Re: [R] debug only top level function

[Martin Maechler]

>>>>> Duncan Murdoch 
>>>>> on Thu, 6 Jun 2019 07:38:40 -0400 writes:

> On 06/06/2019 6:00 a.m., PIKAL Petr wrote:
>> Thanks Duncan.
>> 
>> I think you found it. I have an object called s within my function. I 
wanted to check it, so I hit "s". This did not bring the object but instead it 
change behaviour of debug function. I did not find this in help pages nor in R 
exts or R intro manual. Maybe it would be worth considering to add something 
about it to debug help page.

> It's in the ?browser help page, which is linked from ?debug.

> Duncan Murdoch

Indeed.
As it is not the first time, users did not "find" this, I have
made the links a bit more visible (for future R versions), now.

I'd  use  '(s)'  instead of 's'  [and more often and
importantly, I have a variable 'n' somewhere and need to use
'(n)'  very regularly.

For smallish situations, btw, the use of   ls.str()  comes very handy.

It has to be noted that unfortunately, the difference between
'n' and 's' and 'c'  has been a bit "blurred" for byte compiled
functions, and as the default JIT level is high, 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 
>>> 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 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 <- function(x) mean(x, na.rm=T)
>>>> 
>>>> when I issue
>>>>> debug(fff)
>>>>> fff(1:10)
>>>> debugging in: fff(1:10)
>>>> debug at #1: mean(x, na.rm = T)
>>>> Browse[2]>
>>>> debugging in: mean(x, na.rm = T)
>>>> debug: UseMethod("mean")
>>>> Browse[3]>
>>>> debugging in: mean.default(x, na.rm = T) ...
>>>> it starts debugging mean function. I understand that it is indicated by
>>> Browse[n] but it could be quite messy if I have many embedded functions 
and
>>> difficult to follow.
>>>> 
>>>> Can I persuade debug function not to bother with embedded functions 
(e.g.
>>> mean, median, mad, ...) and debug only my top level code?
>>> 
>>> There are several commands available.  Type "help" to see them:
>>> 
>>> n  next
>>> s  step into
>>> f  finish
>>> c or cont  continue
>>> Q  quit
>>> where  show stack
>>> help   show help
>>>  evaluate expression
>>> 
>>> 
>>> You want "n", and are getting "s".  I believe if you hit Enter without 
choosing
>>> one, it will do the same as the previous time, so you've probably used 
"s"
>>> sometime in the past.
>>> 
>>> Duncan Murdoch
>>> 
>>>> 
>>>> Best regards
>>>> Petr
>>>> 
>>>>> sessionInfo()
>>>> R Under development (unstable) (2018-03-07 r74369)
>>>> Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10
>>>> x64 (build 17763)
>>>> 
>>>> Matrix products: default
>>>> 
>>>> locale:
>>>> [1] LC_COLLATE=Czech_Czechia.1250  LC_CTYPE=Czech_Czechia.1250 [3]
>>>> LC_MONETARY=Czech_Czechia.1250 LC_NUMERIC=C [5]
>>>> LC_TIME=Czech_Czechia.1250
>>>> 
>>>> attached base packages:
>>>> [1] stats datasets  utils grDevices graphics  methods   base
>>>> 
>>>> other attached packages:
>>>> [1] MASS_7.3-49 readxl_1.0.0lattice_0.20-35 fun_0.1
>>>> 
>>>> loaded via a namespace (and not attached):
>>>> [1] Rcpp_0.12.16 cellranger_1.1.0 grid_3.5.0   plyr_1.8.4
>>>> [5] gtable_0.2.0 scales_0.5.0 ggplot2_2.2.1pillar_1.2.1
>>>> [9] rlang_0.2.0  lazyeval_0.2.1   rpart_4.1-13 tools_3.5.0
>>>> [13] munsell_0.4.3compiler_3.5.0   colorspace_1.3-2 tibble_1.4.2

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Re: [R] debug only top level function

[Duncan Murdoch]

On 06/06/2019 6:00 a.m., PIKAL Petr wrote:

Thanks Duncan.

I think you found it. I have an object called s within my function. I wanted to check it, 
so I hit "s". This did not bring the object but instead it change behaviour of 
debug function. I did not find this in help pages nor in R exts or R intro manual. Maybe 
it would be worth considering to add something about it to debug help page.


It's in the ?browser help page, which is linked from ?debug.

Duncan Murdoch



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 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 <- function(x) mean(x, na.rm=T)

when I issue

debug(fff)
fff(1:10)

debugging in: fff(1:10)
debug at #1: mean(x, na.rm = T)
Browse[2]>
debugging in: mean(x, na.rm = T)
debug: UseMethod("mean")
Browse[3]>
debugging in: mean.default(x, na.rm = T) ...
it starts debugging mean function. I understand that it is indicated by

Browse[n] but it could be quite messy if I have many embedded functions and
difficult to follow.


Can I persuade debug function not to bother with embedded functions (e.g.

mean, median, mad, ...) and debug only my top level code?

There are several commands available.  Type "help" to see them:

n  next
s  step into
f  finish
c or cont  continue
Q  quit
where  show stack
help   show help
 evaluate expression


You want "n", and are getting "s".  I believe if you hit Enter without choosing
one, it will do the same as the previous time, so you've probably used "s"
sometime in the past.

Duncan Murdoch



Best regards
Petr


sessionInfo()

R Under development (unstable) (2018-03-07 r74369)
Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10
x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=Czech_Czechia.1250  LC_CTYPE=Czech_Czechia.1250 [3]
LC_MONETARY=Czech_Czechia.1250 LC_NUMERIC=C [5]
LC_TIME=Czech_Czechia.1250

attached base packages:
[1] stats datasets  utils grDevices graphics  methods   base

other attached packages:
[1] MASS_7.3-49 readxl_1.0.0lattice_0.20-35 fun_0.1

loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 cellranger_1.1.0 grid_3.5.0   plyr_1.8.4
   [5] gtable_0.2.0 scales_0.5.0 ggplot2_2.2.1pillar_1.2.1
   [9] rlang_0.2.0  lazyeval_0.2.1   rpart_4.1-13 tools_3.5.0
[13] munsell_0.4.3compiler_3.5.0   colorspace_1.3-2 tibble_1.4.2



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Re: [R] debug only top level function

[PIKAL Petr]

Thanks Duncan.

I think you found it. I have an object called s within my function. I wanted to 
check it, so I hit "s". This did not bring the object but instead it change 
behaviour of debug function. I did not find this in help pages nor in R exts or 
R intro manual. Maybe it would 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 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 <- function(x) mean(x, na.rm=T)
> >
> > when I issue
> >> debug(fff)
> >> fff(1:10)
> > debugging in: fff(1:10)
> > debug at #1: mean(x, na.rm = T)
> > Browse[2]>
> > debugging in: mean(x, na.rm = T)
> > debug: UseMethod("mean")
> > Browse[3]>
> > debugging in: mean.default(x, na.rm = T) ...
> > it starts debugging mean function. I understand that it is indicated by
> Browse[n] but it could be quite messy if I have many embedded functions and
> difficult to follow.
> >
> > Can I persuade debug function not to bother with embedded functions (e.g.
> mean, median, mad, ...) and debug only my top level code?
>
> There are several commands available.  Type "help" to see them:
>
> n  next
> s  step into
> f  finish
> c or cont  continue
> Q  quit
> where  show stack
> help   show help
>  evaluate expression
>
>
> You want "n", and are getting "s".  I believe if you hit Enter without 
> choosing
> one, it will do the same as the previous time, so you've probably used "s"
> sometime in the past.
>
> Duncan Murdoch
>
> >
> > Best regards
> > Petr
> >
> >> sessionInfo()
> > R Under development (unstable) (2018-03-07 r74369)
> > Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10
> > x64 (build 17763)
> >
> > Matrix products: default
> >
> > locale:
> > [1] LC_COLLATE=Czech_Czechia.1250  LC_CTYPE=Czech_Czechia.1250 [3]
> > LC_MONETARY=Czech_Czechia.1250 LC_NUMERIC=C [5]
> > LC_TIME=Czech_Czechia.1250
> >
> > attached base packages:
> > [1] stats datasets  utils grDevices graphics  methods   base
> >
> > other attached packages:
> > [1] MASS_7.3-49 readxl_1.0.0lattice_0.20-35 fun_0.1
> >
> > loaded via a namespace (and not attached):
> > [1] Rcpp_0.12.16 cellranger_1.1.0 grid_3.5.0   plyr_1.8.4
> >   [5] gtable_0.2.0 scales_0.5.0 ggplot2_2.2.1pillar_1.2.1
> >   [9] rlang_0.2.0  lazyeval_0.2.1   rpart_4.1-13 tools_3.5.0
> > [13] munsell_0.4.3compiler_3.5.0   colorspace_1.3-2 tibble_1.4.2
> >>
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > 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.
> >

Osobní údaje: Informace o zpracování a ochraně osobních údajů obchodních 
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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.

Re: [R] debug only top level function

[Duncan Murdoch]

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 <- function(x) mean(x, na.rm=T)

when I issue

debug(fff)
fff(1:10)

debugging in: fff(1:10)
debug at #1: mean(x, na.rm = T)
Browse[2]>
debugging in: mean(x, na.rm = T)
debug: UseMethod("mean")
Browse[3]>
debugging in: mean.default(x, na.rm = T)
...
it starts debugging mean function. I understand that it is indicated by 
Browse[n] but it could be quite messy if I have many embedded functions and 
difficult to follow.

