bugs-r-devel

Re: [Bugs-r-devel] SF.net SVN: bugs-r:[108] trunk/R2WinBUGS

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

Gorjanc Gregor wrote:
> I guess so since we have a bugfix and a hack/solution that eases the
> work on Macs. If you have time of course.

Will do shortly!

Uwe



> ________________________________________
> From: Uwe Ligges [li...@st...]
> Sent: Wednesday, March 25, 2009 5:27 PM
> To: gg...@us...
> Cc: bug...@li...
> Subject: Re: [Bugs-r-devel] SF.net SVN: bugs-r:[108] trunk/R2WinBUGS
> 
> Thanks, do we need to release soon?
> 
> Uwe
> 
> 
> gg...@us... wrote:
>> Revision: 108
>>           http://bugs-r.svn.sourceforge.net/bugs-r/?rev=108&view=rev
>> Author:   ggorjan
>> Date:     2009-03-25 12:45:56 +0000 (Wed, 25 Mar 2009)
>>
>> Log Message:
>> -----------
>> hack: adding group write permission for a temporary working directory in order to avoid problems with WINE emulator on Mac OS X
>>
>> Modified Paths:
>> --------------
>>     trunk/R2WinBUGS/DESCRIPTION
>>     trunk/R2WinBUGS/R/bugs.R
>>     trunk/R2WinBUGS/inst/NEWS
>>
>> Modified: trunk/R2WinBUGS/DESCRIPTION
>> ===================================================================
>> --- trunk/R2WinBUGS/DESCRIPTION       2009-02-20 15:11:48 UTC (rev 107)
>> +++ trunk/R2WinBUGS/DESCRIPTION       2009-03-25 12:45:56 UTC (rev 108)
>> @@ -1,7 +1,7 @@
>>  Package: R2WinBUGS
>>  Title: Running WinBUGS and OpenBUGS from R / S-PLUS
>>  Date: 2009-02-11
>> -Version: 2.1-12
>> +Version: 2.1-13
>>  Author: originally written by Andrew Gelman <ge...@st...>;
>>   changes and packaged by Sibylle Sturtz <st...@st...>
>>   and Uwe Ligges <li...@st...>.
>>
>> Modified: trunk/R2WinBUGS/R/bugs.R
>> ===================================================================
>> --- trunk/R2WinBUGS/R/bugs.R  2009-02-20 15:11:48 UTC (rev 107)
>> +++ trunk/R2WinBUGS/R/bugs.R  2009-03-25 12:45:56 UTC (rev 108)
>> @@ -48,7 +48,7 @@
>>      if(useWINE){
>>          ## Some tweaks for wine (particularly required for Mac OS)
>>          working.directory <- gsub("//", "/", working.directory)
>> -        Sys.chmod(working.directory, mode="750")
>> +        Sys.chmod(working.directory, mode="770")
>>          on.exit(Sys.chmod(working.directory, mode="700"), add = TRUE)
>>      }
>>      savedWD <- getwd()
>>
>> Modified: trunk/R2WinBUGS/inst/NEWS
>> ===================================================================
>> --- trunk/R2WinBUGS/inst/NEWS 2009-02-20 15:11:48 UTC (rev 107)
>> +++ trunk/R2WinBUGS/inst/NEWS 2009-03-25 12:45:56 UTC (rev 108)
>> @@ -2,7 +2,9 @@
>>  =====================
>>
>>  Update 2.1-13
>> -- properly using chain parameters in as.mcmc.list.bugs
>> +- hack: adding group write permission for a temporary working directory in order to
>> +  avoid problems with WINE emulator on Mac OS X
>> +- bugfix: properly using chain parameters in as.mcmc.list.bugs
>>  - documentation fix
>>
>>  Update 2.1-12
>>
>>
>> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
>>
>> ------------------------------------------------------------------------------
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>> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
>> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
>> software that enables intelligent coding and step-through debugging.
>> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
>> _______________________________________________
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>> https://lists.sourceforge.net/lists/listinfo/bugs-r-devel
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Re: [Bugs-r-devel] SF.net SVN: bugs-r:[108] trunk/R2WinBUGS

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

I guess so since we have a bugfix and a hack/solution that eases the
work on Macs. If you have time of course.
________________________________________
From: Uwe Ligges [li...@st...]
Sent: Wednesday, March 25, 2009 5:27 PM
To: gg...@us...
Cc: bug...@li...
Subject: Re: [Bugs-r-devel] SF.net SVN: bugs-r:[108] trunk/R2WinBUGS

Thanks, do we need to release soon?

Uwe


gg...@us... wrote:
> Revision: 108
>           http://bugs-r.svn.sourceforge.net/bugs-r/?rev=108&view=rev
> Author:   ggorjan
> Date:     2009-03-25 12:45:56 +0000 (Wed, 25 Mar 2009)
>
> Log Message:
> -----------
> hack: adding group write permission for a temporary working directory in order to avoid problems with WINE emulator on Mac OS X
>
> Modified Paths:
> --------------
>     trunk/R2WinBUGS/DESCRIPTION
>     trunk/R2WinBUGS/R/bugs.R
>     trunk/R2WinBUGS/inst/NEWS
>
> Modified: trunk/R2WinBUGS/DESCRIPTION
> ===================================================================
> --- trunk/R2WinBUGS/DESCRIPTION       2009-02-20 15:11:48 UTC (rev 107)
> +++ trunk/R2WinBUGS/DESCRIPTION       2009-03-25 12:45:56 UTC (rev 108)
> @@ -1,7 +1,7 @@
>  Package: R2WinBUGS
>  Title: Running WinBUGS and OpenBUGS from R / S-PLUS
>  Date: 2009-02-11
> -Version: 2.1-12
> +Version: 2.1-13
>  Author: originally written by Andrew Gelman <ge...@st...>;
>   changes and packaged by Sibylle Sturtz <st...@st...>
>   and Uwe Ligges <li...@st...>.
>
> Modified: trunk/R2WinBUGS/R/bugs.R
> ===================================================================
> --- trunk/R2WinBUGS/R/bugs.R  2009-02-20 15:11:48 UTC (rev 107)
> +++ trunk/R2WinBUGS/R/bugs.R  2009-03-25 12:45:56 UTC (rev 108)
> @@ -48,7 +48,7 @@
>      if(useWINE){
>          ## Some tweaks for wine (particularly required for Mac OS)
>          working.directory <- gsub("//", "/", working.directory)
> -        Sys.chmod(working.directory, mode="750")
> +        Sys.chmod(working.directory, mode="770")
>          on.exit(Sys.chmod(working.directory, mode="700"), add = TRUE)
>      }
>      savedWD <- getwd()
>
> Modified: trunk/R2WinBUGS/inst/NEWS
> ===================================================================
> --- trunk/R2WinBUGS/inst/NEWS 2009-02-20 15:11:48 UTC (rev 107)
> +++ trunk/R2WinBUGS/inst/NEWS 2009-03-25 12:45:56 UTC (rev 108)
> @@ -2,7 +2,9 @@
>  =====================
>
>  Update 2.1-13
> -- properly using chain parameters in as.mcmc.list.bugs
> +- hack: adding group write permission for a temporary working directory in order to
> +  avoid problems with WINE emulator on Mac OS X
> +- bugfix: properly using chain parameters in as.mcmc.list.bugs
>  - documentation fix
>
>  Update 2.1-12
>
>
> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
>
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
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Re: [Bugs-r-devel] SF.net SVN: bugs-r:[108] trunk/R2WinBUGS

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

Thanks, do we need to release soon?

