bugs-r-devel

Re: [Bugs-r-devel] R2WinBUGS on Solaris

[Rodney S. <rsp...@mc...>]

Uwe Ligges wrote:
>
>> Hi Uwe:
>>
>> But, you have the command setwd("d:/temp") and I don't.  However, 
>> this does
>> not work around the problem either:
>>
>> library(R2WinBUGS)
>> schools <- read.table ("/usr/local/doc/r2winbugs/schools.dat", header=T)
>> J <- nrow (schools)
>> y <- schools$estimate
>> sigma.y <- schools$sd
>> data <- list ("J", "y", "sigma.y")
>> inits <- function()
>>  list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
>>        sigma.theta=runif(1,0,100))
>> parameters <- c("theta", "mu.theta", "sigma.theta")
>> setwd(".")
>> schools.sim <- bugs (data, inits, parameters, 
>> "/usr/local/doc/r2winbugs/schools.bug",
>>                     n.chains=3, n.iter=1000, working.directory=".")
>>
>>
>> Warning message:
>> In file.create(to[okay]) :
>>  cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason 
>> 'Permission denied'
>
>
>
> So, what exactly is your working directory? If it is 
> "/usr/local/doc/r2winbugs/schools.txt", I am not surprised.
>
> Uwe Ligges
>
As I said in the original post, $HOME

-- 
Rodney Sparapani      Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician              Department of Medicine
Was 'Name That Tune' rigged?     Medical College of Wisconsin (MCW)
WWLD: What Would Lombardi Do     Milwaukee, WI, USA

Re: [Bugs-r-devel] R2WinBUGS on Solaris

[Uwe L. <li...@st...>]

Rodney Sparapani wrote:
> Uwe Ligges wrote:
>> I cannot reproduce on Windows even when using 3 different directories:
>>
>> - one for data
>> - one as working directory
>> - one for the model file
>>
>>
>>
>>  schools <- read.table ("d:/schools.dat", header=T)
>>  J <- nrow (schools)
>>  y <- schools$estimate
>>  sigma.y <- schools$sd
>>  data <- list ("J", "y", "sigma.y")
>>  inits <- function()
>>    list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
>>          sigma.theta=runif(1,0,100))
>>   parameters <- c("theta", "mu.theta", "sigma.theta")
>>  setwd("d:/temp")
>>  schools.sim <- bugs (data, inits, parameters, "d:/uwe/schools.bug",
>>                n.chains=3, n.iter=1000, working.directory="d:/temp")
>>
>>
>> Simply works for me ....
>>
>> Uwe
> Hi Uwe:
> 
> But, you have the command setwd("d:/temp") and I don't.  However, this does
> not work around the problem either:
> 
> library(R2WinBUGS)
> schools <- read.table ("/usr/local/doc/r2winbugs/schools.dat", header=T)
> J <- nrow (schools)
> y <- schools$estimate
> sigma.y <- schools$sd
> data <- list ("J", "y", "sigma.y")
> inits <- function()
>  list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
>        sigma.theta=runif(1,0,100))
> parameters <- c("theta", "mu.theta", "sigma.theta")
> setwd(".")
> schools.sim <- bugs (data, inits, parameters, 
> "/usr/local/doc/r2winbugs/schools.bug",
>                     n.chains=3, n.iter=1000, working.directory=".")
> 
> 
> Warning message:
> In file.create(to[okay]) :
>  cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason 
> 'Permission denied'



So, what exactly is your working directory? If it is 
"/usr/local/doc/r2winbugs/schools.txt", I am not surprised.

Uwe Ligges

Re: [Bugs-r-devel] R2WinBUGS on Solaris

[Rodney S. <rsp...@mc...>]

Uwe Ligges wrote:
> I cannot reproduce on Windows even when using 3 different directories:
>
> - one for data
> - one as working directory
> - one for the model file
>
>
>
>  schools <- read.table ("d:/schools.dat", header=T)
>  J <- nrow (schools)
>  y <- schools$estimate
>  sigma.y <- schools$sd
>  data <- list ("J", "y", "sigma.y")
>  inits <- function()
>    list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
>          sigma.theta=runif(1,0,100))
>   parameters <- c("theta", "mu.theta", "sigma.theta")
>  setwd("d:/temp")
>  schools.sim <- bugs (data, inits, parameters, "d:/uwe/schools.bug",
>                n.chains=3, n.iter=1000, working.directory="d:/temp")
>
>
> Simply works for me ....
>
> Uwe
Hi Uwe:

But, you have the command setwd("d:/temp") and I don't.  However, this does
not work around the problem either:

library(R2WinBUGS)
schools <- read.table ("/usr/local/doc/r2winbugs/schools.dat", header=T)
J <- nrow (schools)
y <- schools$estimate
sigma.y <- schools$sd
data <- list ("J", "y", "sigma.y")
inits <- function()
  list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
        sigma.theta=runif(1,0,100))
parameters <- c("theta", "mu.theta", "sigma.theta")
setwd(".")
schools.sim <- bugs (data, inits, parameters, 
"/usr/local/doc/r2winbugs/schools.bug",
                     n.chains=3, n.iter=1000, working.directory=".")