Can I persuade debug function not to bother with embedded functions (e.g. mean, 
median, mad, ...) and debug only my top level code?


There are several commands available.  Type "help" to see them:

n  next
s  step into
f  finish
c or cont  continue
Q  quit
where  show stack
help   show help
 evaluate expression


You want "n", and are getting "s".  I believe if you hit Enter without 
choosing one, it will do the same as the previous time, so you've 
probably used "s" sometime in the past.


Duncan Murdoch



Best regards
Petr


sessionInfo()

R Under development (unstable) (2018-03-07 r74369)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=Czech_Czechia.1250  LC_CTYPE=Czech_Czechia.1250
[3] LC_MONETARY=Czech_Czechia.1250 LC_NUMERIC=C
[5] LC_TIME=Czech_Czechia.1250

attached base packages:
[1] stats datasets  utils grDevices graphics  methods   base

other attached packages:
[1] MASS_7.3-49 readxl_1.0.0lattice_0.20-35 fun_0.1

loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 cellranger_1.1.0 grid_3.5.0   plyr_1.8.4
  [5] gtable_0.2.0 scales_0.5.0 ggplot2_2.2.1pillar_1.2.1
  [9] rlang_0.2.0  lazyeval_0.2.1   rpart_4.1-13 tools_3.5.0
[13] munsell_0.4.3compiler_3.5.0   colorspace_1.3-2 tibble_1.4.2



Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj? obchodn?ch 
partner? PRECHEZA a.s. jsou zve?ejn?ny na: 
https://www.precheza.cz/zasady-ochrany-osobnich-udaju/ | Information about 
processing and protection of business partner's personal data are available on 
website: https://www.precheza.cz/en/personal-data-protection-principles/
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[R] debug only top level function

[PIKAL Petr]

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
> debug(fff)
> fff(1:10)
debugging in: fff(1:10)
debug at #1: mean(x, na.rm = T)
Browse[2]>
debugging in: mean(x, na.rm = T)
debug: UseMethod("mean")
Browse[3]>
debugging in: mean.default(x, na.rm = T)
...
it starts debugging mean function. I understand that it is indicated by 
Browse[n] but it could be quite messy if I have many embedded functions and 
difficult to follow.

Can I persuade debug function not to bother with embedded functions (e.g. mean, 
median, mad, ...) and debug only my top level code?

Best regards
Petr

> sessionInfo()
R Under development (unstable) (2018-03-07 r74369)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=Czech_Czechia.1250  LC_CTYPE=Czech_Czechia.1250
[3] LC_MONETARY=Czech_Czechia.1250 LC_NUMERIC=C
[5] LC_TIME=Czech_Czechia.1250

attached base packages:
[1] stats datasets  utils grDevices graphics  methods   base

other attached packages:
[1] MASS_7.3-49 readxl_1.0.0lattice_0.20-35 fun_0.1

loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 cellranger_1.1.0 grid_3.5.0   plyr_1.8.4
 [5] gtable_0.2.0 scales_0.5.0 ggplot2_2.2.1pillar_1.2.1
 [9] rlang_0.2.0  lazyeval_0.2.1   rpart_4.1-13 tools_3.5.0
[13] munsell_0.4.3compiler_3.5.0   colorspace_1.3-2 tibble_1.4.2
>
Osobn? ?daje: Informace o zpracov?n? a ochran? osobn?ch ?daj? obchodn?ch 
partner? PRECHEZA a.s. jsou zve?ejn?ny na: 
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processing and protection of business partner's personal data are available on 
website: https://www.precheza.cz/en/personal-data-protection-principles/
D?v?rnost: Tento e-mail a jak?koliv k n?mu p?ipojen? dokumenty jsou d?v?rn? a 
podl?haj? tomuto pr?vn? z?vazn?mu prohl??en? o vylou?en? odpov?dnosti: 
https://www.precheza.cz/01-dovetek/ | This email and any documents attached to 
it may be confidential and are subject to the legally binding disclaimer: 
https://www.precheza.cz/en/01-disclaimer/


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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Debug package options

[Keith S Weintraub]

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 have the right size font and Tk window to be able to do 
debugging using the debug package.

In case you are interested I use Windows 7 on my Mac via Parallels.

Thanks again,
Best,
KW



 On Mar 30, 2015, at 2:05 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote:
 
 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 environment so when debug starts up I 
 have all the options set up the way I want them?
 
 Do I do this in a .First file? Does the .First file have to load the debug 
 package every time I start up R?
 
 No need to do my work for me. Just point me to the right doc.
 
 See the ?Startup help topic.  You probably want to use one of the
 profile files rather than .First, because .First needs to be in a
 workspace, and you shouldn't be loading a workspace every time.
 
 Duncan Murdoch

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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.

Re: [R] Debug package options

[Duncan Murdoch]

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 environment so when debug starts up I 
 have all the options set up the way I want them?
 
 Do I do this in a .First file? Does the .First file have to load the debug 
 package every time I start up R?
 
 No need to do my work for me. Just point me to the right doc.

See the ?Startup help topic.  You probably want to use one of the
profile files rather than .First, because .First needs to be in a
workspace, and you shouldn't be loading a workspace every time.

Duncan Murdoch

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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.

[R] Debug package options

[Keith S Weintraub]

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 up the way I want them?

Do I do this in a .First file? Does the .First file have to load the debug 
package every time I start up R?

No need to do my work for me. Just point me to the right doc.

Best,
KW

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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.

[R] debug on lapply

[Asis Hallab]

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( test )

*Start debug:*
 test()
debugging in: test()
debug bei #1:{
lapply(1:10, function(x) x + 1)
}
Browse[2] n
debug bei #2:lapply(1:10, function(x) x + 1)

*The next n does not allow me to inspect the inner function,*
*but gives me the result directly:*
Browse[2] n
exiting from: test()
[[1]]
[1] 2

[[2]]
[1] 3

[[3]]
[1] 4

Can anyone help me, please?
Kind regards!

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] debug on lapply

[jim holtman]

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 modified code I used:

lapply( 1:3, function( x ){
browser()
x + 1
}
  )



Here is the output from the console after sourcing in the statements above:

 source('clipboard')
Called from: FUN(1:3[[1L]], ...)
Browse[1] ls()
[1] x
Browse[1] x
[1] 1
Browse[1] n
debug at clipboard#3: x + 1
Browse[2] x
[1] 1
Browse[2] n
Called from: FUN(1:3[[2L]], ...)
Browse[1] x
[1] 2
Browse[1] n
debug at clipboard#3: x + 1
Browse[2]
Called from: FUN(1:3[[3L]], ...)
Browse[1] n
debug at clipboard#3: x + 1
Browse[2] x
[1] 3
Browse[2] n



On Tue, Dec 11, 2012 at 1:17 PM, Asis Hallab asis.hal...@gmail.com 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?

 *For example:*
 test - function( ) {
   lapply( 1:3, function( x ) x + 1 )
 }
 debug( test )

 *Start debug:*
 test()
 debugging in: test()
 debug bei #1:{
 lapply(1:10, function(x) x + 1)
 }
 Browse[2] n
 debug bei #2:lapply(1:10, function(x) x + 1)

 *The next n does not allow me to inspect the inner function,*
 *but gives me the result directly:*
 Browse[2] n
 exiting from: test()
 [[1]]
 [1] 2

 [[2]]
 [1] 3

 [[3]]
 [1] 4

 Can anyone help me, please?
 Kind regards!

 [[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.



-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] debug on lapply

[Duncan Murdoch]

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 is to debug lapply, and when 
stepping through it, debug(FUN) after it is created on the first line.  
Jim's method is more convenient if you are particularly interested in a 
complicated function, this method is better if you are already in the 
middle of debugging and just want to look at a possibly anonymous 
function being passed to lapply.


Duncan Murdoch


*For example:*
test - function( ) {
   lapply( 1:3, function( x ) x + 1 )
}
debug( test )

*Start debug:*
 test()
debugging in: test()
debug bei #1:{
 lapply(1:10, function(x) x + 1)
}
Browse[2] n
debug bei #2:lapply(1:10, function(x) x + 1)

*The next n does not allow me to inspect the inner function,*
*but gives me the result directly:*
Browse[2] n
exiting from: test()
[[1]]
[1] 2

[[2]]
[1] 3

[[3]]
[1] 4

Can anyone help me, please?
Kind regards!

[[alternative HTML version deleted]]

__
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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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and provide commented, minimal, self-contained, reproducible code.

[R] Debug newbie

[Ana Richardson]

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 they must be in line 366 in sites variable in cosmo.R:

 Code:

for (i in 1:com$selNumSites){
  site - seqMat[com$alignStarts[i]:(com$alignStarts[i]+com$selWidth-1),
 com$alignSeqs[i]]
  sites - c(sites, toString(site))

But when I try to debug it I need first to load the cosmo library, then
read the data and then run cosmo:

 Code:

library(cosmo)
seqal - system.file(Exfiles/short702k.FASTA, package=cosmo)
res - cosmo(seqs=seqal, constraints=None, minW=10, maxW=10, models=TCM )



For debugging line 366 I think I should:
 Code:

library(cosmo)
seqal - system.file(Exfiles/short702k.FASTA, package=cosmo)
setBreakpoint(cosmo.R,366)
res - cosmo(seqs=seqal, constraints=None, minW=10, maxW=10, models=TCM )

But I don't get any value of any variable..

