Ubuntu and R

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Ubuntu and R

Tyler Smith
You could try the stable/sarge backport from Cran. That's less likely
to cause problems than using the Etch version, but I'm not using Ubuntu
so I can't confirm this. Add the following to your sources.list and see
how it goes:

     deb http://cran.R-project.org/bin/linux/debian stable/

--
Tyler Smith

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Re: Ubuntu and R

Fernando Mayer
I did this in my Ubuntu 5.10 and it works very well...

Fernando Mayer.

Tyler Smith escreveu:

>You could try the stable/sarge backport from Cran. That's less likely
>to cause problems than using the Etch version, but I'm not using Ubuntu
>so I can't confirm this. Add the following to your sources.list and see
>how it goes:
>
>     deb http://cran.R-project.org/bin/linux/debian stable/
>
>  
>

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Re: Ubuntu and R

Clint Harshaw
Thanks for the advice, everyone. I've done what Tyler suggested and have
a fresh install of R now using the Debian binaries.

Clint

Fernando Mayer wrote:

> I did this in my Ubuntu 5.10 and it works very well...
>
> Fernando Mayer.
>
> Tyler Smith escreveu:
>
>> You could try the stable/sarge backport from Cran. That's less likely
>> to cause problems than using the Etch version, but I'm not using
>> Ubuntu so I can't confirm this. Add the following to your sources.list
>> and see how it goes:
>>
>>     deb http://cran.R-project.org/bin/linux/debian stable/
>>
>>  
>>
>

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Variance for Vector of Constants is Not Zero

Barry Zajdlik
In reply to this post by Tyler Smith

Hi All,

An annoying but not critical problem I am having is that the variance of
a vector of constants is reported as > 0. I imagine there is a simple
workaround for the following but could not find it after having spent an
embarrassing amount of time.

In Splus:

> x<-rep(0.02,10)
> var(x)
> 0

In R:

x<-rep(0.02,10)
var(x)
1.337451e-35

I assumed the problem had to do with machine precision and suitably
modified .Machine$double.eps and .Machine$double.neg.eps which I thought
would fix the problem but without success. Any pointers to a solution
would be appreciated!

Cheers,
Barry Zajdlik

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Re: Variance for Vector of Constants is Not Zero

JohnDee
On Thursday 16 February 2006 11:29, Barry Zajdlik wrote:
> 1.337451e-35

Well, its nearly zero ;-)

JD

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Re: Variance for Vector of Constants is Not Zero

Spencer Graves
In reply to this post by Barry Zajdlik
          Could you please provide "sessionInfo()";  I can't replicate the
problem:

 > var(x)
[1] 0
 > sessionInfo()
R version 2.2.1, 2005-12-20, i386-pc-mingw32

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

          spencer graves

Barry Zajdlik wrote:

> Hi All,
>
> An annoying but not critical problem I am having is that the variance of
> a vector of constants is reported as > 0. I imagine there is a simple
> workaround for the following but could not find it after having spent an
> embarrassing amount of time.
>
> In Splus:
>
>
>>x<-rep(0.02,10)
>>var(x)
>>0
>
>
> In R:
>
> x<-rep(0.02,10)
> var(x)
> 1.337451e-35
>
> I assumed the problem had to do with machine precision and suitably
> modified .Machine$double.eps and .Machine$double.neg.eps which I thought
> would fix the problem but without success. Any pointers to a solution
> would be appreciated!
>
> Cheers,
> Barry Zajdlik
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Re: Variance for Vector of Constants is Not Zero

Uwe Ligges
In reply to this post by Barry Zajdlik
Barry Zajdlik wrote:

> Hi All,
>
> An annoying but not critical problem I am having is that the variance of
> a vector of constants is reported as > 0. I imagine there is a simple
> workaround for the following but could not find it after having spent an
> embarrassing amount of time.
>
> In Splus:
>
>
>>x<-rep(0.02,10)
>>var(x)
>>0
>
>
> In R:
>
> x<-rep(0.02,10)
> var(x)
> 1.337451e-35


Which version of R and which OS is this? I get 0 for both Linux and
Windows with R-2.2.1.
Anyway, 0.02 is not well representable and hence can be very well the
cause for such a numerical inaccuracy.

> I assumed the problem had to do with machine precision and suitably
> modified .Machine$double.eps and .Machine$double.neg.eps which I thought
> would fix the problem but without success. Any pointers to a solution
> would be appreciated!

Changing .Machine$double.eps does not help to calculate more accurate ...

Uwe Ligges


> Cheers,
> Barry Zajdlik
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Re: Variance for Vector of Constants is Not Zero

Prof Brian Ripley
This looks like the known problem, PR#1228.