Warning message:
In file.create(to[okay]) :
  cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason 
'Permission denied'

-- 
Rodney Sparapani      Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician              Department of Medicine
Was 'Name That Tune' rigged?     Medical College of Wisconsin (MCW)
WWLD: What Would Lombardi Do     Milwaukee, WI, USA

Re: [Bugs-r-devel] R2WinBUGS on Solaris

[Uwe L. <li...@st...>]

I cannot reproduce on Windows even when using 3 different directories:

- one for data
- one as working directory
- one for the model file



  schools <- read.table ("d:/schools.dat", header=T)
  J <- nrow (schools)
  y <- schools$estimate
  sigma.y <- schools$sd
  data <- list ("J", "y", "sigma.y")
  inits <- function()
    list (theta=rnorm(J,0,100), mu.theta=rnorm(1,0,100),
          sigma.theta=runif(1,0,100))
   parameters <- c("theta", "mu.theta", "sigma.theta")
  setwd("d:/temp")
  schools.sim <- bugs (data, inits, parameters, "d:/uwe/schools.bug",
                n.chains=3, n.iter=1000, working.directory="d:/temp")


Simply works for me ....

Uwe



Rodney Sparapani wrote:
> Gorjanc Gregor wrote:
>>
>> Can you please post a reproducible example so that we can check what
>> is going on.
>>
>> gg
>>
>>
>>
>>   
> You will find it attached.
> 

Re: [Bugs-r-devel] R2WinBUGS on Solaris

[Rodney S. <rsp...@mc...>]

Gorjanc Gregor wrote:
>
> Can you please post a reproducible example so that we can check what
> is going on.
>
> gg
>
>
>
>   
You will find it attached.

-- 
Rodney Sparapani      Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician              Department of Medicine
Was 'Name That Tune' rigged?     Medical College of Wisconsin (MCW)
WWLD: What Would Lombardi Do     Milwaukee, WI, USA

Re: [Bugs-r-devel] R2WinBUGS on Solaris

[Gorjanc G. <Gre...@bf...>]

Hi Rodney,

> My current working directory is $HOME which is writeable.
> R2WinBUGS is ignoring that and using the directory of the source file.
> Attempting to over-ride this behavior with working-directory does not
> workaround the problem. Please fix.

Can you please post a reproducible example so that we can check what
is going on.

gg

Re: [Bugs-r-devel] R2WinBUGS on Solaris

[Rodney S. <rsp...@mc...>]

Gorjanc Gregor wrote:
> ...
>   
>>>> 1. The working.directory is assumed to be the same directory as the
>>>> model.file and setting working.directory to something else doesn't help.
>>>>         
>>> Working directory and model.file can be in separate directories, you
>>> can you tell me an example where it does not work.
>>>
>>>       
>> Doesn't work.  See below:
>>
>>  > schools.sim <- bugs (data, inits, parameters,
>> "/usr/local/doc/r2winbugs/schools.bug",
>> +                     n.chains=3, n.iter=1000, working.directory=".")
>> Warning message:
>> In file.create(to[okay]) :
>>   cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason
>> 'Permission denied'
>>     
>
> Rodney, this is a problem with permissions and not with R2WinBUGS! /usr/local/doc folders
> are usually not writable for regular users. If you want to avoid this problem, you can do either:
>
> A. Put modelfile somewhere else. If there will be many users (say a whole class), you do not want
> that they will be overwritting the same files, do you? Putting the modelfile to a home folder of each
> user, makes much more sense.
>
> B. You also might change the permissions of the  /usr/local/doc/r2winbugs/ folder. Actually, this is needed
> since the R2WinBUGS package changes some parameters related to burnin and metropolis acceptance rate in
> a file that resides in /usr/local/doc/r2winbugs/. I am not really aware what actually is done, since the code
> was written by Andrew Gelman and I just make it sure that some bits run under linux.
>
> So my recommendation is:
> - change permissions in /usr/local/doc/r2winbugs/ via chmod -R uga+w /usr/local/doc/r2winbugs/
>
> - make sure that each user is using its own modelfile
>
> Regards, Gregor
>   
Hi Gregor:

My current working directory is $HOME which is writeable.
R2WinBUGS is ignoring that and using the directory of the source file.
Attempting to over-ride this behavior with working-directory does not
workaround the problem. Please fix.

Thanks,

Rodney

-- 
Rodney Sparapani      Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician              Department of Medicine
Was 'Name That Tune' rigged?     Medical College of Wisconsin (MCW)
WWLD: What Would Lombardi Do     Milwaukee, WI, USA

Re: [Bugs-r-devel] R2WinBUGS on Solaris

[Gorjanc G. <Gre...@bf...>]

...
>>> 1. The working.directory is assumed to be the same directory as the
>>> model.file and setting working.directory to something else doesn't help.
>>
>> Working directory and model.file can be in separate directories, you
>> can you tell me an example where it does not work.
>>
> Doesn't work.  See below:
>
>  > schools.sim <- bugs (data, inits, parameters,
> "/usr/local/doc/r2winbugs/schools.bug",
> +                     n.chains=3, n.iter=1000, working.directory=".")
> Warning message:
> In file.create(to[okay]) :
>   cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason
> 'Permission denied'

Rodney, this is a problem with permissions and not with R2WinBUGS! /usr/local/doc folders
are usually not writable for regular users. If you want to avoid this problem, you can do either:

A. Put modelfile somewhere else. If there will be many users (say a whole class), you do not want
that they will be overwritting the same files, do you? Putting the modelfile to a home folder of each
user, makes much more sense.