And it doesn't seem to be the easiest way to get the sites variable values..

Ana

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] debug vs regular mode

[Henric (Nilsson) Winell]

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 segmentation fault.


There's some information missing here, notably the output from 
'sessionInfo()', but I guess this is under GNU/Linux.  I can confirm a 
seg. fault under Fedora FC17 x86_64.


Under Windows 7 64-bit, however, we get some further info:

 library(glmulti)
Loading required package: rJava
 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)
Initialization...
Error in .jnew(glmulti/ModelGenerator, y, .jarray(xc), .jarray(xq),  :
  java.lang.ArrayIndexOutOfBoundsException: 15

 sessionInfo()
R version 2.15.1 Patched (2012-08-06 r60178)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252
[3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
[5] LC_TIME=Swedish_Sweden.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] glmulti_1.0.4 rJava_0.9-3


So, this doesn't seem to be a bug in R and is thus likely to need the 
attention of the 'glmulti' package's maintainer.



HTH,
Henric




But I have troubles to
extract the exact information from this S4 class to make a simpler
example because of my limited knowledge on S4 class. The author of the
package is busy at the moment, and does not have time to look into it.

Peng

On 08/09/2012 10:25 PM, R. Michael Weylandt michael.weyla...@gmail.com
wrote:


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 regular
mode?

I cannot help you there.


Though a reproducible segfault is certainly worth a bug report if you can do 
so, in debug or regular modes.

You may wish to search stackoverflow for tips on how to make a great 
reproducible example in R.

Michael

**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues

__
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.



__
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.

Re: [R] debug vs regular mode

[Zhang, Peng]

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)))
  glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16, 
data= testdata, level = 2)
Segmentation fault

Is this information Error in .jnew(glmulti/ModelGenerator, y, 
.jarray(xc), .jarray(xq),  : java.lang.ArrayIndexOutOfBoundsException: 
15 only in Windows, or did you see it under Fedora as well?

Thank you!

Peng

BTW:

$ uname -a
Linux Precision 3.4.7-1-ARCH #1 SMP PREEMPT Sun Jul 29 22:02:56 CEST 
2012 x86_64 GNU/Linux

  sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=C LC_NAME=C
  [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base


On 08/10/2012 09:25 AM, Henric (Nilsson) Winell wrote:
 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 segmentation fault.

 There's some information missing here, notably the output from 
 'sessionInfo()', but I guess this is under GNU/Linux.  I can confirm a 
 seg. fault under Fedora FC17 x86_64.

 Under Windows 7 64-bit, however, we get some further info:

  library(glmulti)
 Loading required package: rJava
  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)
 Initialization...
 Error in .jnew(glmulti/ModelGenerator, y, .jarray(xc), .jarray(xq),  :
   java.lang.ArrayIndexOutOfBoundsException: 15
 
  sessionInfo()
 R version 2.15.1 Patched (2012-08-06 r60178)
 Platform: x86_64-w64-mingw32/x64 (64-bit)

 locale:
 [1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252
 [3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
 [5] LC_TIME=Swedish_Sweden.1252

 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods base

 other attached packages:
 [1] glmulti_1.0.4 rJava_0.9-3
 

 So, this doesn't seem to be a bug in R and is thus likely to need the 
 attention of the 'glmulti' package's maintainer.


 HTH,
 Henric



 But I have troubles to
 extract the exact information from this S4 class to make a simpler
 example because of my limited knowledge on S4 class. The author of the
 package is busy at the moment, and does not have time to look into it.

 Peng

 On 08/09/2012 10:25 PM, R. Michael Weylandt michael.weyla...@gmail.com
 wrote:

 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 
 regular
 mode?
 I cannot help you there.

 Though a reproducible segfault is certainly worth a bug report if 
 you can do so, in debug or regular modes.

 You may wish to search stackoverflow for tips on how to make a great 
 reproducible example in R.

 Michael
 **
 Electronic Mail is not secure, may not be read every day, and should 
 not be used for urgent or sensitive issues

 __
 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.


**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues 

__
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.

Re: [R] debug vs regular mode

[Henric (Nilsson) Winell]

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
= 50)))
   glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16,
data= testdata, level = 2)
Segmentation fault

Is this information Error in .jnew(glmulti/ModelGenerator, y,
jarray(xc), .jarray(xq),  : java.lang.ArrayIndexOutOfBoundsException:
15 only in Windows, or did you see it under Fedora as well?


Windows only.  Fedora just returned Segmentation fault.


//Henric





Thank you!

Peng

BTW:

$ uname -a
Linux Precision 3.4.7-1-ARCH #1 SMP PREEMPT Sun Jul 29 22:02:56 CEST
2012 x86_64 GNU/Linux

   sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
   [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
   [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
   [7] LC_PAPER=C LC_NAME=C
   [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base


On 08/10/2012 09:25 AM, Henric (Nilsson) Winell wrote:

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 segmentation fault.


There's some information missing here, notably the output from
'sessionInfo()', but I guess this is under GNU/Linux.  I can confirm a
seg. fault under Fedora FC17 x86_64.

Under Windows 7 64-bit, however, we get some further info:


library(glmulti)

Loading required package: rJava

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)
Initialization...
Error in .jnew(glmulti/ModelGenerator, y, .jarray(xc), .jarray(xq),  :
   java.lang.ArrayIndexOutOfBoundsException: 15


sessionInfo()

R version 2.15.1 Patched (2012-08-06 r60178)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=Swedish_Sweden.1252  LC_CTYPE=Swedish_Sweden.1252
[3] LC_MONETARY=Swedish_Sweden.1252 LC_NUMERIC=C
[5] LC_TIME=Swedish_Sweden.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base

other attached packages:
[1] glmulti_1.0.4 rJava_0.9-3




So, this doesn't seem to be a bug in R and is thus likely to need the
attention of the 'glmulti' package's maintainer.


HTH,
Henric




But I have troubles to
extract the exact information from this S4 class to make a simpler
example because of my limited knowledge on S4 class. The author of the
package is busy at the moment, and does not have time to look into it.

Peng

On 08/09/2012 10:25 PM, R. Michael Weylandt michael.weyla...@gmail.com
wrote:


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
regular
mode?

I cannot help you there.


Though a reproducible segfault is certainly worth a bug report if
you can do so, in debug or regular modes.

You may wish to search stackoverflow for tips on how to make a great
reproducible example in R.

Michael

**
Electronic Mail is not secure, may not be read every day, and should
not be used for urgent or sensitive issues

__
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.




**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues




__
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.

Re: [R] debug vs regular mode

[Zhang, Peng]

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 fault will appear when I step to neotete = 
terms(as.formula(paste(h~,paste(preds, collapse=*. That is why 
I have asked my initial question on the board.

The more interesting thing is that if I don't run library(glmulti), but 
just the following lines, I won't have problem when I stepped to that 
terms function.

I am totally lost. It is not clear to me how to debug S4 class.

Best,
Peng

### beginning
library(glmulti)

testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol = 50)))

glmulti =
function(y, xr, data, exclude, name, intercept, marginality , bunch, 
chunk, chunks,
 level, minsize, maxsize, minK, maxK, 
method,crit,confsetsize,popsize,mutrate,
 sexrate,imm, plotty,  report, deltaM, deltaB, conseq, 
fitfunction, resumefile, includeobjects, ...) {
 if (missing(data))
 tete = terms(y)
 else
 tete = terms(y, data=data)
 oo = attr(tete,order)
 dep = as.character(attr(tete,variables))[2]
 int = attr(tete,intercept)
 preds = as.character(attr(tete,variables))[-(1:2)]
 if (level==2  max(oo)1) {
 # get all possible interactions
 interac = attr(tete,term.labels)[oo==2]
 neotete = terms(as.formula(paste(h~,paste(preds, collapse=*
 neointerac= attr(neotete,term.labels)[attr(neotete,order)==2]
 # get exclusions
 for (i in interac)
 neointerac=neointerac[neointerac!=i]
 # same for main effects
 mama = attr(tete,term.labels)[oo==1]
 exma = preds
 for (j in mama)
 exma = exma[exma!=j]
 exma = c(exma,neointerac)
 } else {
 preds = attr(tete,term.labels)[oo==1]
 exma=c(1)
 }
 call = match.call()
 call[[match(y, names(call))]] = dep
 call[[length(names(call))+1]] = preds
 names(call)[length(names(call))] =xr
 call[[length(names(call))+1]] = exma
 names(call)[length(names(call))] =exclude

 if (missing(data)) {
 call[[length(names(call))+1]] = environment(y)
 names(call)[length(names(call))] =data
 }
 eval(call)
}

debug(glmulti)

glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16, 
xr=NULL, data = testdata, level = 2)
###end

On 08/10/2012 11:47 AM, Henric (Nilsson) Winell wrote:
 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
 = 50)))
glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16,
 data= testdata, level = 2)
 Segmentation fault

 Is this information Error in .jnew(glmulti/ModelGenerator, y,
 jarray(xc), .jarray(xq),  : java.lang.ArrayIndexOutOfBoundsException:
 15 only in Windows, or did you see it under Fedora as well?