Uwe


gg...@us... wrote:
> Revision: 108
>           http://bugs-r.svn.sourceforge.net/bugs-r/?rev=108&view=rev
> Author:   ggorjan
> Date:     2009-03-25 12:45:56 +0000 (Wed, 25 Mar 2009)
> 
> Log Message:
> -----------
> hack: adding group write permission for a temporary working directory in order to avoid problems with WINE emulator on Mac OS X
> 
> Modified Paths:
> --------------
>     trunk/R2WinBUGS/DESCRIPTION
>     trunk/R2WinBUGS/R/bugs.R
>     trunk/R2WinBUGS/inst/NEWS
> 
> Modified: trunk/R2WinBUGS/DESCRIPTION
> ===================================================================
> --- trunk/R2WinBUGS/DESCRIPTION	2009-02-20 15:11:48 UTC (rev 107)
> +++ trunk/R2WinBUGS/DESCRIPTION	2009-03-25 12:45:56 UTC (rev 108)
> @@ -1,7 +1,7 @@
>  Package: R2WinBUGS
>  Title: Running WinBUGS and OpenBUGS from R / S-PLUS
>  Date: 2009-02-11
> -Version: 2.1-12
> +Version: 2.1-13
>  Author: originally written by Andrew Gelman <ge...@st...>;
>   changes and packaged by Sibylle Sturtz <st...@st...>
>   and Uwe Ligges <li...@st...>.
> 
> Modified: trunk/R2WinBUGS/R/bugs.R
> ===================================================================
> --- trunk/R2WinBUGS/R/bugs.R	2009-02-20 15:11:48 UTC (rev 107)
> +++ trunk/R2WinBUGS/R/bugs.R	2009-03-25 12:45:56 UTC (rev 108)
> @@ -48,7 +48,7 @@
>      if(useWINE){
>          ## Some tweaks for wine (particularly required for Mac OS)
>          working.directory <- gsub("//", "/", working.directory)
> -        Sys.chmod(working.directory, mode="750")
> +        Sys.chmod(working.directory, mode="770")
>          on.exit(Sys.chmod(working.directory, mode="700"), add = TRUE)
>      }
>      savedWD <- getwd()
> 
> Modified: trunk/R2WinBUGS/inst/NEWS
> ===================================================================
> --- trunk/R2WinBUGS/inst/NEWS	2009-02-20 15:11:48 UTC (rev 107)
> +++ trunk/R2WinBUGS/inst/NEWS	2009-03-25 12:45:56 UTC (rev 108)
> @@ -2,7 +2,9 @@
>  =====================
>  
>  Update 2.1-13
> -- properly using chain parameters in as.mcmc.list.bugs
> +- hack: adding group write permission for a temporary working directory in order to
> +  avoid problems with WINE emulator on Mac OS X
> +- bugfix: properly using chain parameters in as.mcmc.list.bugs
>  - documentation fix
>  
>  Update 2.1-12
> 
> 
> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
> 
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Bugs-r-devel mailing list
> Bug...@li...
> https://lists.sourceforge.net/lists/listinfo/bugs-r-devel

[Bugs-r-devel] SF.net SVN: bugs-r:[108] trunk/R2WinBUGS

[<gg...@us...>]

Revision: 108
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=108&view=rev
Author:   ggorjan
Date:     2009-03-25 12:45:56 +0000 (Wed, 25 Mar 2009)

Log Message:
-----------
hack: adding group write permission for a temporary working directory in order to avoid problems with WINE emulator on Mac OS X

Modified Paths:
--------------
    trunk/R2WinBUGS/DESCRIPTION
    trunk/R2WinBUGS/R/bugs.R
    trunk/R2WinBUGS/inst/NEWS

Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION	2009-02-20 15:11:48 UTC (rev 107)
+++ trunk/R2WinBUGS/DESCRIPTION	2009-03-25 12:45:56 UTC (rev 108)
@@ -1,7 +1,7 @@
 Package: R2WinBUGS
 Title: Running WinBUGS and OpenBUGS from R / S-PLUS
 Date: 2009-02-11
-Version: 2.1-12
+Version: 2.1-13
 Author: originally written by Andrew Gelman <ge...@st...>;
  changes and packaged by Sibylle Sturtz <st...@st...>
  and Uwe Ligges <li...@st...>.

Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R	2009-02-20 15:11:48 UTC (rev 107)
+++ trunk/R2WinBUGS/R/bugs.R	2009-03-25 12:45:56 UTC (rev 108)
@@ -48,7 +48,7 @@
     if(useWINE){
         ## Some tweaks for wine (particularly required for Mac OS)
         working.directory <- gsub("//", "/", working.directory)
-        Sys.chmod(working.directory, mode="750")
+        Sys.chmod(working.directory, mode="770")
         on.exit(Sys.chmod(working.directory, mode="700"), add = TRUE)
     }
     savedWD <- getwd()

Modified: trunk/R2WinBUGS/inst/NEWS
===================================================================
--- trunk/R2WinBUGS/inst/NEWS	2009-02-20 15:11:48 UTC (rev 107)
+++ trunk/R2WinBUGS/inst/NEWS	2009-03-25 12:45:56 UTC (rev 108)
@@ -2,7 +2,9 @@
 =====================
 
 Update 2.1-13
-- properly using chain parameters in as.mcmc.list.bugs
+- hack: adding group write permission for a temporary working directory in order to
+  avoid problems with WINE emulator on Mac OS X
+- bugfix: properly using chain parameters in as.mcmc.list.bugs
 - documentation fix
 
 Update 2.1-12


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Re: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]

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

Gorjanc Gregor wrote:
> I think this should be safe enough. Uwe do you see any problem?

I'm fine (although I always see a problem when changing those permissions).

Uwe


> gg
> ________________________________________
> From: Rodney Sparapani [rsp...@mc...]
> Sent: Tuesday, March 24, 2009 3:12 PM
> To: Uwe Ligges
> Cc: Gorjanc Gregor; bug...@li...
> Subject: Re: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]
> 
> Uwe Ligges wrote:
>>
>> Sparapani, Rodney wrote:
>>> Hi Gregor:
>>>
>>> Good suggestion!  777 works for me.   Please commit.
>>
>> And 770 does not?
> Oh, good suggestion!  770 does work.  Please commit.  Thanks.
> 
> --
> 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
> 

Re: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]

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

I think this should be safe enough. Uwe do you see any problem?

gg
________________________________________
From: Rodney Sparapani [rsp...@mc...]
Sent: Tuesday, March 24, 2009 3:12 PM
To: Uwe Ligges
Cc: Gorjanc Gregor; bug...@li...
Subject: Re: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]

Uwe Ligges wrote:
>
>
> Sparapani, Rodney wrote:
>> Hi Gregor:
>>
>> Good suggestion!  777 works for me.   Please commit.
>
>
> And 770 does not?
Oh, good suggestion!  770 does work.  Please commit.  Thanks.

--
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

Re: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]

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

Uwe Ligges wrote:
>
>
> Sparapani, Rodney wrote:
>> Hi Gregor:
>>
>> Good suggestion!  777 works for me.   Please commit.  
>
>
> And 770 does not? 
Oh, good suggestion!  770 does work.  Please commit.  Thanks.

-- 
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

Re: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]

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

Sparapani, Rodney wrote:
> Hi Gregor:
> 
> Good suggestion!  777 works for me.   Please commit.  


And 770 does not? What about 775?

Anyway, I am a bit reluctant to commit right away:
tempdir() is created by R on startup and used by the R process and other 
packages. Making that directory open is a security issue for those who 
are doing more or less confidential analyses / working on confidential 
data. I'd be happier if people could tell wine to run under their own 
credentials (and not some wine account or so), but I am not sure if that 
is possible or what the problems are to run under the users credentials.