B. You also might change the permissions of the  /usr/local/doc/r2winbugs/ folder. Actually, this is needed
since the R2WinBUGS package changes some parameters related to burnin and metropolis acceptance rate in
a file that resides in /usr/local/doc/r2winbugs/. I am not really aware what actually is done, since the code
was written by Andrew Gelman and I just make it sure that some bits run under linux.

So my recommendation is:
- change permissions in /usr/local/doc/r2winbugs/ via chmod -R uga+w /usr/local/doc/r2winbugs/

- make sure that each user is using its own modelfile

Regards, Gregor

Re: [Bugs-r-devel] R2WinBUGS on Solaris

[Rodney S. <rsp...@mc...>]

Uwe Ligges wrote:
>
>
> Rodney Sparapani wrote:
>> Hi Gang:
>>
>> Recent versions of WINE (1.1.3 and 1.1.4) actually work on Solaris 10
>> and OpenSolaris.  And, R2WinBUGS works as well with WinBUGS.  However,
>> there seem to be 2 bugs.
>> 1. The working.directory is assumed to be the same directory as the
>> model.file and setting working.directory to something else doesn't help. 
>
>
> Working directory and model.file can be in separate directories, you 
> can you tell me an example where it does not work.
>
Doesn't work.  See below:

 > schools.sim <- bugs (data, inits, parameters, 
"/usr/local/doc/r2winbugs/schools.bug",
+                     n.chains=3, n.iter=1000, working.directory=".")
Warning message:
In file.create(to[okay]) :
  cannot create file '/usr/local/doc/r2winbugs/schools.txt', reason 
'Permission denied'

-- 
Rodney Sparapani      Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician              Department of Medicine
Was 'Name That Tune' rigged?     Medical College of Wisconsin (MCW)
WWLD: What Would Lombardi Do     Milwaukee, WI, USA

Re: [Bugs-r-devel] R2WinBUGS on Solaris

[Uwe L. <li...@st...>]

Rodney Sparapani wrote:
> Hi Gang:
> 
> Recent versions of WINE (1.1.3 and 1.1.4) actually work on Solaris 10
> and OpenSolaris.  And, R2WinBUGS works as well with WinBUGS.  However,
> there seem to be 2 bugs. 
> 
> 1. The working.directory is assumed to be the same directory as the
> model.file and setting working.directory to something else doesn't help. 


Working directory and model.file can be in separate directories, you can 
you tell me an example where it does not work.


> 2. Attempting to use OpenBUGS fails due to a requirement for the BRugs
> package.  However, no such package exists on CRAN.  There is the rbugs
> package.  But, loading that package doesn't help.  The same error message
> is displayed.  What/where is the BRugs package?

BRugs is avaibale from CRANextras hosted by Brian Ripley. A Windows 
version of R will install BRugs from there automatically if you say

install.packages("BRugs")

The package won't run under Solaris (there is no toolchain to compile 
ComponentPascal under Solaris, as far as IO know).

Best wishes,
Uwe Ligges


> It will be exciting to see R2WinBUGS running on the Solaris platform after
> these are fixed!  Our students are just starting a year-long course in
> Bayesian indoctrination and they will benefit immensely from your efforts.
> 

[Bugs-r-devel] R2WinBUGS on Solaris

[Rodney S. <rsp...@mc...>]

Hi Gang:

Recent versions of WINE (1.1.3 and 1.1.4) actually work on Solaris 10
and OpenSolaris.  And, R2WinBUGS works as well with WinBUGS.  However,
there seem to be 2 bugs. 

1. The working.directory is assumed to be the same directory as the
model.file and setting working.directory to something else doesn't help. 

2. Attempting to use OpenBUGS fails due to a requirement for the BRugs
package.  However, no such package exists on CRAN.  There is the rbugs
package.  But, loading that package doesn't help.  The same error message
is displayed.  What/where is the BRugs package?

It will be exciting to see R2WinBUGS running on the Solaris platform after
these are fixed!  Our students are just starting a year-long course in
Bayesian indoctrination and they will benefit immensely from your efforts.

-- 
Rodney Sparapani      Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician              Department of Medicine
Was 'Name That Tune' rigged?     Medical College of Wisconsin (MCW)
WWLD: What Would Lombardi Do     Milwaukee, WI, USA

Re: [Bugs-r-devel] move BRugs from CRAN to CRAN extras

[Uwe L. <li...@st...>]

Since nobody objected, I will proceed.