 Windows only.  Fedora just returned Segmentation fault.


 //Henric




 Thank you!

 Peng

 BTW:

 $ uname -a
 Linux Precision 3.4.7-1-ARCH #1 SMP PREEMPT Sun Jul 29 22:02:56 CEST
 2012 x86_64 GNU/Linux

sessionInfo()
 R version 2.15.1 (2012-06-22)
 Platform: x86_64-unknown-linux-gnu (64-bit)

 locale:
[1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C   LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods base


 On 08/10/2012 09:25 AM, Henric (Nilsson) Winell wrote:
 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 segmentation fault.

 There's some information missing here, notably the output from
 'sessionInfo()', but I guess this is under GNU/Linux.  I can confirm a
 seg. fault under Fedora FC17 x86_64.

 Under Windows 7 64-bit, however, we get some further info:

 library(glmulti)
 Loading required package: rJava
 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)
 Initialization...
 Error in .jnew(glmulti/ModelGenerator, y, .jarray(xc), 
 .jarray(xq),  :
java.lang.ArrayIndexOutOfBoundsException: 15

 sessionInfo()
 R version 2.15.1 Patched (2012-08-06 r60178)
 Platform: 

Re: [R] debug vs regular mode

[peter dalgaard]

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 Aug 10, 2012, at 19:51 , Zhang, Peng wrote:

 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 fault will appear when I step to neotete = 
 terms(as.formula(paste(h~,paste(preds, collapse=*. That is why 
 I have asked my initial question on the board.
 
 The more interesting thing is that if I don't run library(glmulti), but 
 just the following lines, I won't have problem when I stepped to that 
 terms function.
 
 I am totally lost. It is not clear to me how to debug S4 class.
 
 Best,
 Peng
 
 ### beginning
 library(glmulti)
 
 testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol = 50)))
 
 glmulti =
 function(y, xr, data, exclude, name, intercept, marginality , bunch, 
 chunk, chunks,
 level, minsize, maxsize, minK, maxK, 
 method,crit,confsetsize,popsize,mutrate,
 sexrate,imm, plotty,  report, deltaM, deltaB, conseq, 
 fitfunction, resumefile, includeobjects, ...) {
 if (missing(data))
 tete = terms(y)
 else
 tete = terms(y, data=data)
 oo = attr(tete,order)
 dep = as.character(attr(tete,variables))[2]
 int = attr(tete,intercept)
 preds = as.character(attr(tete,variables))[-(1:2)]
 if (level==2  max(oo)1) {
 # get all possible interactions
 interac = attr(tete,term.labels)[oo==2]
 neotete = terms(as.formula(paste(h~,paste(preds, collapse=*
 neointerac= attr(neotete,term.labels)[attr(neotete,order)==2]
 # get exclusions
 for (i in interac)
 neointerac=neointerac[neointerac!=i]
 # same for main effects
 mama = attr(tete,term.labels)[oo==1]
 exma = preds
 for (j in mama)
 exma = exma[exma!=j]
 exma = c(exma,neointerac)
 } else {
 preds = attr(tete,term.labels)[oo==1]
 exma=c(1)
 }
 call = match.call()
 call[[match(y, names(call))]] = dep
 call[[length(names(call))+1]] = preds
 names(call)[length(names(call))] =xr
 call[[length(names(call))+1]] = exma
 names(call)[length(names(call))] =exclude
 
 if (missing(data)) {
 call[[length(names(call))+1]] = environment(y)
 names(call)[length(names(call))] =data
 }
 eval(call)
 }
 
 debug(glmulti)
 
 glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16, 
 xr=NULL, data = testdata, level = 2)
 ###end
 
 On 08/10/2012 11:47 AM, Henric (Nilsson) Winell wrote:
 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
 = 50)))
 glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16,
 data= testdata, level = 2)
 Segmentation fault
 
 Is this information Error in .jnew(glmulti/ModelGenerator, y,
 jarray(xc), .jarray(xq),  : java.lang.ArrayIndexOutOfBoundsException:
 15 only in Windows, or did you see it under Fedora as well?
 
 Windows only.  Fedora just returned Segmentation fault.
 
 
 //Henric
 
 
 
 
 Thank you!
 
 Peng
 
 BTW:
 
 $ uname -a
 Linux Precision 3.4.7-1-ARCH #1 SMP PREEMPT Sun Jul 29 22:02:56 CEST
 2012 x86_64 GNU/Linux
 
 sessionInfo()
 R version 2.15.1 (2012-06-22)
 Platform: x86_64-unknown-linux-gnu (64-bit)
 
 locale:
   [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
   [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
   [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
   [7] LC_PAPER=C LC_NAME=C
   [9] LC_ADDRESS=C   LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
 
 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods base
 
 
 On 08/10/2012 09:25 AM, Henric (Nilsson) Winell wrote:
 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 segmentation fault.
 
 There's some information missing here, notably the output from
 'sessionInfo()', but I guess this is under GNU/Linux.  I can confirm a
 seg. fault under Fedora FC17 x86_64.
 
 Under Windows 7 64-bit, however, we get some further info:
 
 library(glmulti)
 Loading required package: rJava
 

Re: [R] debug vs regular mode

[peter dalgaard]

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 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 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

[much snipped]

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] debug vs regular mode

[Zhang, Peng]

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 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 Aug 10, 2012, at 19:51 , Zhang, Peng wrote:

 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 fault will appear when I step to neotete =
 terms(as.formula(paste(h~,paste(preds, collapse=*. That is why
 I have asked my initial question on the board.

 The more interesting thing is that if I don't run library(glmulti), but
 just the following lines, I won't have problem when I stepped to that
 terms function.

 I am totally lost. It is not clear to me how to debug S4 class.

 Best,
 Peng

 ### beginning
 library(glmulti)

 testdata = cbind(Y=rnorm(100), data.frame(matrix(rnorm(100*50), ncol = 50)))

 glmulti =
 function(y, xr, data, exclude, name, intercept, marginality , bunch,
 chunk, chunks,
  level, minsize, maxsize, minK, maxK,
 method,crit,confsetsize,popsize,mutrate,
  sexrate,imm, plotty,  report, deltaM, deltaB, conseq,
 fitfunction, resumefile, includeobjects, ...) {
  if (missing(data))
  tete = terms(y)
  else
  tete = terms(y, data=data)
  oo = attr(tete,order)
  dep = as.character(attr(tete,variables))[2]
  int = attr(tete,intercept)
  preds = as.character(attr(tete,variables))[-(1:2)]
  if (level==2  max(oo)1) {
  # get all possible interactions
  interac = attr(tete,term.labels)[oo==2]
  neotete = terms(as.formula(paste(h~,paste(preds, collapse=*
  neointerac= attr(neotete,term.labels)[attr(neotete,order)==2]
  # get exclusions
  for (i in interac)
  neointerac=neointerac[neointerac!=i]
  # same for main effects
  mama = attr(tete,term.labels)[oo==1]
  exma = preds
  for (j in mama)
  exma = exma[exma!=j]
  exma = c(exma,neointerac)
  } else {
  preds = attr(tete,term.labels)[oo==1]
  exma=c(1)
  }
  call = match.call()
  call[[match(y, names(call))]] = dep
  call[[length(names(call))+1]] = preds
  names(call)[length(names(call))] =xr
  call[[length(names(call))+1]] = exma
  names(call)[length(names(call))] =exclude

  if (missing(data)) {
  call[[length(names(call))+1]] = environment(y)
  names(call)[length(names(call))] =data
  }
  eval(call)
 }

 debug(glmulti)

 glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16,
 xr=NULL, data = testdata, level = 2)
 ###end

 On 08/10/2012 11:47 AM, Henric (Nilsson) Winell wrote:
 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
 = 50)))
 glmulti(Y~(X1+X2+X3+X4+X5+X6+X7+X8+X9+X10+X11+X12+X13+X14+X15)*X16,
 data= testdata, level = 2)
 Segmentation fault

 Is this information Error in .jnew(glmulti/ModelGenerator, y,
 jarray(xc), .jarray(xq),  : java.lang.ArrayIndexOutOfBoundsException:
 15 only in Windows, or did you see it under Fedora as well?
 Windows only.  Fedora just returned Segmentation fault.


 //Henric



 Thank you!

 Peng

 BTW:

 $ uname -a
 Linux Precision 3.4.7-1-ARCH #1 SMP PREEMPT Sun Jul 29 22:02:56 CEST
 2012 x86_64 GNU/Linux

 sessionInfo()
 R version 2.15.1 (2012-06-22)
 Platform: x86_64-unknown-linux-gnu (64-bit)

 locale:
[1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C   LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

 attached base packages:
 [1] stats graphics  grDevices utils datasets  methods base


 On 08/10/2012 09:25 AM, Henric (Nilsson) Winell wrote:
 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 segmentation fault.
 There's some information missing here, notably the 

Re: [R] debug vs regular mode

[Zhang, Peng]

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, 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 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 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
 [much snipped]

**
Electronic Mail is not secure, may not be read every day, and should not be 
used for urgent or sensitive issues 

__
R-help@r-project.org mailing list
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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.