Best wishes,
Uwe




> Thanks,
> 
> Rodney
> 
> 
> -----Original Message-----
> From: Gorjanc Gregor [mailto:Gre...@bf...]
> Sent: Thu 3/19/2009 12:24 PM
> To: Sparapani, Rodney; bug...@li...
> Subject: RE: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]
>  
> Rodney,
> 
> this is odd since we do tweak the permissions of temporary directory created by
> tempdir (this is done in bugs() function). However, we only use 750, which might
> not be enough. Can you modify the bugs function on your Mac (change to 770 or 777)
> and test if it works without setting the working.directoty=".".
> 
> Thanks, gg
> ________________________________________
> From: Rodney Sparapani [rsp...@mc...]
> Sent: Wednesday, March 18, 2009 9:49 PM
> To: bug...@li...
> Subject: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]
> 
> -------- Original Message --------
> Subject:        Re: strange error with bugs() on Mac OSX
> Date:   Thu, 12 Mar 2009 09:19:02 -0500
> From:   Rodney Sparapani <rsp...@mc...>
> To:     Luca Pozzi <luc...@AS...>
> References:     <BUGS%200...@JI...>
> 
> 
> 
>> ------------------------------------------------------------------------
>> hello, I am trying to run bugs() from a Mac (yes, I really need to
>> use
>> WinBUGS and not JAGS although the latter works better), but some
>> problem
>> occurs and R prints the following
>>
>> fixme:keyboard:RegisterHotKey (0x1002a,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
>> Errore in bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE =
>> useWINE,  :
>>   Look at the log file and
>> try again with 'debug=TRUE' to figure out what went wrong within
>> Bugs.
>>
>> but this message is no use since:
>> -debug=TRUE: this option only keep WB open after the run, so that, if
>> any error message is displayed in WB you will be able to read it. But
>> this time no WB error message appears and so this suggestion from R
>> isquite a default message that is of no help this time.
>>
>> .log file: the problem is that, being the .log file nothing but a
>> trnscription of the lines appearing on the WB command line there is no
>> .log because in my
>> case WB stops before running, before even starting to process the
>> model and so
>> on, the only thing that happens is WB opening and showing the licence
>> agreement.
>> This, together with the message printed out on R command line, make me
>> think to an error in the licence registration, but I can't find it..
>> moreover before the expiration of my previous key the R2B interface
>> worked well, but I have installed the new one (several times, just in
>> case...) but nothing's changed... when I tried again with the old key
>> I received an additional message of expired key, when I run again the
>> immortal key nothing changes (it probably doesn't load the new one
>> correctly).
>>
>> notice that WB runs fine if I run it directly..
>>
>> Please help me...
>>
>> Luca Pozzi
> Hi Luca:
> 
> It looks like you are using R2WinBUGS, correct?  Make sure that you
> have the latest version.  Also, I think there is a bug in R2WinBUGS
> that requires the following workaround.  I always have to set
> working.directory=".".
> 
> --
> 
> Hi Gang:
> 
> Luca assures me that he also needs to set working.directory=".".
> I know you guys aren't interested in debugging on OS X, but
> perhaps there could be an entry in the PROBLEMS file, or
> similar like README.MACOSX, that gives this simple workaround?
> 
> --
> 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
> 
> 
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Bugs-r-devel mailing list
> Bug...@li...
> https://lists.sourceforge.net/lists/listinfo/bugs-r-devel
> 
> 
> ------------------------------------------------------------------------------
> Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
> powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
> easily build your RIAs with Flex Builder, the Eclipse(TM)based development
> software that enables intelligent coding and step-through debugging.
> Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
> _______________________________________________
> Bugs-r-devel mailing list
> Bug...@li...
> https://lists.sourceforge.net/lists/listinfo/bugs-r-devel

Re: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]

[Sparapani, R. <rsp...@mc...>]

Hi Gregor:

Good suggestion!  777 works for me.   Please commit.  

Thanks,

Rodney


-----Original Message-----
From: Gorjanc Gregor [mailto:Gre...@bf...]
Sent: Thu 3/19/2009 12:24 PM
To: Sparapani, Rodney; bug...@li...
Subject: RE: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]
 
Rodney,

this is odd since we do tweak the permissions of temporary directory created by
tempdir (this is done in bugs() function). However, we only use 750, which might
not be enough. Can you modify the bugs function on your Mac (change to 770 or 777)
and test if it works without setting the working.directoty=".".

Thanks, gg
________________________________________
From: Rodney Sparapani [rsp...@mc...]
Sent: Wednesday, March 18, 2009 9:49 PM
To: bug...@li...
Subject: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]

-------- Original Message --------
Subject:        Re: strange error with bugs() on Mac OSX
Date:   Thu, 12 Mar 2009 09:19:02 -0500
From:   Rodney Sparapani <rsp...@mc...>
To:     Luca Pozzi <luc...@AS...>
References:     <BUGS%200...@JI...>



>
> ------------------------------------------------------------------------
> hello, I am trying to run bugs() from a Mac (yes, I really need to
> use
> WinBUGS and not JAGS although the latter works better), but some
> problem
> occurs and R prints the following
>
> fixme:keyboard:RegisterHotKey (0x1002a,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
> Errore in bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE =
> useWINE,  :
>   Look at the log file and
> try again with 'debug=TRUE' to figure out what went wrong within
> Bugs.
>
> but this message is no use since:
> -debug=TRUE: this option only keep WB open after the run, so that, if
> any error message is displayed in WB you will be able to read it. But
> this time no WB error message appears and so this suggestion from R
> isquite a default message that is of no help this time.
>
> .log file: the problem is that, being the .log file nothing but a
> trnscription of the lines appearing on the WB command line there is no
> .log because in my
> case WB stops before running, before even starting to process the
> model and so
> on, the only thing that happens is WB opening and showing the licence
> agreement.
> This, together with the message printed out on R command line, make me
> think to an error in the licence registration, but I can't find it..
> moreover before the expiration of my previous key the R2B interface
> worked well, but I have installed the new one (several times, just in
> case...) but nothing's changed... when I tried again with the old key
> I received an additional message of expired key, when I run again the
> immortal key nothing changes (it probably doesn't load the new one
> correctly).
>
> notice that WB runs fine if I run it directly..
>
> Please help me...
>
> Luca Pozzi
Hi Luca:

It looks like you are using R2WinBUGS, correct?  Make sure that you
have the latest version.  Also, I think there is a bug in R2WinBUGS
that requires the following workaround.  I always have to set
working.directory=".".

--

Hi Gang:

Luca assures me that he also needs to set working.directory=".".
I know you guys aren't interested in debugging on OS X, but
perhaps there could be an entry in the PROBLEMS file, or
similar like README.MACOSX, that gives this simple workaround?

--
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


------------------------------------------------------------------------------
Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
easily build your RIAs with Flex Builder, the Eclipse(TM)based development
software that enables intelligent coding and step-through debugging.
Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
_______________________________________________
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Bug...@li...
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Re: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]

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

Rodney,

this is odd since we do tweak the permissions of temporary directory created by
tempdir (this is done in bugs() function). However, we only use 750, which might
not be enough. Can you modify the bugs function on your Mac (change to 770 or 777)
and test if it works without setting the working.directoty=".".

