Re: [Bugs-r-devel] Mac bug regressions

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

Gorjanc Gregor wrote:
> Hi Rodney,
>
>   
>> I just sent out a bug report.  Did anyone get it?  I hate Outlook!
>>     
>
> Then stop using it! Read further ...
>
>   
Actually, I don't.  But, in order to send the bug report from my Mac, 
where I did the testing, I had to...
>> Bug 1, Priority Secondary:
>>     
>>> if(!exists("baseenv", mode="function")) baseenv <- function() NULL
>>> options(STERM='iESS', editor='emacsclient')
>>> options(warn=2)
>>> library(R2WinBUGS)
>>>       
>> Loading required package: coda
>> Loading required package: lattice
>>     
>>> schools <- read.table ("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, "schools.bug", debug=TRUE,
>>>       
>> +                      n.chains=3, n.iter=1000, working.directory=".")
>> sh: /Volumes/My: No such file or directory
>>     
> ...
>   
>> Error in .fileCopy(file.path(bugs.directory, "System/Rsrc/Registry.odc"),  :
>>  no files to copy from
>> Error in if (!file.exists(dos.location)) stop(paste("WinBUGS executable does not exist in",  :
>>  argument is of length zero
>> Error in .fileCopy(file.path(bugs.directory, "System/Rsrc/Registry_Rsave.odc"),  :
>> no files to copy from
>>
>> This seems to be a bug with bad defaults.  Since supplying the correct defaults
>> works.
>>     
>
> Hmm, there is a problem with bugs.directory default. It is not really a problem, since
> we do not know what is the default place for Mac applications? The default also does
> not work on Linux if WinBUGS is not strictly installed in "c:/Program Files/WinBUGS14/"
> part of wine. The help of bugs() says
>
> ...
> Operation system support:
>
> MS Windows no problem
>
> Linux, Mac OS X and Unix in general possible with Wine emulation via useWINE=TRUE, but only for WinBUGS 1.4.*
>
> If useWINE=TRUE is used, all paths (such as working.directory and model.file, must
> be given in native (Unix) style, but working.directory can be given in Windows path style
> (e.g. “c:/Program Files/WinBUGS14/”) or native (Unix) style (e.g. “/path/to/wine/folder/dosdevices/c:/Program
> Files/WinBUGS14”). This is done to achieve greatest portability with default argument value for
> working.directory.
>
> Unless you can provide a reasonable defaul for Mac, we can not help you!
>
>   
Umm.  According to my notes I did.  Or was that just a patch that I 
applied to my local copy that was not
incorporated into the mainline.  Can't find it right now.  But, the 
default for all Mac applications is
/Applications.  That was in the workaround I sent.  The reason is that 
that the Mac filesystem has
permissions since it is just the Unix filesystem with a few bells and 
whistles.   The /Applications
directory has the permissions necessary to allow any user to install 
applications system-wide, a nice
compromise between security and practicality.  Other directories are 
secure so they are not an option
(and for real Mac applications, they actually need to be in 
/Applications:  this is probably more than
you need or want to know).
> I wonder where "sh: /Volumes/My: No such file or directory" is comming from. It looks like the path has space
> in it. Perhaps we could be more informative in such cases so that users would be warned that bugs.directory
> needs to be accomodated.
>
> I will look into other bug later.
>
> Btw. Why do you use setwd(".")? It does not make sense, since this is changing the working directory to
> the current one.
>
> gg
>   
I don't know.  I got that from the Solaris example that you guys helped 
me with.  I figured you guys know
what you are doing.  My mistake :o)

-- 
Rodney Sparapani      Center for Patient Care & Outcomes Research (PCOR)
Sr. Biostatistician              http://www.mcw.edu/pcor
4 wheels good, 2 wheels better!  Medical College of Wisconsin (MCW)
WWLD?:  What Would Lombardi Do?  Milwaukee, WI, USA