[R] debug vs regular mode

[Zhang, Peng]

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. Is there a known limit of terms for a formula?
2. Why does the same function behave differently under debug and regular 
mode?

Thank you!

Best,
Peng
**
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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] debug vs regular mode

[David Winsemius]

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 though taking long time.

My questions are:
1. Is there a known limit of terms for a formula?


I think so. I seem to remember it was something around 500 characters,  
but was raised a couple of years ago.


This is a 2010 extract of a posting by the indomitable Prof Ripley:

R-devel:
• The previously almost undocumented limit of 256 bytes on a symbol  
name has been raised to 10,000 bytes (a sanity check). Long symbol  
names can sometimes occur when deparsing expressions (for example, in  
model.frame).  


Found with a MarkMail search with this strategy:

list:org.r-project.r-devel maximum length of formula



Subject:Re: [Rd] model.frame problem

From:Prof Brian Ripley (rip...@stats.ox.ac.uk)

Date:Nov 3, 2010 1:37:50 pm

List:org.r-project.r-devel


2. Why does the same function behave differently under debug and  
regular

mode?


I cannot help you there.

--

David Winsemius, MD
Alameda, CA, USA

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] debug vs regular mode

[R. Michael Weylandt michael.weyla...@gmail.com]

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 regular
 mode?
 
 I cannot help you there.
 

Though a reproducible segfault is certainly worth a bug report if you can do 
so, in debug or regular modes. 

You may wish to search stackoverflow for tips on how to make a great 
reproducible example in R. 

Michael
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and provide commented, minimal, self-contained, reproducible code.

Re: [R] debug vs regular mode

[Zhang, Peng]

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 
extract the exact information from this S4 class to make a simpler 
example because of my limited knowledge on S4 class. The author of the 
package is busy at the moment, and does not have time to look into it.

Peng

On 08/09/2012 10:25 PM, R. Michael Weylandt michael.weyla...@gmail.com 
wrote:

 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 regular
 mode?
 I cannot help you there.

 Though a reproducible segfault is certainly worth a bug report if you can do 
 so, in debug or regular modes.

 You may wish to search stackoverflow for tips on how to make a great 
 reproducible example in R.

 Michael
**
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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] debug in a loop

[Duncan Murdoch]

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


setBreakpoint(foo.R#10, tracer=quote(if(is.na(tab[i])) browser()))

Duncan Murdoch



On Fri, Feb 10, 2012 at 7:22 AM, ikuzarraz...@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:

tab = c(1:300)
tab[250] = NA
len = length(tab)
for (i in 1:len){
   if(i != len){


if(is.na(tab[i])) browser()


 tab[i] = tab[i]+tab[i+1]
   }
}

I do not want to do Browse[2]  n for each step ... I'd like to declare a
browser() in the loop with a condition. But how to write stop running
when you encounter NA ?

Thanks for your help

--
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[[alternative HTML version deleted]]

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[R] debug in a loop

[ikuzar]

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 for each step ... I'd like to declare a
browser() in the loop with a condition. But how to write stop running
when you encounter NA ?

Thanks for your help

--
View this message in context: 
http://r.789695.n4.nabble.com/debug-in-a-loop-tp4376563p4376563.html
Sent from the R help mailing list archive at Nabble.com.

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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.

Re: [R] debug in a loop

[Justin Haynes]

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:

 tab = c(1:300)
 tab[250] = NA
 len = length(tab)
 for (i in 1:len){
   if(i != len){

   if(is.na(tab[i])) browser()

 tab[i] = tab[i]+tab[i+1]
   }
 }

 I do not want to do Browse[2] n for each step ... I'd like to declare a
 browser() in the loop with a condition. But how to write stop running
 when you encounter NA ?

 Thanks for your help

 --
 View this message in context:
 http://r.789695.n4.nabble.com/debug-in-a-loop-tp4376563p4376563.html
 Sent from the R help mailing list archive at Nabble.com.

 __
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 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.


[[alternative HTML version deleted]]

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[R] debug package: mtrace fails

[deivit]

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 the times I get the
following error:
Error in x[[i]] : subscript out of bounds

I can't understand whats happening and I couldn't find any help surfing the
net. I have the feeling it might be because of my coding style or something
similar.

Any help will be highly appreciated :)

Thanks in advance!
see ya


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Re: [R] debug package: mtrace fails

[Tal Galili]

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 (Hebrew) |
www.r-statistics.com (English)
--




On Tue, Jan 24, 2012 at 1:40 PM, deivit david.cass...@transmuralbiotech.com
 wrote:

 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 the times I get the
 following error:
 Error in x[[i]] : subscript out of bounds

 I can't understand whats happening and I couldn't find any help surfing the
 net. I have the feeling it might be because of my coding style or something
 similar.

 Any help will be highly appreciated :)

 Thanks in advance!
 see ya


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 __
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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.


[[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.

Re: [R] debug package: mtrace fails

[deivit]

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 bounds

--- code ---

index_remap - function (idx_relation=NULL, idx_vector=NULL, undo=FALSE)
{
if ((! any(duplicated(idx_vector)))  all(idx_vector %in%
idx_relation))
{
updated_idx - {}
for ( i in 1:length(idx_vector) )
{
if (undo == FALSE)
{
updated_idx - c(updated_idx, which
(idx_relation == idx_vector[i]))
} else {
updated_idx - c(updated_idx,
idx_relation[idx_vector[i]])
}
}

return (updated_idx)
} else {
error_msg(Some error message)
}
}

error_msg = function ( msg=NULL)
{
cat(style(msg,fg=red),\n)
}



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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.

[R] debug R code

[Hui Du]

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 (stop at line 123) 
or 'b 123' (break at line 123). Is there any similar commend in R debugger?


Thanks.

HXD


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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.

Re: [R] debug R code

[Duncan Murdoch]

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 or dbx 
debugger) I can run stop at 123 (stop at line 123) or 'b 123' (break at line 
123). Is there any similar commend in R debugger?




See ?setBreakpoint.

You can set a breakpoint from within the browser, or before you run your 
function.  ?trace gives full details on all the (many) options.


Duncan Murdoch

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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.

Re: [R] debug R device plot

[cameron.bracken]

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 it did
not get removed correctly. tikzDevice uses the filehash package to cache
font metrics and it must have gotten interrupted.

-Cameron

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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.

Re: [R] debug R device plot

[Sharpie]

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
location for the metrics dictionary, it will be in a temporary directory.
The tikzDevice prints out a status message with the location of the
temporary dictionary whenever it has to create one.

-
Charlie Sharpsteen
Undergraduate-- Environmental Resources Engineering
Humboldt State University
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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.

[R] debug R device plot

[Michael Bach]

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): cannot create lock file

I see that this is related to my OS, namely Ubuntu 10.04. I already checked
if I have write access to /var/lock via

touch /var/lock/test  rm -f /var/lock/test

which gave no errors...

Now my actual question: How can I inspect which file R wants to create? It
fails both when called from inside emacs via ESS mode and when called from
the command line. I am out of ideas...

Any advice on how to inspect what is going on here?

Thanks in advance

[[alternative HTML version deleted]]

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] debug biglm response error on bigglm model

[Mike Harwood]

Thank you, Greg.  The issue was in the simulation logic, where one of
the values was not changing correctly for some iterations...

On Jan 10, 3:20 pm, Greg Snow greg.s...@imail.org wrote:
 Not sure, but one possible candidate problem is that in your simulations one 
 iteration ended up with fewer levels of a factor than the overall dataset and 
 that caused the error.

 There is no recode function in the default packages, there are at least 6 
 recode functions in other packages, we cannot tell which you were using from 
 the code below.

 --
 Gregory (Greg) L. Snow Ph.D.
 Statistical Data 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 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 from bigglm (in package biglm), and how can I
  debug it?  I am attempting to do Monte Carlo simulations, which may
  explain the loop in the code that follows.  After the code I
  have included the output, which shows that the simulations are
  changing the response and input values, and that there are not any
  atypical values for the
  factors in the seventh iteration.  At the end of the output is the
  aforementioned error message.  Finally, I have included the model from
  biglm.

  Thanks in advance!