Thanks, gg
________________________________________
From: Rodney Sparapani [rsp...@mc...]
Sent: Wednesday, March 18, 2009 9:49 PM
To: bug...@li...
Subject: [Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]

-------- Original Message --------
Subject:        Re: strange error with bugs() on Mac OSX
Date:   Thu, 12 Mar 2009 09:19:02 -0500
From:   Rodney Sparapani <rsp...@mc...>
To:     Luca Pozzi <luc...@AS...>
References:     <BUGS%200...@JI...>



>
> ------------------------------------------------------------------------
> hello, I am trying to run bugs() from a Mac (yes, I really need to
> use
> WinBUGS and not JAGS although the latter works better), but some
> problem
> occurs and R prints the following
>
> fixme:keyboard:RegisterHotKey (0x1002a,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
> Errore in bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE =
> useWINE,  :
>   Look at the log file and
> try again with 'debug=TRUE' to figure out what went wrong within
> Bugs.
>
> but this message is no use since:
> -debug=TRUE: this option only keep WB open after the run, so that, if
> any error message is displayed in WB you will be able to read it. But
> this time no WB error message appears and so this suggestion from R
> isquite a default message that is of no help this time.
>
> .log file: the problem is that, being the .log file nothing but a
> trnscription of the lines appearing on the WB command line there is no
> .log because in my
> case WB stops before running, before even starting to process the
> model and so
> on, the only thing that happens is WB opening and showing the licence
> agreement.
> This, together with the message printed out on R command line, make me
> think to an error in the licence registration, but I can't find it..
> moreover before the expiration of my previous key the R2B interface
> worked well, but I have installed the new one (several times, just in
> case...) but nothing's changed... when I tried again with the old key
> I received an additional message of expired key, when I run again the
> immortal key nothing changes (it probably doesn't load the new one
> correctly).
>
> notice that WB runs fine if I run it directly..
>
> Please help me...
>
> Luca Pozzi
Hi Luca:

It looks like you are using R2WinBUGS, correct?  Make sure that you
have the latest version.  Also, I think there is a bug in R2WinBUGS
that requires the following workaround.  I always have to set
working.directory=".".

--

Hi Gang:

Luca assures me that he also needs to set working.directory=".".
I know you guys aren't interested in debugging on OS X, but
perhaps there could be an entry in the PROBLEMS file, or
similar like README.MACOSX, that gives this simple workaround?

--
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


------------------------------------------------------------------------------
Apps built with the Adobe(R) Flex(R) framework and Flex Builder(TM) are
powering Web 2.0 with engaging, cross-platform capabilities. Quickly and
easily build your RIAs with Flex Builder, the Eclipse(TM)based development
software that enables intelligent coding and step-through debugging.
Download the free 60 day trial. http://p.sf.net/sfu/www-adobe-com
_______________________________________________
Bugs-r-devel mailing list
Bug...@li...
https://lists.sourceforge.net/lists/listinfo/bugs-r-devel

[Bugs-r-devel] [Fwd: Re: strange error with bugs() on Mac OSX]

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

-------- Original Message --------
Subject: 	Re: strange error with bugs() on Mac OSX
Date: 	Thu, 12 Mar 2009 09:19:02 -0500
From: 	Rodney Sparapani <rsp...@mc...>
To: 	Luca Pozzi <luc...@AS...>
References: 	<BUGS%200...@JI...>



>
> ------------------------------------------------------------------------
> hello, I am trying to run bugs() from a Mac (yes, I really need to
> use
> WinBUGS and not JAGS although the latter works better), but some
> problem
> occurs and R prints the following
>
> fixme:keyboard:RegisterHotKey (0x1002a,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
> Errore in bugs.run(n.burnin, bugs.directory, WINE = WINE, useWINE =
> useWINE,  :
>   Look at the log file and
> try again with 'debug=TRUE' to figure out what went wrong within
> Bugs.
>
> but this message is no use since:
> -debug=TRUE: this option only keep WB open after the run, so that, if 
> any error message is displayed in WB you will be able to read it. But 
> this time no WB error message appears and so this suggestion from R 
> isquite a default message that is of no help this time.
>
> .log file: the problem is that, being the .log file nothing but a 
> trnscription of the lines appearing on the WB command line there is no 
> .log because in my
> case WB stops before running, before even starting to process the 
> model and so
> on, the only thing that happens is WB opening and showing the licence
> agreement.
> This, together with the message printed out on R command line, make me
> think to an error in the licence registration, but I can't find it.. 
> moreover before the expiration of my previous key the R2B interface 
> worked well, but I have installed the new one (several times, just in 
> case...) but nothing's changed... when I tried again with the old key 
> I received an additional message of expired key, when I run again the 
> immortal key nothing changes (it probably doesn't load the new one 
> correctly).
>
> notice that WB runs fine if I run it directly..
>
> Please help me...
>
> Luca Pozzi
Hi Luca:

It looks like you are using R2WinBUGS, correct?  Make sure that you
have the latest version.  Also, I think there is a bug in R2WinBUGS
that requires the following workaround.  I always have to set
working.directory=".".

-- 

Hi Gang:

Luca assures me that he also needs to set working.directory=".".
I know you guys aren't interested in debugging on OS X, but 
perhaps there could be an entry in the PROBLEMS file, or
similar like README.MACOSX, that gives this simple workaround?

-- 
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

Re: [Bugs-r-devel] [Fwd: storing WinBUGS simulations in a R list]

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

Rodney Sparapani wrote:
> Hi Gang:
> 
> I didn't know if you had seen this.  It sounds like it might be interesting.

I doubt it is: If you want to save something, use save() on the bugs
object. Or if you have coda files, you can postprocess with the coda
package. In both cases all information are available and I think two
ways are enough for now.

Best wishes,
Uwe


> Rodney
> 
> -------- Original Message --------
> Subject: 	storing WinBUGS simulations in a R list]
> Date: 	Tue, 3 Mar 2009 00:03:37 +0000
> From: 	BUGS automatic digest system <LIS...@JI...>
> Reply-To: 	lau...@YA...
> To: 	BU...@JI...
> 
> 
> Dear BUGS users,
> 
>  
>  I have written a R function to store the MCMC simulations produced by 
> WinBUGS in a R list. The code is available from here: 
> http://forums.cirad.fr/logiciel-R/viewtopic.php?t=1749
>  
>  I have nothing to gain from sharing this code - just hope this could help.
>  
> Below are some explanations:
>  
>   By default, the R function  bugs()  from the R2WinBUGS package, 1) 
> runs WinBUGS, 2) stores simulations in R, 3) produces summary statistics 
> on simulations.
>  
>  The  bugs()  function could crash whereas WinBUGS works well. Or one 
> could be interested only in running WinBUGS and storing the simulations; 
> this could be achieved with option codaPkg=TRUE in the bugs() function 
> and then applying the  read.bugs()  function for further output analysis 
> using the coda package.
>   
>  The function  read.winbugs()  given in the document allows a more 
> straightforward storing of the simulations in a R list, and this list 
> allows a particularly easy access to the simulations, nice for further 
> 'bare-hand' treatment of the simulations.
>  
>  Of course it is also possible to use both an available R function as 
> well as my function  read.winbugs()  to get this friendly list.
>  
>  
>  Hope this could help,
>   
>                            Stéphane
> 
> 

[Bugs-r-devel] [Fwd: storing WinBUGS simulations in a R list]

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

Hi Gang:

I didn't know if you had seen this.  It sounds like it might be interesting.

Rodney

-------- Original Message --------
Subject: 	storing WinBUGS simulations in a R list]
Date: 	Tue, 3 Mar 2009 00:03:37 +0000
From: 	BUGS automatic digest system <LIS...@JI...>
Reply-To: 	lau...@YA...
To: 	BU...@JI...


Dear BUGS users,

 
 I have written a R function to store the MCMC simulations produced by 
WinBUGS in a R list. The code is available from here: 
http://forums.cirad.fr/logiciel-R/viewtopic.php?t=1749
 
 I have nothing to gain from sharing this code - just hope this could help.
 
Below are some explanations:
 
  By default, the R function  bugs()  from the R2WinBUGS package, 1) 
runs WinBUGS, 2) stores simulations in R, 3) produces summary statistics 
on simulations.
 
 The  bugs()  function could crash whereas WinBUGS works well. Or one 
could be interested only in running WinBUGS and storing the simulations; 
this could be achieved with option codaPkg=TRUE in the bugs() function 
and then applying the  read.bugs()  function for further output analysis 
using the coda package.
  