It is possible to do better, but really users should be aware that
numerical inaccuracies will occur, and not expect exact results from
floating-point calculations.

On Thu, 16 Feb 2006, Uwe Ligges wrote:

> Barry Zajdlik wrote:
>
>> Hi All,
>>
>> An annoying but not critical problem I am having is that the variance of
>> a vector of constants is reported as > 0. I imagine there is a simple
>> workaround for the following but could not find it after having spent an
>> embarrassing amount of time.
>>
>> In Splus:
>>
>>
>>> x<-rep(0.02,10)
>>> var(x)
>>> 0
>>
>>
>> In R:
>>
>> x<-rep(0.02,10)
>> var(x)
>> 1.337451e-35
>
>
> Which version of R and which OS is this? I get 0 for both Linux and
> Windows with R-2.2.1.
> Anyway, 0.02 is not well representable and hence can be very well the
> cause for such a numerical inaccuracy.
>
>> I assumed the problem had to do with machine precision and suitably
>> modified .Machine$double.eps and .Machine$double.neg.eps which I thought
>> would fix the problem but without success. Any pointers to a solution
>> would be appreciated!
>
> Changing .Machine$double.eps does not help to calculate more accurate ...
>
> Uwe Ligges
>
>
>> Cheers,
>> Barry Zajdlik
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: Variance for Vector of Constants is Not Zero

Jari Oksanen
In reply to this post by Uwe Ligges

On 16 Feb 2006, at 23:17, Uwe Ligges wrote:

> Barry Zajdlik wrote:
>
>> Hi All,
>>
>> An annoying but not critical problem I am having is that the variance
>> of
>> a vector of constants is reported as > 0. I imagine there is a simple
>> workaround for the following but could not find it after having spent
>> an
>> embarrassing amount of time.
>>
>> In Splus:
>>
>>
>>> x<-rep(0.02,10)
>>> var(x)
>>> 0
>>
>>
>> In R:
>>
>> x<-rep(0.02,10)
>> var(x)
>> 1.337451e-35
>
>
> Which version of R and which OS is this? I get 0 for both Linux and
> Windows with R-2.2.1.
> Anyway, 0.02 is not well representable and hence can be very well the
> cause for such a numerical inaccuracy.
>
>> I assumed the problem had to do with machine precision and suitably
>> modified .Machine$double.eps and .Machine$double.neg.eps which I
>> thought
>> would fix the problem but without success. Any pointers to a solution
>> would be appreciated!
>
> Changing .Machine$double.eps does not help to calculate more accurate
> ...
>
> Uwe Ligges
>
>
>> Cheers,
>> Barry Zajdlik
>>
>> ______________________________________________
>> [hidden email] mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide!
>> http://www.R-project.org/posting-guide.html
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
> http://www.R-project.org/posting-guide.html
>
--
Jari Oksanen, Oulu, Finland

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Variance for Vector of Constants is STILL Not Zero

Barry Zajdlik
In reply to this post by Spencer Graves
Hello all,

Thanks for the responses but I am still annoyed by this seemingly simple
problem; I recorded sessionInfo() as below.

x<-rep(0.02,10)
> var(x)
[1] 1.337451e-35
>  sessionInfo()
R version 2.1.0, 2005-04-18, i386-pc-mingw32

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


I then decided to download the latest version today but obtained the
same result.

> x<-rep(0.02,10)
> var(x)
[1] 1.337451e-35

> sessionInfo()
R version 2.2.1, 2005-12-20, i386-pc-mingw32

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


I Changed .Machine$double.eps to make the calculations LESS accurate.
My thought was that if I reduced the precision, 1-eps would return 1
instead of some number less than 1.  My thought was that if eps were
sufficiently large my sample problem would return a zero.  This didn't
happen though.

Again, any thoughts would be appreciated.

Regards,
Barry Zajdlik

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Re: Variance for Vector of Constants is STILL Not Zero

P Ehlers
Barry,
Try the latest _patched_ version. I'm on 2006-02-12, but that may
already be superseded. I get var(x) = 0.