  Code:
  ===
  iter - nrow(nov.2010)
  predict.nov.2011 - vector(mode='numeric', length=iter)
  for (i in 1:iter) {
      iter.df - nov.2010
      ##-- Update values of dynamic variables --
      iter.df$age - iter.df$age + 12
      iter.df$pct_utilize -
          iter.df$pct_utilize + mc.util.delta[i]

      iter.df$updated_varname1 -
          ceiling(iter.df$updated_varname1 + mc.varname1.delta[i])

      if(iter.df$state==WI)
          iter.df$varname3 - iter.df$varname3 + mc.wi.varname3.delta[i]
      if(iter.df$state==MN)
          iter.df$varname3 - iter.df$varname3 + mc.mn.varname3.delta[i]
      if(iter.df$state==IL)
          iter.df$varname3 - iter.df$varname3 + mc.il.varname3.delta[i]
      if(iter.df$state==US)
          iter.df$varname3 - iter.df$varname3 + mc.us.varname3.delta[i]

      ##--- Bin Variables --
      iter.df$bin_varname1 - as.factor(recode(iter.df$updated_varname1,
          300:499 = '300 - 499';
           500:549 = '500 - 549';
           550:599 = '550 - 599';
           600:649 = '600 - 649';
           650:699 = '650 - 699';
           700:749 = '700 - 749';
           750:799 = '750 - 799'; 800:849 = 'GE 800'; else    =
  'missing';
           ))
      iter.df$bin_age - as.factor(recode(iter.df$age,
          0:23   = '  24mo.';
           24:72  = '24 - 72mo.';
           72:300 = '72 - 300mo'; else   = 'missing';
           ))
      iter.df$bin_util - as.factor(recode(iter.df$pct_utilize,
          0.0:0.2 = '  0 - 20%';
           0.2:0.4 = '  20 - 40%';
           0.4:0.6 = '  40 - 60%';
           0.6:0.8 = '  60 - 80%';
           0.8:1.0 = ' 80 - 100%';
           1.0:1.2 = '100 - 120%'; else    = 'missing';
           ))
      iter.df$bin_varname2 - as.factor(recode(iter.df$varname2_prop,
          0:70 = '     70%';
           70:85 = ' 70 - 85%';
           85:95 = ' 85 - 95%';
           95:110 = '95 - 110%'; else  =  'missing';
           ))
      iter.df$bin_varname1 - relevel(iter.df$bin_varname1, 'missing')
      iter.df$bin_age - relevel(iter.df$bin_age, 'missing')
      iter.df$bin_util - relevel(iter.df$bin_util, 'missing')
      iter.df$bin_varname2 - relevel(iter.df$bin_varname2, 'missing')

  #~     print(head(iter.df))
      if (i=6  i=8){
           print('-')
           browser()
           print(i)
           print(table(iter.df$bin_varname1))
           print(table(iter.df$bin_age))
           print(table(iter.df$bin_util))
           print(table(iter.df$bin_varname2))
  #~         debug(predict.nov.2011[i] -
  #~              sum(predict(logModel.1, newdata=iter.df,
  type='response')))
       }

      predict.nov.2011[i] -
           sum(predict(logModel.1, newdata=iter.df, type='response'))

      print(predict.nov.2011[i])

    }

  Output
  ==
  [1] 36.56073
  [1] 561.4516
  [1] 4.83483
  [1] 5.01398
  [1] 7.984146
  [1] -
  Called from: top level
  Browse[1]
  [1] 6

    missing 300 - 499 500 - 549 550 - 599 600 - 649 650 - 699 700 - 749
  750 - 799    GE 800
        842       283       690      1094      1695      3404
  6659     18374     21562

     missing     24mo. 24 - 72mo. 72 - 300mo
          16       2997      19709      31881

     missing    0 - 20%   20 - 40%   40 - 60%   60 - 80%  80 - 100% 100
  - 120%
       17906

[R] debug biglm response error on bigglm model

[Mike Harwood]

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 in the code that follows.  After the code I
have included the output, which shows that the simulations are
changing the response and input values, and that there are not any
atypical values for the
factors in the seventh iteration.  At the end of the output is the
aforementioned error message.  Finally, I have included the model from
biglm.

Thanks in advance!

Code:
===
iter - nrow(nov.2010)
predict.nov.2011 - vector(mode='numeric', length=iter)
for (i in 1:iter) {
iter.df - nov.2010
##-- Update values of dynamic variables --
iter.df$age - iter.df$age + 12
iter.df$pct_utilize -
iter.df$pct_utilize + mc.util.delta[i]

iter.df$updated_varname1 -
ceiling(iter.df$updated_varname1 + mc.varname1.delta[i])

if(iter.df$state==WI)
iter.df$varname3 - iter.df$varname3 + mc.wi.varname3.delta[i]
if(iter.df$state==MN)
iter.df$varname3 - iter.df$varname3 + mc.mn.varname3.delta[i]
if(iter.df$state==IL)
iter.df$varname3 - iter.df$varname3 + mc.il.varname3.delta[i]
if(iter.df$state==US)
iter.df$varname3 - iter.df$varname3 + mc.us.varname3.delta[i]

##--- Bin Variables --
iter.df$bin_varname1 - as.factor(recode(iter.df$updated_varname1,
300:499 = '300 - 499';
 500:549 = '500 - 549';
 550:599 = '550 - 599';
 600:649 = '600 - 649';
 650:699 = '650 - 699';
 700:749 = '700 - 749';
 750:799 = '750 - 799'; 800:849 = 'GE 800'; else=
'missing';
 ))
iter.df$bin_age - as.factor(recode(iter.df$age,
0:23   = '  24mo.';
 24:72  = '24 - 72mo.';
 72:300 = '72 - 300mo'; else   = 'missing';
 ))
iter.df$bin_util - as.factor(recode(iter.df$pct_utilize,
0.0:0.2 = '  0 - 20%';
 0.2:0.4 = '  20 - 40%';
 0.4:0.6 = '  40 - 60%';
 0.6:0.8 = '  60 - 80%';
 0.8:1.0 = ' 80 - 100%';
 1.0:1.2 = '100 - 120%'; else= 'missing';
 ))
iter.df$bin_varname2 - as.factor(recode(iter.df$varname2_prop,
0:70 = ' 70%';
 70:85 = ' 70 - 85%';
 85:95 = ' 85 - 95%';
 95:110 = '95 - 110%'; else  =  'missing';
 ))
iter.df$bin_varname1 - relevel(iter.df$bin_varname1, 'missing')
iter.df$bin_age - relevel(iter.df$bin_age, 'missing')
iter.df$bin_util - relevel(iter.df$bin_util, 'missing')
iter.df$bin_varname2 - relevel(iter.df$bin_varname2, 'missing')

#~ print(head(iter.df))
if (i=6  i=8){
 print('-')
 browser()
 print(i)
 print(table(iter.df$bin_varname1))
 print(table(iter.df$bin_age))
 print(table(iter.df$bin_util))
 print(table(iter.df$bin_varname2))
#~ debug(predict.nov.2011[i] -
#~  sum(predict(logModel.1, newdata=iter.df,
type='response')))
 }

predict.nov.2011[i] -
 sum(predict(logModel.1, newdata=iter.df, type='response'))

print(predict.nov.2011[i])

  }

Output
==
[1] 36.56073
[1] 561.4516
[1] 4.83483
[1] 5.01398
[1] 7.984146
[1] -
Called from: top level
Browse[1]
[1] 6

  missing 300 - 499 500 - 549 550 - 599 600 - 649 650 - 699 700 - 749
750 - 799GE 800
  842   283   690  1094  1695  3404
6659 18374 21562

   missing 24mo. 24 - 72mo. 72 - 300mo
16   2997  19709  31881

   missing0 - 20%   20 - 40%   40 - 60%   60 - 80%  80 - 100% 100
- 120%
 17906   4832   4599   5154   7205
14865 42

  missing  70%  70 - 85%  85 - 95% 95 - 110%
10423 19429 10568  8350  5833
[1] 11.04090
[1] -
Called from: top level
Browse[1]
[1] 7

  missing 300 - 499 500 - 549 550 - 599 600 - 649 650 - 699 700 - 749
750 - 799
  847   909  1059  1586  3214  6304
16349 24335

   missing 24mo. 24 - 72mo. 72 - 300mo
16   2997  19709  31881

   missing0 - 20%   20 - 40%   40 - 60%   60 - 80%  80 - 100% 100
- 120%
 17145   4972   4617   5020   6634
16139 76

  missing  70%  70 - 85%  85 - 95% 95 - 110%
10423 19429 10568  8350  5833
Error in x %*% coef(object) : non-conformable arguments

Model
===
Large data regression model: bigglm(outcome ~ bin_varname1 +
bin_varname2 + bin_age + bin_util +
state + varname3 + varname3:state, family = binomial(link =
logit),
data = dev.data, maxit = 75, sandwich = FALSE)
Sample size =  1372250

__
R-help@r-project.org mailing list

Re: [R] debug biglm response error on bigglm model

[Greg Snow]

Not sure, but one possible candidate problem is that in your simulations one 
iteration ended up with fewer levels of a factor than the overall dataset and 
that caused the error.

There is no recode function in the default packages, there are at least 6 
recode functions in other packages, we cannot tell which you were using from 
the code below.

-- 
Gregory (Greg) L. Snow Ph.D.
Statistical Data 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-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 from bigglm (in package biglm), and how can I
 debug it?  I am attempting to do Monte Carlo simulations, which may
 explain the loop in the code that follows.  After the code I
 have included the output, which shows that the simulations are
 changing the response and input values, and that there are not any
 atypical values for the
 factors in the seventh iteration.  At the end of the output is the
 aforementioned error message.  Finally, I have included the model from
 biglm.
 
 Thanks in advance!
 