 The function  read.winbugs()  given in the document allows a more 
straightforward storing of the simulations in a R list, and this list 
allows a particularly easy access to the simulations, nice for further 
'bare-hand' treatment of the simulations.
 
 Of course it is also possible to use both an available R function as 
well as my function  read.winbugs()  to get this friendly list.
 
 
 Hope this could help,
  
                           Stéphane


-- 
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

Re: [Bugs-r-devel] as.mcmc.list

[Mike M. <mme...@wc...>]

Hi Uwe and Gorjanc,

Looks like I got the thinning wrong!

Thanks for correcting that.

Cheers, Mike.

At 19:52 20/02/2009, Uwe Ligges wrote:
>Gorjanc Gregor wrote:
>>Hi,
>>Recently as.mcmc.list.bugs has been introduced as contrbuted by 
>>Mike Meredith.
>>I think there are some flaws. For example. I have an bugs object 
>>with the following details:
>>3 chains, each with 1e+05 iterations (first 10000 discarded), 
>>n.thin = 10 n.sims = 27000 iterations saved
>>i.e.
>>List of 24
>>  $ n.chains       : num 3
>>  $ n.iter         : num 1e+05
>>  $ n.burnin       : num 10000
>>  $ n.thin         : num 10
>>  $ n.keep         : num 9000
>>  $ n.sims         : num 27000
>>however, when I create an mcmc object I get
>>List of 3
>>  $ : mcmc [1:9000, 1:59] 12 12.4 12.8 13.1 12.1 ...
>>   ..- attr(*, "dimnames")=List of 2
>>   .. ..$ : chr [1:9000] "1001" "1002" "1003" "1004" ...
>>   .. ..$ : chr [1:59] "alpha" "deviance" "l[10]" "l[11]" ...
>>   ..- attr(*, "mcpar")= num [1:3] 1001 10000 1
>>...
>>The last line, i.e., the mcpar, is wrong. It should be
>>   ..- attr(*, "mcpar")= num [1:3] 10001 100000 10
>>I also do not see the point in setting the rownames, since they are 
>>not reflecting the reality, i.e.,
>>my chains where thinned, but the rownames are 1001, 1002, ...
>>Bellow is the diff of the "fixed" function, but before I commit it, 
>>I would like to make sure
>>there is consensus about this. I could not find Mikes e-mail. Uwe?
>
>Thanks for the fix. I had not tested all possible cases, obviously. 
>I'm fine with it, hence just commit unless anybody else objects. CCing Mike.
>
>Best,
>Uwe
>
>
>
>>Index: as.mcmc.list.bugs.R
>>===================================================================
>>--- as.mcmc.list.bugs.R (revision 105)
>>+++ as.mcmc.list.bugs.R (working copy)
>>@@ -5,14 +5,14 @@
>>      if(dim(x$sims.array)[2] != x$n.chains)
>>          stop("Inconsistancy in bug object regarding the number of chains.")
>>      mclis <- vector("list", x$n.chains)
>>-    strt <- x$n.burnin%/%x$n.thin + 1
>>-    end <- x$n.iter%/%x$n.thin
>>+    strt <- x$n.burnin + 1
>>+    end <- x$n.iter
>>      ord <- order(dimnames(x$sims.array)[[3]])
>>-    if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
>>+    ## This is not necedarry, since strt and end match dims of sims.array
>>+    ## if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
>>      for(i in 1:x$n.chains) {
>>          tmp1 <- x$sims.array[,i,ord]
>>-        rownames(tmp1) <- strt:end
>>-        mclis[[i]] <- mcmc(tmp1, strt, end, 1)
>>+        mclis[[i]] <- mcmc(tmp1, start=strt, end=end, thin=x$n.thin)
>>------------------------------------------------------------------------------
>>Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
>>-OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
>>-Strategies to boost innovation and cut costs with open source participation
>>-Receive a $600 discount off the registration fee with the source code: SFAD
>>http://p.sf.net/sfu/XcvMzF8H
>>_______________________________________________
>>Bugs-r-devel mailing list
>>Bug...@li...
>>https://lists.sourceforge.net/lists/listinfo/bugs-r-devel
>
>===============================================
>Michael E Meredith
>Wildlife Conservation Society (WCS) Malaysia Program
>7 Jalan Ridgeway, 93250 Kuching, Malaysia
>Fax: +60-82-577 443 Mobile: +60-19 888 1533
>email: mme...@wc...
>Program website: http://www.wcsmalaysia.org 

[Bugs-r-devel] SF.net SVN: bugs-r:[107] trunk/R2WinBUGS

[<gg...@us...>]

Revision: 107
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=107&view=rev
Author:   ggorjan
Date:     2009-02-20 15:11:48 +0000 (Fri, 20 Feb 2009)

Log Message:
-----------
- properly using chain parameters in as.mcmc.list.bugs
- documentation fix

Modified Paths:
--------------
    trunk/R2WinBUGS/R/as.mcmc.list.bugs.R
    trunk/R2WinBUGS/inst/NEWS

Modified: trunk/R2WinBUGS/R/as.mcmc.list.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/as.mcmc.list.bugs.R	2009-02-20 00:12:21 UTC (rev 106)
+++ trunk/R2WinBUGS/R/as.mcmc.list.bugs.R	2009-02-20 15:11:48 UTC (rev 107)
@@ -1,18 +1,17 @@
-## Function as.mcmc.list.bugs contributed by Mike Meredith, 12 Feb 2009:
-as.mcmc.list.bugs <- function(x, ...) {
+
+as.mcmc.list.bugs <- function(x, ...)
+{
     if(!inherits(x, "bugs")) 
         stop("Method as.mcmc.list.bugs() is only intended for bugs objects.")
     if(dim(x$sims.array)[2] != x$n.chains)
         stop("Inconsistancy in bug object regarding the number of chains.")
     mclis <- vector("list", x$n.chains)
-    strt <- x$n.burnin%/%x$n.thin + 1
-    end <- x$n.iter%/%x$n.thin
+    strt <- x$n.burnin + 1
+    end <- x$n.iter
     ord <- order(dimnames(x$sims.array)[[3]])
-    if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
     for(i in 1:x$n.chains) {
         tmp1 <- x$sims.array[,i,ord]
-        rownames(tmp1) <- strt:end
-        mclis[[i]] <- mcmc(tmp1, strt, end, 1)
+        mclis[[i]] <- mcmc(tmp1, start=strt, end=end, thin=x$n.thin)
     }
     as.mcmc.list(mclis)
-} 
+} 
\ No newline at end of file

Modified: trunk/R2WinBUGS/inst/NEWS
===================================================================
--- trunk/R2WinBUGS/inst/NEWS	2009-02-20 00:12:21 UTC (rev 106)
+++ trunk/R2WinBUGS/inst/NEWS	2009-02-20 15:11:48 UTC (rev 107)
@@ -1,6 +1,10 @@
 Changes to R2WinBUGS:
 =====================
 
+Update 2.1-13
+- properly using chain parameters in as.mcmc.list.bugs
+- documentation fix
+
 Update 2.1-12
 - new method as.mcmc.list.bugs contributed by Mike Meredith
 - bugfix: plot.bugs() did not reset par(mfrow)


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.