Uwe


Gregor Gorjanc wrote:
> Uwe Ligges wrote:
> ...
>> 1. we can ship BRugs without the OpenBUGS dll, and ask users to install
>> it separately (which most users won't understand)
>>
>> 2. (preferred from my point of view) move BRugs to the CRAN extras
>> repository (automatically included in repository search list under R for
>> Windows) maintained by Brian Ripley, who would also host a copy of the
>> OpenBUGS sources that have been used for the OpenBUGS binaries included
>> in the current version of BRugs - in order to be safely conform to GPL.
>>
>> Any objections to 2. ?
> 
> I agree with 2.
> g
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by the 2008 JavaOne(SM) Conference 
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Re: [Bugs-r-devel] move BRugs from CRAN to CRAN extras

[Gregor G. <gre...@bf...>]

Uwe Ligges wrote:
...
> 1. we can ship BRugs without the OpenBUGS dll, and ask users to install
> it separately (which most users won't understand)
> 
> 2. (preferred from my point of view) move BRugs to the CRAN extras
> repository (automatically included in repository search list under R for
> Windows) maintained by Brian Ripley, who would also host a copy of the
> OpenBUGS sources that have been used for the OpenBUGS binaries included
> in the current version of BRugs - in order to be safely conform to GPL.
> 
> Any objections to 2. ?

I agree with 2.
g

[Bugs-r-devel] move BRugs from CRAN to CRAN extras

[Uwe L. <li...@st...>]

Dear BRugs developers,

since CRAN maintainers will look more closely on problems related to 
license issues in future, CRAN won't allow in any source package:

a) executables, binaries or other stuff that is shipped without sources 
(currently true for BRugs) - hence at least problematic if GPLed

b) executables, dlls and certain other kinds of binaries in general.

This is because we do not want to get into conflict with license issues 
or related problems. Being CRAN maintainer for Windows binary packages 
myself, I was involved in the discussion and I like and will support the 
decision. It makes life much easier for us CRAN people and hence we do 
not have one foot in jail already. ;-)


This means we will have to change the way BRugs is shipped. Since we 
cannot ship BRugs as is without including a binary, we have two options:

1. we can ship BRugs without the OpenBUGS dll, and ask users to install 
it separately (which most users won't understand)

2. (preferred from my point of view) move BRugs to the CRAN extras 
repository (automatically included in repository search list under R for 
Windows) maintained by Brian Ripley, who would also host a copy of the 
OpenBUGS sources that have been used for the OpenBUGS binaries included 
in the current version of BRugs - in order to be safely conform to GPL.

Any objections to 2. ?

Best wishes,
Uwe Ligges

Re: [Bugs-r-devel] [R] Error: expected the collection operator c error pos 98 (error on line 1)

[Uwe L. <li...@st...>]

Quick inspection shows that we cannot do anything.

In BUGS, Y indicates a scalar and Y[] indicates a vector.
For scalar Y, you need Y=0.00000E+00 in your data file, but for vector 
Y[], you need Y=c(0.00000E+00) in your data file.

This means you need to know what Y is in the model and I do not see any 
API I can use to ask the BRugs.dll what Y actually is.

So question redirected to Andrew Thomas (in CC).

Best wishes,
Uwe



Uwe Ligges wrote:
> 
> 
> Blanchard, Suzette wrote:
>> Greetings,
>>
>>  
>>
>>       I implemented BRugs to run the EWOC model with a cohort size 
>> N=1.  I output the simulation data using bugsdata(data),  where data 
>> is the following list.
>>
>>  
>>> data
>>
>> $Dose
>>
>> [1] 140
>>
>>  
>>
>> $Y
>>
>> [1] 0
>>
>>  
>>
>> bugsdata(data)  puts out the file data.txt as follows.
>>
>>  
>>
>> list(Dose=1.40000E+02, Y=0.00000E+00)
>>
>>  
>>
>> after I type the following line
>>
>> modelData("data.txt")              # read data file
>>
>>  
>>
>> I get the ERROR:
>> expected the collection operator c error pos 98 (error on line 1)
>>
>>  
>>
>> If I rewrite the file
>>
>>
>>
>> list(Dose=c(1.40000E+02), c(Y=0.00000E+00))
>>
>>  
>>
>> it runs fine.  Can you suggest a way to get the output dataset to 
>> automatically put the
>>
>> c( ) on the data when the sample size is 1?
> 
> Hmmm, I will take a look how to implement it.
> 
> I guess you have modeled Y to be a vector by indexing with brackets in 
> your BUGS model? It works for me if I use Y without index brackets in a 
> BUGS model file.

