating the response values
for
newdata with a model from bigglm (in package biglm), and how can I
debug it? I am attempting to do Monte Carlo simulations, which may
explain the loop
Sent: Monday, January 10, 2011 6:29 AM
To: r-help@r-project.org
Subject: [R] debug biglm response error on bigglm model
G'morning
What does the error message Error in x %*% coef(object) : non-
conformable arguments indicate when calculating the response values
for
newdata with a model
-Original Message-
From: Liviu Andronic [mailto:landronim...@gmail.com]
Sent: Sunday, December 13, 2009 4:05 AM
To: Duncan Murdoch
Cc: r-help@r-project.org Help
Subject: Re: [R] debug an error that incapacitates R?
Hello
And thank you for the quick answer.
On 12/13/09, Duncan
Murdoch
Cc: r-help@r-project.org Help
Subject: Re: [R] debug an error that incapacitates R?
Hello
And thank you for the quick answer.
On 12/13/09, Duncan Murdoch murd...@stats.uwo.ca wrote:
I think you need to go back to old-fashioned debugging methods.
Identify
the line the triggers the error
-Original Message-
From: Rolf Turner [mailto:r.tur...@auckland.ac.nz]
Sent: Monday, December 14, 2009 2:07 PM
To: Brian Diggs
Cc: r-help@r-project.org Help
Subject: Re: [R] debug an error that incapacitates R?
Wouldn't sink.number() give you a handle on whether
the problem
Dear all
How should I attempt debugging this error?
sosInit()
Error: invalid connection
When this happens R refuses to run anything:
2+2
Error: invalid connection
sessionInfo ()
Error in stdout() : invalid connection
Debugging it seems impossible.
options(error=recover)
sosInit()
Error:
On 13/12/2009 5:31 AM, Liviu Andronic wrote:
Dear all
How should I attempt debugging this error?
sosInit()
Error: invalid connection
When this happens R refuses to run anything:
2+2
Error: invalid connection
sessionInfo ()
Error in stdout() : invalid connection
Debugging it seems
Hello
And thank you for the quick answer.
On 12/13/09, Duncan Murdoch murd...@stats.uwo.ca wrote:
I think you need to go back to old-fashioned debugging methods. Identify
the line the triggers the error, by using debug() and single stepping
through sosInit(), or by adding print() or cat()
Hi,
I'm working through R-debug-tools.pdf and on page 7 it describes doing:
Browse[1] debug(sum) ## Flag sum for debugging
however, when I try this, I get:
Browse[1] debug(sum)Error in debug(fun) : argument must be a closure
Does anyone know why I get this error, and how to work around it?
Thanks
On 10/10/2009 7:00 PM, Another Oneforyou wrote:
Hi,
I'm working through R-debug-tools.pdf and on page 7 it describes doing:
Browse[1] debug(sum) ## Flag sum for debugging
however, when I try this, I get:
Browse[1] debug(sum)Error in debug(fun) : argument must be a closure
Does anyone know why I
On Oct 1, 2009, at 11:04 AM, Tammy Ma wrote:
provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
__
R-help@r-project.org mailing list
From: metal_lical...@live.com
To: r-help@r-project.org
Subject: Debug
Date: Thu, 1 Oct 2009 15:21:42 +0300
Hi, R-Users,'
I have written a programe to process the bunch of files in one folder.
But there is a error came out;
How can I know which file returns error when being processed?
I
Hi Tammy,
On Oct 1, 2009, at 11:04 AM, Tammy Ma wrote:
Hi, R-Users,'
I have written a programe to process the bunch of files in one folder.
But there is a error came out;
How can I know which file returns error when being processed?
I have tested the first 1-10th files, no any problem. But the
Hello,
In the past I have used intensively the mtrace function from the debug
package, but now with my actual version of R(2.8.1) , it is impossible
to use it anymore.
I've updated all my packages, and I don't understand how solve this
problem...
Here is an example code :
Hi, All
I have so many files in my directory. I got the following error. At this time,
I couldn't use debug() to check error one by one because so many files getting
invloved. How can I get some idea about my error??
.
Skipping book_log-20060222T143612.txt
Skipping
Tammy Ma wrote:
Hi, All
I have so many files in my directory. I got the following error. At this time,
I couldn't use debug() to check error one by one because so many files getting
invloved. How can I get some idea about my error??
The usual advice: simplify the problem until it's
Hi,
I am getting the following error: argument is of length zero
My code:
temp - 0
for (j in 1 : 3) {
for (k in 1 : 12) {
temp - temp + as.double(C[k, (q - 1) * 3 + j]) * as.double(m_ret_reb[i + k
- 1, j+1])
}
}
Why would R handle my temp variable as numeric(0)?
Thanks
--
View this message
On 2/4/2009 6:28 AM, ehxpieterse wrote:
Hi,
I am getting the following error: argument is of length zero
My code:
temp - 0
for (j in 1 : 3) {
for (k in 1 : 12) {
temp - temp + as.double(C[k, (q - 1) * 3 + j]) * as.double(m_ret_reb[i + k
- 1, j+1])
}
}
Why would R handle my temp variable as
,
Eduard
-Original Message-
From: Duncan Murdoch [mailto:murd...@stats.uwo.ca]
Sent: 04 February 2009 14:04
To: Eduard Pieterse (Macquarie Securities)
Cc: r-help@r-project.org
Subject: Re: [R] Debug help
On 2/4/2009 6:28 AM, ehxpieterse wrote:
Hi,
I am getting the following error
What is 'debug' defined as? Include at least the assignment or
'str(debug)'. If you have not assigned anything to it, then 'debug'
is a function in the basic set of R functions and may be giving you a
message like:
if (debug) 1
Error in if (debug) 1 : argument is not interpretable as logical
Thanks a lot...I realised where I was going wrongif I declare debug
= F then my problem is getting solved.
-Original Message-
From: jim holtman [mailto:[EMAIL PROTECTED]
Sent: Wednesday, November 12, 2008 9:12 AM
To: Agarwal, Rahul-A
Cc: r-help@r-project.org
Subject: Re: [R
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