Re: [Bugs-r-devel] as.mcmc.list

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

Gorjanc Gregor wrote:
> Hi,
> 
> Recently as.mcmc.list.bugs has been introduced as contrbuted by Mike Meredith.
> I think there are some flaws. For example. I have an bugs object with the following details:
> 
> 3 chains, each with 1e+05 iterations (first 10000 discarded), n.thin = 10 n.sims = 27000 iterations saved
> 
> i.e.
> 
> List of 24
>  $ n.chains       : num 3
>  $ n.iter         : num 1e+05
>  $ n.burnin       : num 10000
>  $ n.thin         : num 10
>  $ n.keep         : num 9000
>  $ n.sims         : num 27000
> 
> however, when I create an mcmc object I get
> 
> List of 3
>  $ : mcmc [1:9000, 1:59] 12 12.4 12.8 13.1 12.1 ...
>   ..- attr(*, "dimnames")=List of 2
>   .. ..$ : chr [1:9000] "1001" "1002" "1003" "1004" ...
>   .. ..$ : chr [1:59] "alpha" "deviance" "l[10]" "l[11]" ...
>   ..- attr(*, "mcpar")= num [1:3] 1001 10000 1
> ...
> 
> The last line, i.e., the mcpar, is wrong. It should be
> 
>   ..- attr(*, "mcpar")= num [1:3] 10001 100000 10
> 
> I also do not see the point in setting the rownames, since they are not reflecting the reality, i.e.,
> my chains where thinned, but the rownames are 1001, 1002, ...
> 
> Bellow is the diff of the "fixed" function, but before I commit it, I would like to make sure
> there is consensus about this. I could not find Mikes e-mail. Uwe?

Thanks for the fix. I had not tested all possible cases, obviously. I'm 
fine with it, hence just commit unless anybody else objects. CCing Mike.

Best,
Uwe



> Index: as.mcmc.list.bugs.R
> ===================================================================
> --- as.mcmc.list.bugs.R (revision 105)
> +++ as.mcmc.list.bugs.R (working copy)
> @@ -5,14 +5,14 @@
>      if(dim(x$sims.array)[2] != x$n.chains)
>          stop("Inconsistancy in bug object regarding the number of chains.")
>      mclis <- vector("list", x$n.chains)
> -    strt <- x$n.burnin%/%x$n.thin + 1
> -    end <- x$n.iter%/%x$n.thin
> +    strt <- x$n.burnin + 1
> +    end <- x$n.iter
>      ord <- order(dimnames(x$sims.array)[[3]])
> -    if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
> +    ## This is not necedarry, since strt and end match dims of sims.array
> +    ## if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
>      for(i in 1:x$n.chains) {
>          tmp1 <- x$sims.array[,i,ord]
> -        rownames(tmp1) <- strt:end
> -        mclis[[i]] <- mcmc(tmp1, strt, end, 1)
> +        mclis[[i]] <- mcmc(tmp1, start=strt, end=end, thin=x$n.thin)
> 
> ------------------------------------------------------------------------------
> Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA
> -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise
> -Strategies to boost innovation and cut costs with open source participation
> -Receive a $600 discount off the registration fee with the source code: SFAD
> http://p.sf.net/sfu/XcvMzF8H
> _______________________________________________
> Bugs-r-devel mailing list
> Bug...@li...
> https://lists.sourceforge.net/lists/listinfo/bugs-r-devel

[Bugs-r-devel] as.mcmc.list

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

Hi,

Recently as.mcmc.list.bugs has been introduced as contrbuted by Mike Meredith.
I think there are some flaws. For example. I have an bugs object with the following details:

3 chains, each with 1e+05 iterations (first 10000 discarded), n.thin = 10 n.sims = 27000 iterations saved

i.e.

List of 24
 $ n.chains       : num 3
 $ n.iter         : num 1e+05
 $ n.burnin       : num 10000
 $ n.thin         : num 10
 $ n.keep         : num 9000
 $ n.sims         : num 27000

however, when I create an mcmc object I get

List of 3
 $ : mcmc [1:9000, 1:59] 12 12.4 12.8 13.1 12.1 ...
  ..- attr(*, "dimnames")=List of 2
  .. ..$ : chr [1:9000] "1001" "1002" "1003" "1004" ...
  .. ..$ : chr [1:59] "alpha" "deviance" "l[10]" "l[11]" ...
  ..- attr(*, "mcpar")= num [1:3] 1001 10000 1
...

The last line, i.e., the mcpar, is wrong. It should be

  ..- attr(*, "mcpar")= num [1:3] 10001 100000 10

I also do not see the point in setting the rownames, since they are not reflecting the reality, i.e.,
my chains where thinned, but the rownames are 1001, 1002, ...

Bellow is the diff of the "fixed" function, but before I commit it, I would like to make sure
there is consensus about this. I could not find Mikes e-mail. Uwe?

Index: as.mcmc.list.bugs.R
===================================================================
--- as.mcmc.list.bugs.R (revision 105)
+++ as.mcmc.list.bugs.R (working copy)
@@ -5,14 +5,14 @@
     if(dim(x$sims.array)[2] != x$n.chains)
         stop("Inconsistancy in bug object regarding the number of chains.")
     mclis <- vector("list", x$n.chains)
-    strt <- x$n.burnin%/%x$n.thin + 1
-    end <- x$n.iter%/%x$n.thin
+    strt <- x$n.burnin + 1
+    end <- x$n.iter
     ord <- order(dimnames(x$sims.array)[[3]])
-    if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
+    ## This is not necedarry, since strt and end match dims of sims.array
+    ## if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
     for(i in 1:x$n.chains) {
         tmp1 <- x$sims.array[,i,ord]
-        rownames(tmp1) <- strt:end
-        mclis[[i]] <- mcmc(tmp1, strt, end, 1)
+        mclis[[i]] <- mcmc(tmp1, start=strt, end=end, thin=x$n.thin)

[Bugs-r-devel] SF.net SVN: bugs-r:[106] trunk/R2WinBUGS/man/bugs.Rd

[<gg...@us...>]

Revision: 106
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=106&view=rev
Author:   ggorjan
Date:     2009-02-20 00:12:21 +0000 (Fri, 20 Feb 2009)

Log Message:
-----------
Fixed typo.

Modified Paths:
--------------
    trunk/R2WinBUGS/man/bugs.Rd

Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd	2009-02-15 18:56:29 UTC (rev 105)
+++ trunk/R2WinBUGS/man/bugs.Rd	2009-02-20 00:12:21 UTC (rev 106)
@@ -142,12 +142,12 @@
 
   If \code{useWINE=TRUE} is used, all paths (such as
   \code{working.directory} and \code{model.file}, must be given in
-  native (Unix) style, but \code{working.directory} can be given in
+  native (Unix) style, but \code{bugs.directory} can be given in
   Windows path style (e.g. \dQuote{c:/Program Files/WinBUGS14/}) or
   native (Unix) style
   (e.g. \dQuote{/path/to/wine/folder/dosdevices/c:/Program
   Files/WinBUGS14}).  This is done to achieve greatest portability with
-  default argument value for \code{working.directory}.
+  default argument value for \code{bugs.directory}.
 
 }
 


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[Bugs-r-devel] SF.net SVN: bugs-r:[105] trunk/BRugs

[<li...@us...>]

Revision: 105
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=105&view=rev
Author:   ligges
Date:     2009-02-15 18:56:29 +0000 (Sun, 15 Feb 2009)

Log Message:
-----------
move to tempdir() usage in BRugs

Modified Paths:
--------------
    trunk/BRugs/DESCRIPTION
    trunk/BRugs/NAMESPACE
    trunk/BRugs/R/BRugsFit.R
    trunk/BRugs/R/bugs.data.R
    trunk/BRugs/R/bugs.inits.R
    trunk/BRugs/man/BRugsFit.Rd
    trunk/BRugs/man/bugs.data.Rd
    trunk/BRugs/man/bugs.inits.Rd

Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION	2009-02-13 11:19:57 UTC (rev 104)
+++ trunk/BRugs/DESCRIPTION	2009-02-15 18:56:29 UTC (rev 105)
@@ -1,7 +1,7 @@
 Package: BRugs
 Title: OpenBUGS and its R / S-PLUS interface BRugs
-Version: 0.4-3
-Date: 2009-01-20
+Version: 0.5-0
+Date: 2009-02-15
 Author: The Chief Software Bug is Andrew Thomas, with web assistance from Real Bug Bob O'Hara. Other members of the BUGS team are statisticians David Spiegelhalter, Nicky Best, Dave Lunn and Ken Rice. Dave Lunn has also made major contributions to the software development. R Code modified, extended and packaged for R by Uwe Ligges and Sibylle Sturtz. Some ideas taken from the R2WinBUGS package based on code by Andrew Gelman.
 Description: An R / S-PLUS package containing OpenBUGS and its R / S-PLUS interface BRugs.
 Maintainer: Uwe Ligges <li...@st...>