> Best wishes,
> Uwe
> 
> 
> 
>>  
>>
>> Thank you,
>>
>> Suzette
>>
>>  
>>
>> Suzette Blanchard, Ph.D.
>> Assistant Professor, Dept. of Biostatistics
>> City of Hope
>> 1500 East Duarte Rd
>> Duarte, CA 91010-3000
>> ph: (626) 256-4673 ext:64446
>> sbl...@co...
>>  
>>
>>
>> ---------------------------------------------------------------------
>>
>> SECURITY/CONFIDENTIALITY WARNING:  \ This message an...{{dropped:24}}
>>
>> ______________________________________________
>> R-...@r-... 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: [Bugs-r-devel] [R] Error: expected the collection operator c error pos 98 (error on line 1)

[Uwe L. <li...@st...>]

Blanchard, Suzette wrote:
> Greetings,
> 
>  
> 
>       I implemented BRugs to run the EWOC model with a cohort size N=1.  I output the simulation data using bugsdata(data),  where data is the following list.
> 
>   
> 
>> data
> 
> $Dose
> 
> [1] 140
> 
>  
> 
> $Y
> 
> [1] 0
> 
>  
> 
> bugsdata(data)  puts out the file data.txt as follows.
> 
>  
> 
> list(Dose=1.40000E+02, Y=0.00000E+00)
> 
>  
> 
> after I type the following line
> 
> modelData("data.txt")              # read data file
> 
>  
> 
> I get the ERROR: 
> 
> expected the collection operator c error pos 98 (error on line 1)
> 
>  
> 
> If I rewrite the file
> 
> 
> 
> list(Dose=c(1.40000E+02), c(Y=0.00000E+00))
> 
>  
> 
> it runs fine.  Can you suggest a way to get the output dataset to automatically put the
> 
> c( ) on the data when the sample size is 1?

Hmmm, I will take a look how to implement it.

I guess you have modeled Y to be a vector by indexing with brackets in 
your BUGS model? It works for me if I use Y without index brackets in a 
BUGS model file.

Best wishes,
Uwe



>  
> 
> Thank you,
> 
> Suzette
> 
>  
> 
> Suzette Blanchard, Ph.D.
> Assistant Professor, Dept. of Biostatistics
> City of Hope
> 1500 East Duarte Rd
> Duarte, CA 91010-3000
> ph: (626) 256-4673 ext:64446
> sbl...@co...
>  
> 
> 
> ---------------------------------------------------------------------
> 
> SECURITY/CONFIDENTIALITY WARNING:  \ This message an...{{dropped:24}}
> 
> ______________________________________________
> R-...@r-... 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: [Bugs-r-devel] R2WinBUGS and Crossover in GNU/Linux

[Gorjanc G. <Gre...@bf...>]

Sebastian,

sorry for late reply. The "errors" you are getting are meaningless. This set
is from WinBUGS - even if launched directly from wine.

fixme:keyboard:RegisterHotKey (0x20024,13,0x00000002,3): stub
fixme:ole:GetHGlobalFromILockBytes cbSize is 13824
err:ole:CoGetClassObject class {0003000a-0000-0000-c000-000000000046} not registered
err:ole:CoGetClassObject class {0003000a-0000-0000-c000-000000000046} not registered
err:ole:CoGetClassObject no class object {0003000a-0000-0000-c000-000000000046} could be created for context 0x3
fixme:ntdll:RtlNtStatusToDosErrorNoTeb no mapping for 8000000a
err:ole:local_server_thread Failure during ConnectNamedPipe 317

Hower, I have not seen before the following

Wine exited with a successful status

Since this does not indicate un-successful exit I would use R2WinBUGS in your case.

You need to use debug=FALSE (I think) if you want to close WinBUGS automatically
after the end of sampling.

Gregor
________________________________________
From: Sebastian P. Luque [sl...@mu...]
Sent: Saturday, February 16, 2008 4:39 AM
To: Gorjanc Gregor
Cc: bug...@li...
Subject: Re: R2WinBUGS and Crossover in GNU/Linux

Hi,

I gave up, I took another route and decided to install Wine in a
different Debian machine that I can access in my network.  Installed
Wine without problems, installed WinBUGS the same, which even runs ok
there too.  Tried the example from locally at that machine with:

---<---------------cut here---------------start-------------->---
bugs.directory <- "/home/sluque/.wine/drive_c/Program Files/WinBUGS14"
WINE <- "/usr/bin/wine"
WINEPATH <- "/usr/bin/winepath"
schools.sim <- bugs(data, inits, parameters, model.file,
                    n.chains=3, n.iter=5000,
                    bugs.directory=bugs.directory,
                    clearWD=TRUE, WINE=WINE, newWINE=TRUE,
                    WINEPATH=WINEPATH)
---<---------------cut here---------------end---------------->---

which gave this output:

---<---------------cut here---------------start-------------->---
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
fixme:keyboard:RegisterHotKey (0x20024,13,0x00000002,3): stub
fixme:ole:GetHGlobalFromILockBytes cbSize is 13824
err:ole:CoGetClassObject class {0003000a-0000-0000-c000-000000000046} not registered
err:ole:CoGetClassObject class {0003000a-0000-0000-c000-000000000046} not registered
err:ole:CoGetClassObject no class object {0003000a-0000-0000-c000-000000000046} could be created for context 0x3
fixme:ntdll:RtlNtStatusToDosErrorNoTeb no mapping for 8000000a
err:ole:local_server_thread Failure during ConnectNamedPipe 317

Wine exited with a successful status
---<---------------cut here---------------end---------------->---

R just hung right before that last line, and I had to manually exit from
WinBUGS, but otherwise returned ok to the prompt.  The schools.sim
object was created properly, the files in the working directory were
also created without problems, and WinBUGS also showed a graph and
output in the log window.  I don't want to be too exquisite at this
point, but I need to run bugs() inside an lapply(), so this will surely
wreck havoc.