Peter Ehlers

Barry Zajdlik wrote:

> Hello all,
>
> Thanks for the responses but I am still annoyed by this seemingly simple
> problem; I recorded sessionInfo() as below.
>
> x<-rep(0.02,10)
>
>>var(x)
>
> [1] 1.337451e-35
>
>> sessionInfo()
>
> R version 2.1.0, 2005-04-18, i386-pc-mingw32
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"
> [7] "base"    
>
>
>
> I then decided to download the latest version today but obtained the
> same result.
>
>
>>x<-rep(0.02,10)
>>var(x)
>
> [1] 1.337451e-35
>
>
>>sessionInfo()
>
> R version 2.2.1, 2005-12-20, i386-pc-mingw32
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"
> [7] "base"    
>
>
> I Changed .Machine$double.eps to make the calculations LESS accurate.
> My thought was that if I reduced the precision, 1-eps would return 1
> instead of some number less than 1.  My thought was that if eps were
> sufficiently large my sample problem would return a zero.  This didn't
> happen though.
>
> Again, any thoughts would be appreciated.
>
> Regards,
> Barry Zajdlik
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Re: Variance for Vector of Constants is STILL Not Zero

Thomas Lumley
In reply to this post by Barry Zajdlik
On Fri, 17 Feb 2006, Barry Zajdlik wrote:
> Hello all,
>
> Thanks for the responses but I am still annoyed by this seemingly simple
> problem; I recorded sessionInfo() as below.
>
> x<-rep(0.02,10)
>> var(x)
> [1] 1.337451e-35

Well, yes, it is accurate only to 35 digits and this is a bit unfortunate
since it could be more accurate in this case. The exact result is probably
system-dependent, but there has been a bug report for a long time
(PR#1228) that var() is not as accurate as it could possibly be, and
patches would be welcome.  They obviously aren't a very high priority for
anyone.

> I Changed .Machine$double.eps to make the calculations LESS accurate.
> My thought was that if I reduced the precision, 1-eps would return 1
> instead of some number less than 1.  My thought was that if eps were
> sufficiently large my sample problem would return a zero.  This didn't
> happen though.
>

.Machine is a set of constants that describe your hardware and C
implementation.  They are right when you start. If you change them all
that happens is that they become wrong -- R doesn't go in and re-engineer
the floating point hardware.

  -thomas

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Re: Variance for Vector of Constants is STILL Not Zero

Duncan Murdoch
In reply to this post by Barry Zajdlik
On 2/17/2006 1:17 PM, Barry Zajdlik wrote:

> Hello all,
>
> Thanks for the responses but I am still annoyed by this seemingly simple
> problem; I recorded sessionInfo() as below.
>
> x<-rep(0.02,10)
>> var(x)
> [1] 1.337451e-35
>>  sessionInfo()
> R version 2.1.0, 2005-04-18, i386-pc-mingw32
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"
> [7] "base"    
>
>
> I then decided to download the latest version today but obtained the
> same result.
>
>> x<-rep(0.02,10)
>> var(x)
> [1] 1.337451e-35

My guess is that you've got a video driver or some other software that's
messing with your floating point processor, reducing the precision from
64 bit to 53 or less.  I can reproduce the error after running
RSiteSearch, which messes with my fpu in that way:

 > var(rep(0.2, 100))
[1] 0
 > RSiteSearch('fpu')
A search query has been submitted to http://search.r-project.org
The results page should open in your browser shortly
 > var(rep(0.2, 100))
[1] 1.525181e-31

(I'm not blaming RSiteSearch for doing something bad, it's the system
DLLs that it calls that are at fault.)

I think this is something we should address, but it's not easy.

Duncan Murdoch

>
>> sessionInfo()
> R version 2.2.1, 2005-12-20, i386-pc-mingw32
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
> "datasets"
> [7] "base"    
>
>
> I Changed .Machine$double.eps to make the calculations LESS accurate.
> My thought was that if I reduced the precision, 1-eps would return 1
> instead of some number less than 1.  My thought was that if eps were
> sufficiently large my sample problem would return a zero.  This didn't
> happen though.
>
> Again, any thoughts would be appreciated.
>
> Regards,
> Barry Zajdlik
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Re: Variance for Vector of Constants is STILL Not Zero

Spencer Graves
          I got the same thing as Duncan:

 > var(rep(0.2, 100))
[1] 0
 > RSiteSearch('fpu')
A search query has been submitted to http://search.r-project.org
The results page should open in your browser shortly
 > var(rep(0.2, 100))
[1] 1.525181e-31
 > sessionInfo()
R version 2.2.1, 2005-12-20, i386-pc-mingw32

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

          spencer graves

Duncan Murdoch wrote:

> On 2/17/2006 1:17 PM, Barry Zajdlik wrote:
>
>>Hello all,
>>
>>Thanks for the responses but I am still annoyed by this seemingly simple
>>problem; I recorded sessionInfo() as below.
>>
>>x<-rep(0.02,10)
>>
>>>var(x)
>>
>>[1] 1.337451e-35
>>
>>> sessionInfo()
>>
>>R version 2.1.0, 2005-04-18, i386-pc-mingw32
>>
>>attached base packages:
>>[1] "methods"   "stats"     "graphics"  "grDevices" "utils"
>>"datasets"
>>[7] "base"    
>>
>>
>>I then decided to download the latest version today but obtained the
>>same result.
>>
>>
>>>x<-rep(0.02,10)
>>>var(x)
>>
>>[1] 1.337451e-35
>
>
> My guess is that you've got a video driver or some other software that's
> messing with your floating point processor, reducing the precision from
> 64 bit to 53 or less.  I can reproduce the error after running
> RSiteSearch, which messes with my fpu in that way:
>
>  > var(rep(0.2, 100))
> [1] 0
>  > RSiteSearch('fpu')
> A search query has been submitted to http://search.r-project.org
> The results page should open in your browser shortly
>  > var(rep(0.2, 100))
> [1] 1.525181e-31
>
> (I'm not blaming RSiteSearch for doing something bad, it's the system
> DLLs that it calls that are at fault.)
>
> I think this is something we should address, but it's not easy.
>
> Duncan Murdoch
>
>
>>>sessionInfo()
>>
>>R version 2.2.1, 2005-12-20, i386-pc-mingw32
>>
>>attached base packages:
>>[1] "methods"   "stats"     "graphics"  "grDevices" "utils"
>>"datasets"
>>[7] "base"    
>>
>>
>>I Changed .Machine$double.eps to make the calculations LESS accurate.
>>My thought was that if I reduced the precision, 1-eps would return 1
>>instead of some number less than 1.  My thought was that if eps were
>>sufficiently large my sample problem would return a zero.  This didn't
>>happen though.
>>
>>Again, any thoughts would be appreciated.
>>
>>Regards,
>>Barry Zajdlik
>>
>>______________________________________________
>>[hidden email] mailing list
>>https://stat.ethz.ch/mailman/listinfo/r-help
>>PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
>
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html

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Re: Variance for Vector of Constants is STILL Not Zero

Prof Brian Ripley
Note though that this is already giving 0 in both cases in R-devel on
Windows (the only platform on which this difference occurs).


On Sat, 18 Feb 2006, Spencer Graves wrote:

>  I got the same thing as Duncan:
>
> > var(rep(0.2, 100))
> [1] 0
> > RSiteSearch('fpu')
> A search query has been submitted to http://search.r-project.org
> The results page should open in your browser shortly
> > var(rep(0.2, 100))
> [1] 1.525181e-31
> > sessionInfo()
> R version 2.2.1, 2005-12-20, i386-pc-mingw32
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "base"
>
>  spencer graves
>
> Duncan Murdoch wrote:
>
>> On 2/17/2006 1:17 PM, Barry Zajdlik wrote:
>>
>>> Hello all,
>>>
>>> Thanks for the responses but I am still annoyed by this seemingly simple
>>> problem; I recorded sessionInfo() as below.
>>>
>>> x<-rep(0.02,10)
>>>
>>>> var(x)
>>>
>>> [1] 1.337451e-35
>>>
>>>> sessionInfo()
>>>
>>> R version 2.1.0, 2005-04-18, i386-pc-mingw32
>>>
>>> attached base packages:
>>> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
>>> "datasets"
>>> [7] "base"
>>>
>>>
>>> I then decided to download the latest version today but obtained the
>>> same result.
>>>
>>>
>>>> x<-rep(0.02,10)
>>>> var(x)
>>>
>>> [1] 1.337451e-35
>>
>>
>> My guess is that you've got a video driver or some other software that's
>> messing with your floating point processor, reducing the precision from
>> 64 bit to 53 or less.  I can reproduce the error after running
>> RSiteSearch, which messes with my fpu in that way:
>>
>> > var(rep(0.2, 100))
>> [1] 0
>> > RSiteSearch('fpu')
>> A search query has been submitted to http://search.r-project.org
>> The results page should open in your browser shortly
>> > var(rep(0.2, 100))
>> [1] 1.525181e-31
>>
>> (I'm not blaming RSiteSearch for doing something bad, it's the system
>> DLLs that it calls that are at fault.)
>>
>> I think this is something we should address, but it's not easy.
>>
>> Duncan Murdoch
>>
>>
>>>> sessionInfo()
>>>
>>> R version 2.2.1, 2005-12-20, i386-pc-mingw32
>>>
>>> attached base packages:
>>> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"
>>> "datasets"
>>> [7] "base"
>>>
>>>
>>> I Changed .Machine$double.eps to make the calculations LESS accurate.
>>> My thought was that if I reduced the precision, 1-eps would return 1
>>> instead of some number less than 1.  My thought was that if eps were
>>> sufficiently large my sample problem would return a zero.  This didn't
>>> happen though.
>>>
>>> Again, any thoughts would be appreciated.
>>>
>>> Regards,
>>> Barry Zajdlik
>>>
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--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
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