Modified: trunk/BRugs/NAMESPACE
===================================================================
--- trunk/BRugs/NAMESPACE	2009-02-13 11:19:57 UTC (rev 104)
+++ trunk/BRugs/NAMESPACE	2009-02-15 18:56:29 UTC (rev 105)
@@ -1,5 +1,5 @@
 useDynLib(BRugs)
-importFrom(coda, mcmc)
+importFrom(coda, mcmc, mcmc.list)
 export(BRugsFit, bugsData, bugsInits, buildMCMC, currentValues,
 dicClear, dicSet, dicStats,
 getNumChains, help.BRugs, help.WinBUGS,

Modified: trunk/BRugs/R/BRugsFit.R
===================================================================
--- trunk/BRugs/R/BRugsFit.R	2009-02-13 11:19:57 UTC (rev 104)
+++ trunk/BRugs/R/BRugsFit.R	2009-02-15 18:56:29 UTC (rev 105)
@@ -1,6 +1,6 @@
 BRugsFit <-
 function(modelFile, data, inits, numChains = 3, parametersToSave,
-    nBurnin = 1000, nIter = 1000, nThin = 1,
+    nBurnin = 1000, nIter = 1000, nThin = 1, coda = FALSE,
     DIC = TRUE, working.directory = NULL, digits = 5, 
     BRugsVerbose = getOption("BRugsVerbose")){
 
@@ -43,5 +43,8 @@
   modelUpdate(nIter)
   sims <- samplesStats("*")
 #  class(sims) <- "BRugsFit"
-  return(list(Stats = sims, DIC = if(DIC) dicStats()))
+  if(coda)
+    return(buildMCMC("*"))
+  else 
+    return(list(Stats = sims, DIC = if(DIC) dicStats()))
 }

Modified: trunk/BRugs/R/bugs.data.R
===================================================================
--- trunk/BRugs/R/bugs.data.R	2009-02-13 11:19:57 UTC (rev 104)
+++ trunk/BRugs/R/bugs.data.R	2009-02-15 18:56:29 UTC (rev 105)
@@ -1,5 +1,5 @@
 "bugsData" <- 
-function(data, fileName = file.path(getwd(), "data.txt"), digits = 5){
+function(data, fileName = file.path(tempdir(), "data.txt"), digits = 5){
   if(is.numeric(unlist(data)))
         if(is.R()) {
             write.datafile(lapply(data, formatC, digits = digits, format = "E"), fileName)

Modified: trunk/BRugs/R/bugs.inits.R
===================================================================
--- trunk/BRugs/R/bugs.inits.R	2009-02-13 11:19:57 UTC (rev 104)
+++ trunk/BRugs/R/bugs.inits.R	2009-02-15 18:56:29 UTC (rev 105)
@@ -1,7 +1,7 @@
 "bugsInits" <-
 function (inits, numChains = 1, fileName, digits = 5){
     if(missing(fileName))
-        fileName <- file.path(getwd(), paste("inits", 1:numChains, ".txt", sep = ""))
+        fileName <- file.path(tempdir(), paste("inits", 1:numChains, ".txt", sep = ""))
     if(length(fileName) != numChains)
         stop("numChains = ", numChains, " filenames must be specified")
     if(!is.null(inits)){

Modified: trunk/BRugs/man/BRugsFit.Rd
===================================================================
--- trunk/BRugs/man/BRugsFit.Rd	2009-02-13 11:19:57 UTC (rev 104)
+++ trunk/BRugs/man/BRugsFit.Rd	2009-02-15 18:56:29 UTC (rev 105)
@@ -4,7 +4,7 @@
 \description{This function takes model, data and starting values as input and automatically runs a simulation in BRugs.}
 \usage{
 BRugsFit(modelFile, data, inits, numChains = 3, parametersToSave,
-    nBurnin = 1000, nIter = 1000, nThin = 1,
+    nBurnin = 1000, nIter = 1000, nThin = 1, coda = FALSE,
     DIC = TRUE, working.directory = NULL, digits = 5, 
     BRugsVerbose = getOption("BRugsVerbose"))
 }
@@ -14,13 +14,13 @@
 \item{data}{Either a named list (names corresponding to variable names in the \code{modelFile}) 
     of the data for the OpenBUGS model, \emph{or}
     a vector or list of the names of the data objects used by the model.
-    In these cases data are written into a file \file{data.txt} into the working directory.
+    In these cases data are written into a file \file{data.txt} into the temporary directory of the current R session.
     
     If a filename of an existing file is given, data are read from that file.}
 \item{inits}{A list with \code{numChains} elements; each element of the list is
     itself a list of starting values for the OpenBUGS model, \emph{or}
     a function creating (possibly random) initial values.
-    In these cases inits are written into files \file{inits1.txt}, \dots, \file{initsN.txt} into the working directory.
+    In these cases inits are written into files \file{inits1.txt}, \dots, \file{initsN.txt} into the temporary directory of the current R session.
 
     If a vector of filenames of existing files is given, inits are read from those files.
     Alternatively, if \code{inits} is not specified, initial values are generated by OpenBUGS.}
@@ -29,6 +29,8 @@
 \item{nBurnin}{Length of burn in (before \code{nIter} iterations start).}
 \item{nIter}{Number of iterations (without burn in).}
 \item{nThin}{Every \code{nThin}-th iteration of each chain is stored.}
+\item{coda}{Determines the output format: if \code{FALSE} (default), a list containing sample and DIC statistics is returned.
+    If \code{TRUE}, an \code{\link[coda]{mcmc.list}} object as known from the \pkg{coda} package is returned.}
 \item{DIC}{Logical, whether to calculate and return the DIC.}
 \item{working.directory}{Sets working directory during execution of this function;
     \code{data}, \code{inits} and other files are written to / read from this directory if no other directory 
@@ -39,7 +41,8 @@
     This can be controlled for the whole BRugs package by by the option \sQuote{BRugsVerbose} (see \code{\link{options}})
     which is set to \code{TRUE} by default.}
 }
-\value{A list containg components
+\value{If \code{coda} is set to \kbd{TRUE}, an \code{\link[coda]{mcmc.list}} object as known from the \pkg{coda} package is returned, 
+otherwise a list containg components
 \item{Stats}{A data frame containing sample statistics. See \code{\link{samplesStats}}.}
 \item{DIC}{The DIC statistics, if \code{DIC=TRUE}, else \code{NULL}. See \code{\link{dicStats}}.}
 }

Modified: trunk/BRugs/man/bugs.data.Rd
===================================================================
--- trunk/BRugs/man/bugs.data.Rd	2009-02-13 11:19:57 UTC (rev 104)
+++ trunk/BRugs/man/bugs.data.Rd	2009-02-15 18:56:29 UTC (rev 105)
@@ -3,13 +3,13 @@
 \title{Writing input for OpenBUGS}
 \description{Write data file for OpenBUGS.}
 \usage{
-bugsData(data, fileName = file.path(getwd(), "data.txt"), digits = 5)
+bugsData(data, fileName = file.path(tempdir(), "data.txt"), digits = 5)
 }
 \arguments{
   \item{data}{either a named list (names corresponding to variable names in the model file)
     of the data for the OpenBUGS model, \emph{or}
     a vector or list of the names of the data objects used by the model}
-  \item{fileName}{the filename, defaults to \file{data.txt} in the current working directory}
+  \item{fileName}{the filename, defaults to \file{data.txt} in the temporary directory of the current R session}
   \item{digits}{number of significant digits used for OpenBUGS input, see \code{\link{formatC}}}
 }
 \value{