Has anybody actually gotten R2WinBUGS running without problems with Wine
on GNU/Linux?  Have you gotten these errors?  Any tips on getting over
them?  Thanks again.


Cheers,

--
Seb

Re: [Bugs-r-devel] R2WinBUGS and Crossover in GNU/Linux

[Sebastian P. L. <sl...@mu...>]

Hi,

I gave up, I took another route and decided to install Wine in a
different Debian machine that I can access in my network.  Installed
Wine without problems, installed WinBUGS the same, which even runs ok
there too.  Tried the example from locally at that machine with:

---<---------------cut here---------------start-------------->---
bugs.directory <- "/home/sluque/.wine/drive_c/Program Files/WinBUGS14"
WINE <- "/usr/bin/wine"
WINEPATH <- "/usr/bin/winepath"
schools.sim <- bugs(data, inits, parameters, model.file,
                    n.chains=3, n.iter=5000,
                    bugs.directory=bugs.directory,
                    clearWD=TRUE, WINE=WINE, newWINE=TRUE,
                    WINEPATH=WINEPATH)
---<---------------cut here---------------end---------------->---

which gave this output:

---<---------------cut here---------------start-------------->---
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
Wine exited with a successful status
fixme:keyboard:RegisterHotKey (0x20024,13,0x00000002,3): stub
fixme:ole:GetHGlobalFromILockBytes cbSize is 13824
err:ole:CoGetClassObject class {0003000a-0000-0000-c000-000000000046} not registered
err:ole:CoGetClassObject class {0003000a-0000-0000-c000-000000000046} not registered
err:ole:CoGetClassObject no class object {0003000a-0000-0000-c000-000000000046} could be created for context 0x3
fixme:ntdll:RtlNtStatusToDosErrorNoTeb no mapping for 8000000a
err:ole:local_server_thread Failure during ConnectNamedPipe 317

Wine exited with a successful status
---<---------------cut here---------------end---------------->---

R just hung right before that last line, and I had to manually exit from
WinBUGS, but otherwise returned ok to the prompt.  The schools.sim
object was created properly, the files in the working directory were
also created without problems, and WinBUGS also showed a graph and
output in the log window.  I don't want to be too exquisite at this
point, but I need to run bugs() inside an lapply(), so this will surely
wreck havoc.

Has anybody actually gotten R2WinBUGS running without problems with Wine
on GNU/Linux?  Have you gotten these errors?  Any tips on getting over
them?  Thanks again.


Cheers,

-- 
Seb

Re: [Bugs-r-devel] R2WinBUGS and Crossover in GNU/Linux

[Gorjanc G. <Gre...@bf...>]

Hi,

sorry for late response - I am out of office these days. Read bellow

> Ok, to debug this a bit better, I'm following the example in ?bugs.  For
> the actual calling of bugs() I did:
>
> ---<---------------cut here---------------start-------------->---
> bugs.directory <- "/home/sluque/.cxoffice/WinBUGS/drive_c/Program Files/WinBUGS14"
> WINE <- "/opt/cxoffice/bin/wine"
> schools.sim <- bugs(data, inits, parameters, model.file,
>                     n.chains=3, n.iter=5000,
>                     bugs.directory=bugs.directory,
>                     working.directory=NULL, clearWD=TRUE,
>                     WINE=WINE, newWINE=FALSE)
> ---<---------------cut here---------------end---------------->---
>
> using as much information as I can gather from Crossover.

This should be OK, but the problem is that winepath binary is not available as
we have discussed earlier. You could perhaps try if a copy of winepath binary
from wine could be of some use. You can also contact Crossover makers, why
they strip out winepath binary - perhaps this is provided somewhere else?

> This uses Gregor's suggestion (newWINE=FALSE), although the result was the same.
> Again, this is the error message:
>
> ---<---------------cut here---------------start-------------->---
> R> schools.sim <- bugs(data, inits, parameters, model.file,
> +                     n.chains=3, n.iter=5000,
> +                     bugs.directory=bugs.directory,
> +                     working.directory=NULL, clearWD=TRUE,
> +                     WINE=WINE, newWINE=FALSE)
> Error in findUnixBinary(x = "winepath") :
>   couldn't find winepath binary file
> ---<---------------cut here---------------end---------------->---

That is odd. Using newWINE=FALSE should try to use ~/.wine/config file. Do you
have this file?