 Code:
 ===
 iter - nrow(nov.2010)
 predict.nov.2011 - vector(mode='numeric', length=iter)
 for (i in 1:iter) {
 iter.df - nov.2010
 ##-- Update values of dynamic variables --
 iter.df$age - iter.df$age + 12
 iter.df$pct_utilize -
 iter.df$pct_utilize + mc.util.delta[i]
 
 iter.df$updated_varname1 -
 ceiling(iter.df$updated_varname1 + mc.varname1.delta[i])
 
 if(iter.df$state==WI)
 iter.df$varname3 - iter.df$varname3 + mc.wi.varname3.delta[i]
 if(iter.df$state==MN)
 iter.df$varname3 - iter.df$varname3 + mc.mn.varname3.delta[i]
 if(iter.df$state==IL)
 iter.df$varname3 - iter.df$varname3 + mc.il.varname3.delta[i]
 if(iter.df$state==US)
 iter.df$varname3 - iter.df$varname3 + mc.us.varname3.delta[i]
 
 ##--- Bin Variables --
 iter.df$bin_varname1 - as.factor(recode(iter.df$updated_varname1,
 300:499 = '300 - 499';
  500:549 = '500 - 549';
  550:599 = '550 - 599';
  600:649 = '600 - 649';
  650:699 = '650 - 699';
  700:749 = '700 - 749';
  750:799 = '750 - 799'; 800:849 = 'GE 800'; else=
 'missing';
  ))
 iter.df$bin_age - as.factor(recode(iter.df$age,
 0:23   = '  24mo.';
  24:72  = '24 - 72mo.';
  72:300 = '72 - 300mo'; else   = 'missing';
  ))
 iter.df$bin_util - as.factor(recode(iter.df$pct_utilize,
 0.0:0.2 = '  0 - 20%';
  0.2:0.4 = '  20 - 40%';
  0.4:0.6 = '  40 - 60%';
  0.6:0.8 = '  60 - 80%';
  0.8:1.0 = ' 80 - 100%';
  1.0:1.2 = '100 - 120%'; else= 'missing';
  ))
 iter.df$bin_varname2 - as.factor(recode(iter.df$varname2_prop,
 0:70 = ' 70%';
  70:85 = ' 70 - 85%';
  85:95 = ' 85 - 95%';
  95:110 = '95 - 110%'; else  =  'missing';
  ))
 iter.df$bin_varname1 - relevel(iter.df$bin_varname1, 'missing')
 iter.df$bin_age - relevel(iter.df$bin_age, 'missing')
 iter.df$bin_util - relevel(iter.df$bin_util, 'missing')
 iter.df$bin_varname2 - relevel(iter.df$bin_varname2, 'missing')
 
 #~ print(head(iter.df))
 if (i=6  i=8){
  print('-')
  browser()
  print(i)
  print(table(iter.df$bin_varname1))
  print(table(iter.df$bin_age))
  print(table(iter.df$bin_util))
  print(table(iter.df$bin_varname2))
 #~ debug(predict.nov.2011[i] -
 #~  sum(predict(logModel.1, newdata=iter.df,
 type='response')))
  }
 
 predict.nov.2011[i] -
  sum(predict(logModel.1, newdata=iter.df, type='response'))
 
 print(predict.nov.2011[i])
 
   }
 
 Output
 ==
 [1] 36.56073
 [1] 561.4516
 [1] 4.83483
 [1] 5.01398
 [1] 7.984146
 [1] -
 Called from: top level
 Browse[1]
 [1] 6
 
   missing 300 - 499 500 - 549 550 - 599 600 - 649 650 - 699 700 - 749
 750 - 799GE 800
   842   283   690  1094  1695  3404
 6659 18374 21562
 
missing 24mo. 24 - 72mo. 72 - 300mo
 16   2997  19709  31881
 
missing0 - 20%   20 - 40%   40 - 60%   60 - 80%  80 - 100% 100
 - 120%
  17906   4832   4599   5154   7205
 14865 42
 
   missing  70%  70 - 85%  85 - 95% 95 - 110%
 10423 19429 10568  8350  5833
 [1] 11.04090
 [1] -
 Called from: top level
 Browse[1]
 [1] 7
 
   missing 300 - 499 500 - 549 550 - 599

Re: [R] debug an error that incapacitates R?

[Brian Diggs]

 -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 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() statements to it (or
  setting tracepoints with trace()), and seeing how many succeed before
  things
  go bad.
 
 Experimenting with browser() and subsequently with the step-through
 debug() I managed to identify the first line that triggers the
 invalid connection error:
 doItAndPrint(paste(## Launching RSiteSearch, please be patient..))

I have seen this invalid connection type error when there is a sink()
active that does not have a valid connection associated with it.  In that
case, any output generates the error.  Try issuing sink() commands (without
any arguments) to remove any active sinks.  When there are not any more 
sinks you will get the message:

Warning message:
In sink() : no sink to remove

   Once you see the bad line, it may be obvious what's wrong with it,
  or you
  may need to ask for help, by putting together a minimal example that
  triggers it.
 
 Unfortunately, there is nothing obviously wrong with the call, nor
 with the environment. Omitting the line makes the function work in all
 my test cases. I will contact John Fox on this.

If it is an invalid sink, this would just be the first call that generates
output.  It would be a sink somewhere before that that is setting up a bad
connection (which doesn't cause problems until something is to be written).

 Thank you
 Liviu
 

--
Brian Diggs, Ph.D.
Senior Research Associate, Department of Surgery, Oregon Health  Science 
University




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Re: [R] debug an error that incapacitates R?

[Rolf Turner]

Wouldn't sink.number() give you a handle on whether
the problem is that there is an invalid sink() in effect?

On 15/12/2009, at 10:55 AM, Brian Diggs wrote:


-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 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() statements to it  
(or
setting tracepoints with trace()), and seeing how many succeed  
before

things
go bad.


Experimenting with browser() and subsequently with the step-through
debug() I managed to identify the first line that triggers the
invalid connection error:
doItAndPrint(paste(## Launching RSiteSearch, please be patient..))


I have seen this invalid connection type error when there is a  
sink()
active that does not have a valid connection associated with it.   
In that
case, any output generates the error.  Try issuing sink() commands  
(without
any arguments) to remove any active sinks.  When there are not any  
more

sinks you will get the message:

Warning message:
In sink() : no sink to remove


 Once you see the bad line, it may be obvious what's wrong with it,
or you
may need to ask for help, by putting together a minimal example that
triggers it.


Unfortunately, there is nothing obviously wrong with the call, nor
with the environment. Omitting the line makes the function work in  
all

my test cases. I will contact John Fox on this.


If it is an invalid sink, this would just be the first call that  
generates
output.  It would be a sink somewhere before that that is setting  
up a bad
connection (which doesn't cause problems until something is to be  
written).



Thank you
Liviu



--
Brian Diggs, Ph.D.
Senior Research Associate, Department of Surgery, Oregon Health   
Science University





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Re: [R] debug an error that incapacitates R?

[Brian Diggs]

 -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 is that there is an invalid sink() in effect?

It would.  I had forgotten about that function.

On 15/12/2009, at 10:55 AM, Brian Diggs wrote:
 
  -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 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() statements to it
  (or
  setting tracepoints with trace()), and seeing how many succeed
  before
  things
  go bad.
 
  Experimenting with browser() and subsequently with the step-through
  debug() I managed to identify the first line that triggers the
  invalid connection error:
  doItAndPrint(paste(## Launching RSiteSearch, please be patient..))
 
  I have seen this invalid connection type error when there is a
  sink()
  active that does not have a valid connection associated with it.
  In that
  case, any output generates the error.  Try issuing sink() commands
  (without
  any arguments) to remove any active sinks.  When there are not any
  more
  sinks you will get the message:
 
  Warning message:
  In sink() : no sink to remove
 
   Once you see the bad line, it may be obvious what's wrong with it,
  or you
  may need to ask for help, by putting together a minimal example
 that
  triggers it.
 
  Unfortunately, there is nothing obviously wrong with the call, nor
  with the environment. Omitting the line makes the function work in
  all
  my test cases. I will contact John Fox on this.
 
  If it is an invalid sink, this would just be the first call that
  generates
  output.  It would be a sink somewhere before that that is setting
  up a bad
  connection (which doesn't cause problems until something is to be
  written).
 
  Thank you
  Liviu
 
 
  --
  Brian Diggs, Ph.D.
  Senior Research Associate, Department of Surgery, Oregon Health 
  Science University
 
 
 
 
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  guide.html
  and provide commented, minimal, self-contained, reproducible code.
 
 
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[R] debug an error that incapacitates R?

[Liviu Andronic]

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: invalid connection
Error during wrapup: invalid connection


The error also crashes browser().
Browse[1] n
debug at 
/home/liviu/Devel/Rcmdr-dev/Rcmdr.sos/RcmdrPlugin.sos-0.1-0/R/sosInit.R#51:
doItAndPrint(paste(## Launching RSiteSearch, please be patient..))
Browse[2]
Error in function ()  : invalid connection
Error: invalid connection


To reproduce the example, you would need to source the following file [1]. Then
require(Rcmdr)
require(sos)
sosInit()

and in the box enter a string similar to asdf ; HTMLgrid. If you
enter simple strings such as asdf, the function will perform as
expected and R will not become non-responsive.
[1] http://s000.tinyupload.com/index.php?file_id=15379960405416742593

Please let me know of any ideas that would help tackle this one. Thank you
Liviu


This is a sessionInfo() prior to running the crash-function.
 sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_GB.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_GB.UTF-8LC_COLLATE=en_GB.UTF-8
 [5] LC_MONETARY=C  LC_MESSAGES=en_GB.UTF-8
 [7] LC_PAPER=en_GB.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

attached base packages:
 [1] datasets  grid  splines   graphics  stats utils grDevices
 [8] tcltk methods   base

other attached packages:
 [1] fortunes_1.3-6   RcmdrPlugin.HH_1.1-25HH_2.1-32
 [4] leaps_2.9multcomp_1.1-2   mvtnorm_0.9-8
 [7] lattice_0.17-26  RcmdrPlugin.sos_0.1-0RcmdrPlugin.Export_0.3-0
[10] Hmisc_3.7-0  survival_2.35-7  xtable_1.5-6
[13] Rcmdr_1.5-4  car_1.2-16   relimp_1.0-1
[16] sos_1.1-7brew_1.0-3   hints_1.0.1-1

loaded via a namespace (and not attached):
[1] cluster_1.12.1

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Re: [R] debug an error that incapacitates R?

