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

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

Hi!

> No, it doesn't.  But, this does:
>
>     schools.sim <- bugs(data, inits, parameters, model.file,
>         n.chains=3, n.iter=5000,
>         bugs.directory="/Applications/WinBUGS14", working.directory=".",
>                         WINE="/Applications/Darwine/Wine.bundle/Contents/bin/wine",
>                     WINEPATH="/Applications/Darwine/Wine.bundle/Contents/bin/winepath",
>         clearWD=TRUE)

Then we are not successfull in finding wine binaries in Mac. This is done by R2WinBUGS:::findUnixBinary
function. It goes like this (returning the result on the first success):

* check if there is x (WINE or WINEPATH) environmental variable
* check if there is /usr/bin/x
* try with which x
* try with locate x

I thought that there is which command in Mac also. Afterall Mac uses unix internally. Can you please check in
the terminal the result of the following commands:

which wine
which winepath

locate wine
locate winepath

Btw. As stated last time, working.directory="." is not really needed unless you do want
to keep the intermediate files in current working directory.


-----Original Message-----
From: Gorjanc Gregor [mailto:Gre...@bf...]
Sent: Mon 10/6/2008 3:01 PM
To: Sparapani, Rodney
Cc: bug...@li...
Subject: RE: [Bugs-r-devel] Mac bug regressions

...
>> 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).

Thank you for this details. /Applications/WinBUGS14 then seems to be a good default
for Mac. Does anyone have any other opinion? Additionally, I wonder how can we
set this default. There is already a bunch of arguments for the bugs() functions. Should
we use

bugs.directory=ifelse(???, "c:/Program Files/WinBUGS14/", "/Applications/WinBUGS14")

or should we change the bugs.directory in the code conditionally on the OS? Uwe?

>> Btw. Why do you use setwd(".")? It does not make sense, since this is changing the working directory to
>> the current one.

> 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)

Actually, you came up with the example and I (we) did not bother ;) What you need is
basically the same as example in ?bugs:

     model.file <- system.file(package="R2WinBUGS", "model", "schools.txt")
     # Some example data (see ?schools for details):
     data(schools)
     schools

     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")
     schools.sim <- bugs(data, inits, parameters, model.file,
         n.chains=3, n.iter=5000,
         bugs.directory="/Applications/WinBUGS14",
         clearWD=TRUE)

Can you please test if this works for you? I would like to know if
wine variables are properly initialized.

gg