Regards, gregor

Re: [Bugs-r-devel] R2WinBUGS and Crossover in GNU/Linux

[Gorjanc G. <Gre...@bf...>]

Ben,

as far as I see, you have:

Plain wine
  1582 2007-10-10 18:21 /usr/bin/winepath
  98027 2007-10-10 18:21 /usr/lib/wine/winepath.exe.so

Crossovers' wine
   79764 2007-09-13 16:51 /home/ben/cxoffice/lib/wine/winepath.exe.so

lpg
________________________________________
From: Ben Bolker [bo...@zo...]
Sent: Thursday, February 14, 2008 4:39 AM
To: Gorjanc Gregor
Cc: Sebastian P. Luque; bug...@li...
Subject: Re: [Bugs-r-devel] R2WinBUGS and Crossover in GNU/Linux

   Weird.  I have

ben@bolker-lap2:~/lib/R/pkgs/phylobase$ locate winepath | xargs ls -l

  (first two columns deleted)

   79764 2007-09-13 16:51 /home/ben/cxoffice/lib/wine/winepath.exe.so
  1582 2007-10-10 18:21 /usr/bin/winepath
  98027 2007-10-10 18:21 /usr/lib/wine/winepath.exe.so

   but I do have both crossover and plain old WINE installed,
so it's hard for me to tell which bits are which.

   Ben




Gorjanc Gregor wrote:
> Sebastian,
>
> please try with
>
> newWINE=FALSE
>
> However, this methods relies on file ~/.wine/config and its contents. New versions
> of wine do not have it anymore. I find it very odd that winepath is not available in
> crossover. winepath is used to transform paths between linux and windows paths -
> not just switching \  and /, but the whole transformation between disk trees. Are you
> sure you have the whole package. My ubuntu packages has binary and library:
>
> $ dpkg -L wine | grep winepath
> /usr/bin/winepath
> /usr/lib/wine/winepath.exe.so
>
> Regards, Gregor
>
> ________________________________________
> From: Sebastian P. Luque [sl...@mu...]
> Sent: Thursday, February 14, 2008 12:01 AM
> To: Uwe Ligges
> Cc: Gorjanc Gregor; Jouni Kerman
> Subject: R2WinBUGS and Crossover in GNU/Linux
>
> Hi,
>
> I'm trying to use R2WinBUGS in GNU/Linux, using Codeweavers' Crossover
> Linux Professional (version 6.2.0).  WinBUGS installed and runs fine
> from Crossover.  However, bugs() fails with the error:
>
> ---<---------------cut here---------------start-------------->---
> Error in findUnixBinary(x = "winepath") :
>   couldn't find winepath binary file
> ---<---------------cut here---------------end---------------->---
>
> I've called it using the arguments:
>
> bugs.directory="/home/sluque/.cxoffice/WinBUGS/drive_c/Program Files/WinBUGS14"
> useWINE=TRUE
> newWINE=TRUE
> WINE="/opt/cxoffice/bin/wine"
>
> It seems the winepath binary isn't even available in Crossover:
>
> ,-----[ find /opt/cxoffice \( -name \*winepath\* \) -exec ls -ld \{\} \; ]
> | -rwxr-xr-x 1 root root 79764 2008-01-05 13:21 /opt/cxoffice/lib/wine/winepath.exe.so
> `-----
>
> Any ideas on how to give bugs what's needed to run WinBUGS in Crossover
> would be appreciated.  Thanks in advance.
>
>
> Cheers,
>
> --
> Seb
>
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Bugs-r-devel mailing list
> Bug...@li...
> https://lists.sourceforge.net/lists/listinfo/bugs-r-devel

Re: [Bugs-r-devel] R2WinBUGS and Crossover in GNU/Linux

[Sebastian P. L. <sl...@mu...>]

On Thu, 14 Feb 2008 04:17:03 +0100,
Gorjanc Gregor <Gre...@bf...> wrote:

> Sebastian, please try with

> newWINE=FALSE

> However, this methods relies on file ~/.wine/config and its
> contents. New versions of wine do not have it anymore. I find it very
> odd that winepath is not available in crossover. winepath is used to
> transform paths between linux and windows paths - not just switching \
> and /, but the whole transformation between disk trees. Are you sure
> you have the whole package. My ubuntu packages has binary and library:

> $ dpkg -L wine | grep winepath /usr/bin/winepath
> /usr/lib/wine/winepath.exe.so

Thanks Gregor, yes I searched for this binary in the Crossover
installation path, so I'm sure it's not there.  Perhaps Crossover has
substituted winepath for something else to do that job?  Perhaps Wine
still has this binary, but I'd prefer to find a way to stay with
Crossover, since I'm afraid mixing both Crossover and Wine may mess up
my environment.  Anyway, I will try with newWine=FALSE in a while.

-- 
Seb

Re: [Bugs-r-devel] R2WinBUGS and Crossover in GNU/Linux

[Ben B. <bo...@zo...>]

   Weird.  I have

ben@bolker-lap2:~/lib/R/pkgs/phylobase$ locate winepath | xargs ls -l

  (first two columns deleted)

   79764 2007-09-13 16:51 /home/ben/cxoffice/lib/wine/winepath.exe.so
  1582 2007-10-10 18:21 /usr/bin/winepath
  98027 2007-10-10 18:21 /usr/lib/wine/winepath.exe.so

   but I do have both crossover and plain old WINE installed,
so it's hard for me to tell which bits are which.