[Duncan Murdoch]

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 impossible.

options(error=recover)
sosInit()

Error: invalid connection
Error during wrapup: invalid connection


The error also crashes browser().
Browse[1] n
debug at 
/home/liviu/Devel/Rcmdr-dev/Rcmdr.sos/RcmdrPlugin.sos-0.1-0/R/sosInit.R#51:
doItAndPrint(paste(## Launching RSiteSearch, please be patient..))
Browse[2]
Error in function ()  : invalid connection
Error: invalid connection

To reproduce the example, you would need to source the following file [1]. Then
require(Rcmdr)
require(sos)
sosInit()

and in the box enter a string similar to asdf ; HTMLgrid. If you
enter simple strings such as asdf, the function will perform as
expected and R will not become non-responsive.
[1] http://s000.tinyupload.com/index.php?file_id=15379960405416742593

Please let me know of any ideas that would help tackle this one. Thank you


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() statements to 
it (or setting tracepoints with trace()), and seeing how many succeed 
before things go bad.


Once you see the bad line, it may be obvious what's wrong with it, or 
you may need to ask for help, by putting together a minimal example that 
triggers it.


Duncan Murdoch

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Re: [R] debug an error that incapacitates R?

[Liviu Andronic]

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() statements to it (or
 setting tracepoints with trace()), and seeing how many succeed before things
 go bad.

Experimenting with browser() and subsequently with the step-through
debug() I managed to identify the first line that triggers the
invalid connection error:
doItAndPrint(paste(## Launching RSiteSearch, please be patient..))



  Once you see the bad line, it may be obvious what's wrong with it, or you
 may need to ask for help, by putting together a minimal example that
 triggers it.

Unfortunately, there is nothing obviously wrong with the call, nor
with the environment. Omitting the line makes the function work in all
my test cases. I will contact John Fox on this.

Thank you
Liviu

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[R] debug(sum) error

[Another Oneforyou]

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.   
_
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Re: [R] debug(sum) error

[Duncan Murdoch]

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 get this error, and how to work around it?


debug() only works on regular functions (which are called closures). 
sum() is a special built in function, because it is so frequently used, 
and because it needs to be fast.  So you can't debug it.


Whoever wrote those instructions should update them to use a different 
example.  (Google suggests that the document was written in 2002, so 
someone may very well have already done so.)


Duncan

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Re: [R] Debug

[David Winsemius]

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

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Re: [R] Debug

[Tammy Ma]

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 have tested the first 1-10th files, no any problem. But the problems is I 
have more than 500 files. How can I know which file has the problem?

Thanks 
Tammy
  
Invite your mail contacts to join your friends list with Windows Live Spaces. 
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Re: [R] Debug

[Steve Lianoglou]

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  
problems is I have more than 500 files. How can I know which file  
has the problem?


See ?tryCatch

Here's some (untested) code that should give you an idea of what to do:

which.files - dir(path=/directory/with/files, full.names=TRUE)
for (file.name in which.files) {
  result - tryCatch(process.file(file.name), error=function(err) err)
  if (inherits(result, 'error')) {
cat(File, file.name, is hosed\n)
  }
}

This assumes you have a function called 'process.file' that does what  
you want. If the function throws an error, it will be caught and  
stored in the result variable. In this case, the file.name will be  
written to your workspace.


Instead of just printing to your workspace, you could consider storing  
the bad file names in a list and post-process later.


Hope that helps,
-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
  |  Memorial Sloan-Kettering Cancer Center
  |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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[R] debug/mtrace problem

[Cuvelier Etienne]

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 :

 foo-function(){cat(Test Function)}
 mtrace(foo)
 foo() # A tcl/tk windows open and close immediately
Erreur dans FUN(l[[1L]], ...) :
 l'argument l est manquant, avec aucune valeur par défaut
 #argument l is missing without default value...


I've tried to look in with traceback(), but it does not help me.

 traceback()
21: FUN(l[[1L]], ...)
20: lapply(savers, get, envir = nlocal.env)
19: mlocal(index(nchar(names(line.list))  0)[l] - 1)
18: screen.line(lno)
17: assign(answer, {


Here is some technical informations :

 Sys.info()
sysname   release versionnodename
Windows Vista build  6001, Service Pack 1  XXX-HOME-VISTA
machinelogin  user
x86  xxx  xxx

 R.Version()
$platform
[1] i386-pc-mingw32
$arch
[1] i386
$os
[1] mingw32
$system
[1] i386, mingw32
$status
[1] 
$major
[1] 2
$minor
[1] 8.1
$year
[1] 2008
$month
[1] 12
$day
[1] 22
$`svn rev`
[1] 47281
$language
[1] R
$version.string
[1] R version 2.8.1 (2008-12-22)


Sincerely

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[R] debug

[Tammy Ma]

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  book_log-20060222T162828.txt 
Skipping  book_log-20060222T162833.txt 
Skipping  book_log-20060222T183742.txt 
Skipping  book_log-20060222T201442.txt 
Skipping  book_log-20060224T153841.txt 
Skipping  book_log-20060224T184225.txt 
Skipping  book_log-20060224T193621.txt 
Skipping  book_log-20060224T193957.txt 
Skipping  book_log-20060225T110011.txt 
Skipping  book_log-20060225T125836.txt 
Skipping  book_log-20060225T131002.txt 
Processing  book_log-20060225T165935.txt 
Error in as.POSIXlt.character(x, tz, ...) : 
  character string is not in a standard unambiguous format


Thanks a lot.

Tammy

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Re: [R] debug

[Duncan Murdoch]

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 obvious. I don't know 
if you consider the skipping messages to be a problem, but if not, it 
sure looks as though the problem is in


book_log-20060225T165935.txt 

so you can simplify things a lot by creating a copy of that file in a 
separate directory, and using debug or other techniques (e.g. 
options(error=recover) ) to diagnose it.


Duncan Murdoch

.
Skipping  book_log-20060222T143612.txt 
Skipping  book_log-20060222T162828.txt 
Skipping  book_log-20060222T162833.txt 
Skipping  book_log-20060222T183742.txt 
Skipping  book_log-20060222T201442.txt 
Skipping  book_log-20060224T153841.txt 
Skipping  book_log-20060224T184225.txt 
Skipping  book_log-20060224T193621.txt 
Skipping  book_log-20060224T193957.txt 
Skipping  book_log-20060225T110011.txt 
Skipping  book_log-20060225T125836.txt 
Skipping  book_log-20060225T131002.txt 
Processing  book_log-20060225T165935.txt 
Error in as.POSIXlt.character(x, tz, ...) : 
  character string is not in a standard unambiguous format
  


Thanks a lot.

Tammy

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[R] Debug help

[ehxpieterse]

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

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Re: [R] Debug help

[Duncan Murdoch]

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 numeric(0)?


You need to send a reproducible example if you want an answer.  It's 
more likely a problem with C or m_ret_reb or q, and we don't have those.


Duncan Murdoch

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Re: [R] Debug help

[Eduard Pieterse (Macquarie Securities)]

Thanks Duncan,

I am translating code from Matlab into R and am still finding my feet in
R.
I first run TriskellData and the compute_strategy. In Matlab this is a
function, so I would be looking to do the same in R. 
The bug is in compute_strategy. I would appreciate any help you can
give.

Thanks,
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: 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)?

You need to send a reproducible example if you want an answer.  It's
more likely a problem with C or m_ret_reb or q, and we don't have those.

Duncan Murdoch

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R-help@r-project.org mailing list
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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.

Re: [R] Debug command-how to use

[jim holtman]

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
 str(debug)   # here is what it is defined as
function (fun)

On Tue, Nov 11, 2008 at 9:50 PM,  [EMAIL PROTECTED] wrote:
 I am getting this error could any one tell me why?
  if(debug) cat(rahul)
 Error in if (debug) cat(rahul) :
  argument is not interpretable as logical

 __
 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.




-- 
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

__
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.

Re: [R] Debug command-how to use

[Rahul-A.Agarwal]

 
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] Debug command-how to use

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
 str(debug)   # here is what it is defined as
function (fun)

On Tue, Nov 11, 2008 at 9:50 PM,  [EMAIL PROTECTED] wrote:
 I am getting this error could any one tell me why?
  if(debug) cat(rahul)
 Error in if (debug) cat(rahul) :
  argument is not interpretable as logical

 __
 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.




--
Jim Holtman
Cincinnati, OH
+1 513 646 9390

What is the problem that you are trying to solve?

__
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.