   Ben




Gorjanc Gregor wrote:
> Sebastian,
> 
> please try with
> 
> newWINE=FALSE
> 
> However, this methods relies on file ~/.wine/config and its contents. New versions
> of wine do not have it anymore. I find it very odd that winepath is not available in
> crossover. winepath is used to transform paths between linux and windows paths -
> not just switching \  and /, but the whole transformation between disk trees. Are you
> sure you have the whole package. My ubuntu packages has binary and library:
> 
> $ dpkg -L wine | grep winepath
> /usr/bin/winepath
> /usr/lib/wine/winepath.exe.so
> 
> Regards, Gregor
> 
> ________________________________________
> From: Sebastian P. Luque [sl...@mu...]
> Sent: Thursday, February 14, 2008 12:01 AM
> To: Uwe Ligges
> Cc: Gorjanc Gregor; Jouni Kerman
> Subject: R2WinBUGS and Crossover in GNU/Linux
> 
> Hi,
> 
> I'm trying to use R2WinBUGS in GNU/Linux, using Codeweavers' Crossover
> Linux Professional (version 6.2.0).  WinBUGS installed and runs fine
> from Crossover.  However, bugs() fails with the error:
> 
> ---<---------------cut here---------------start-------------->---
> Error in findUnixBinary(x = "winepath") :
>   couldn't find winepath binary file
> ---<---------------cut here---------------end---------------->---
> 
> I've called it using the arguments:
> 
> bugs.directory="/home/sluque/.cxoffice/WinBUGS/drive_c/Program Files/WinBUGS14"
> useWINE=TRUE
> newWINE=TRUE
> WINE="/opt/cxoffice/bin/wine"
> 
> It seems the winepath binary isn't even available in Crossover:
> 
> ,-----[ find /opt/cxoffice \( -name \*winepath\* \) -exec ls -ld \{\} \; ]
> | -rwxr-xr-x 1 root root 79764 2008-01-05 13:21 /opt/cxoffice/lib/wine/winepath.exe.so
> `-----
> 
> Any ideas on how to give bugs what's needed to run WinBUGS in Crossover
> would be appreciated.  Thanks in advance.
> 
> 
> Cheers,
> 
> --
> Seb
> 
> -------------------------------------------------------------------------
> This SF.net email is sponsored by: Microsoft
> Defy all challenges. Microsoft(R) Visual Studio 2008.
> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
> _______________________________________________
> Bugs-r-devel mailing list
> Bug...@li...
> https://lists.sourceforge.net/lists/listinfo/bugs-r-devel

Re: [Bugs-r-devel] R2WinBUGS and Crossover in GNU/Linux

[Gorjanc G. <Gre...@bf...>]

Sebastian,

please try with

newWINE=FALSE

However, this methods relies on file ~/.wine/config and its contents. New versions
of wine do not have it anymore. I find it very odd that winepath is not available in
crossover. winepath is used to transform paths between linux and windows paths -
not just switching \  and /, but the whole transformation between disk trees. Are you
sure you have the whole package. My ubuntu packages has binary and library:

$ dpkg -L wine | grep winepath
/usr/bin/winepath
/usr/lib/wine/winepath.exe.so

Regards, Gregor

________________________________________
From: Sebastian P. Luque [sl...@mu...]
Sent: Thursday, February 14, 2008 12:01 AM
To: Uwe Ligges
Cc: Gorjanc Gregor; Jouni Kerman
Subject: R2WinBUGS and Crossover in GNU/Linux

Hi,

I'm trying to use R2WinBUGS in GNU/Linux, using Codeweavers' Crossover
Linux Professional (version 6.2.0).  WinBUGS installed and runs fine
from Crossover.  However, bugs() fails with the error:

---<---------------cut here---------------start-------------->---
Error in findUnixBinary(x = "winepath") :
  couldn't find winepath binary file
---<---------------cut here---------------end---------------->---

I've called it using the arguments:

bugs.directory="/home/sluque/.cxoffice/WinBUGS/drive_c/Program Files/WinBUGS14"
useWINE=TRUE
newWINE=TRUE
WINE="/opt/cxoffice/bin/wine"

It seems the winepath binary isn't even available in Crossover:

,-----[ find /opt/cxoffice \( -name \*winepath\* \) -exec ls -ld \{\} \; ]
| -rwxr-xr-x 1 root root 79764 2008-01-05 13:21 /opt/cxoffice/lib/wine/winepath.exe.so
`-----

Any ideas on how to give bugs what's needed to run WinBUGS in Crossover
would be appreciated.  Thanks in advance.


Cheers,

--
Seb

Re: [Bugs-r-devel] R2WinBUGS

[Kurt H. <Kur...@wu...>]

>>>>> Uwe Ligges writes:

> Kurt,
> R2WinBUGS_2.1-8.tar.gz in CRAN/incoming

Thanks, on CRAN now.

Best
-k

> Thank you!
> Uwe

[Bugs-r-devel] R2WinBUGS

[Uwe L. <li...@st...>]

Kurt,

R2WinBUGS_2.1-8.tar.gz in CRAN/incoming

Thank you!
Uwe