Modified: trunk/BRugs/man/bugs.inits.Rd
===================================================================
--- trunk/BRugs/man/bugs.inits.Rd	2009-02-13 11:19:57 UTC (rev 104)
+++ trunk/BRugs/man/bugs.inits.Rd	2009-02-15 18:56:29 UTC (rev 105)
@@ -11,7 +11,7 @@
     a function creating (possibly random) initial values}
   \item{numChains}{number of Markov chains}
   \item{fileName}{the filename(s), one for each chain.
-    Defaults to \file{inits1.txt}, ..., \file{initsN.txt} in the current working directory.}
+    Defaults to \file{inits1.txt}, ..., \file{initsN.txt} in the temporary directory of the current R session.}
   \item{digits}{number of significant digits used for OpenBUGS input, see \code{\link{formatC}}}
 }
 \value{
@@ -20,4 +20,3 @@
 \seealso{\code{\link{BRugs}}}
 \keyword{file}
 \concept{init}
-


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[Bugs-r-devel] SF.net SVN: bugs-r:[104] trunk/R2WinBUGS/NAMESPACE

[<li...@us...>]

Revision: 104
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=104&view=rev
Author:   ligges
Date:     2009-02-13 11:19:57 +0000 (Fri, 13 Feb 2009)

Log Message:
-----------
one more import directive forgotten

Modified Paths:
--------------
    trunk/R2WinBUGS/NAMESPACE

Modified: trunk/R2WinBUGS/NAMESPACE
===================================================================
--- trunk/R2WinBUGS/NAMESPACE	2009-02-12 18:51:52 UTC (rev 103)
+++ trunk/R2WinBUGS/NAMESPACE	2009-02-13 11:19:57 UTC (rev 104)
@@ -1,4 +1,4 @@
-importFrom(coda, mcmc.list, read.coda)
+importFrom(coda, mcmc.list, as.mcmc.list, read.coda)
 
 export(bugs,
        attach.all,


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[Bugs-r-devel] SF.net SVN: bugs-r:[103] trunk/R2WinBUGS

[<li...@us...>]

Revision: 103
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=103&view=rev
Author:   ligges
Date:     2009-02-12 18:51:52 +0000 (Thu, 12 Feb 2009)

Log Message:
-----------
let openbugs work in the temporary directory as well, and update the docs

Modified Paths:
--------------
    trunk/R2WinBUGS/R/bugs.R
    trunk/R2WinBUGS/R/openbugs.R
    trunk/R2WinBUGS/man/openbugs.Rd

Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R	2009-02-12 12:28:59 UTC (rev 102)
+++ trunk/R2WinBUGS/R/bugs.R	2009-02-12 18:51:52 UTC (rev 103)
@@ -80,7 +80,7 @@
        (regexpr("\\.txt$", data) > 0))) {
     bugs.data.file <- bugs.data(data, dir = getwd(), digits)
   } else {
-    if(inTempDir && basename(data) == data)
+    if(inTempDir && all(basename(data) == data))
         try(file.copy(file.path(savedWD, data), data, overwrite = TRUE))
     if(!file.exists(data))
         stop("File", data, "does not exist.")

Modified: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R	2009-02-12 12:28:59 UTC (rev 102)
+++ trunk/R2WinBUGS/R/openbugs.R	2009-02-12 18:51:52 UTC (rev 103)
@@ -21,11 +21,14 @@
   ## Move to working drirectory or temporary directory when NULL
   if(is.null(working.directory)) {
     working.directory <- tempdir()
+    inTempDir <- TRUE
   }
   savedWD <- getwd()
   setwd(working.directory)
   on.exit(setwd(savedWD))
 
+  if(inTempDir && basename(model.file) == model.file)
+    try(file.copy(file.path(savedWD, model.file), model.file, overwrite = TRUE))
   if(!file.exists(modelFile)) {
     stop(modelFile, " does not exist")
   }
@@ -42,6 +45,8 @@
   if(!(is.vector(data) && is.character(data) && all(file.exists(data)))) {
     data <- BRugs::bugsData(data, digits = digits)
   }
+  if(inTempDir && all(basename(data) == data))
+    try(file.copy(file.path(savedWD, data), data, overwrite = TRUE))
   BRugs::modelData(data)
   BRugs::modelCompile(numChains)
   if(missing(inits) || is.null(inits)) {
@@ -52,6 +57,8 @@
       inits <- BRugs::bugsInits(inits = inits, numChains = numChains,
                                 digits = digits)
     }
+    if(inTempDir && all(basename(inits) == inits))
+        try(file.copy(file.path(savedWD, inits), inits, overwrite = TRUE))
     BRugs::modelInits(inits)
     BRugs::modelGenInits()
   }
@@ -67,8 +74,10 @@
 #  factories <- sub(".adaptivePhase", "",
 #                   adaptivelines[grep("adaptivePhase",adaptivelines)])
 #  sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
-  cat("Start to sample ...\n")
-  flush.console()
+  if(getOption("BRugsVerbose")){   
+    cat("Sampling has been started ...\n")
+    flush.console()
+  }
   BRugs::modelUpdate(nBurnin)
   ## BRugs::samplesSetThin(nThin)
   if(DIC) {

Modified: trunk/R2WinBUGS/man/openbugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/openbugs.Rd	2009-02-12 12:28:59 UTC (rev 102)
+++ trunk/R2WinBUGS/man/openbugs.Rd	2009-02-12 18:51:52 UTC (rev 103)
@@ -55,7 +55,8 @@
     - currently unused}
   \item{working.directory}{sets working directory during execution of
     this function; \pkg{WinBUGS} in- and output will be stored in this
-    directory; if \code{NULL}, the current working directory is chosen.}
+    directory; if \code{NULL}, a temporary working directory via
+    \code{\link{tempdir}} is used.}
 
 }
 
@@ -68,7 +69,7 @@
 }
 
 \note{By default, BRugs (and hence \code{openbugs()}) is quite verbose. 
-    This can be controlled for the whole BRugs package by by the option \sQuote{BRugsVerbose} (see \code{\link{options}})
+    This can be controlled for the whole BRugs package by the option \sQuote{BRugsVerbose} (see \code{\link{options}})
     which is set to \code{TRUE} by default.
 }
 


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[Bugs-r-devel] SF.net SVN: bugs-r:[102] trunk/R2WinBUGS/inst/NEWS

[<li...@us...>]

Revision: 102
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=102&view=rev
Author:   ligges
Date:     2009-02-12 12:28:59 +0000 (Thu, 12 Feb 2009)

Log Message:
-----------
update

Modified Paths:
--------------
    trunk/R2WinBUGS/inst/NEWS

Modified: trunk/R2WinBUGS/inst/NEWS
===================================================================
--- trunk/R2WinBUGS/inst/NEWS	2009-02-12 12:26:22 UTC (rev 101)
+++ trunk/R2WinBUGS/inst/NEWS	2009-02-12 12:28:59 UTC (rev 102)
@@ -2,6 +2,7 @@
 =====================
 
 Update 2.1-12
+- new method as.mcmc.list.bugs contributed by Mike Meredith
 - bugfix: plot.bugs() did not reset par(mfrow)
 - bugfix: adaptive phase stuff cannot read from files anymore by openbugs(),
           feature has been removed


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[Bugs-r-devel] SF.net SVN: bugs-r:[101] trunk/R2WinBUGS

[<li...@us...>]

Revision: 101
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=101&view=rev
Author:   ligges
Date:     2009-02-12 12:26:22 +0000 (Thu, 12 Feb 2009)

Log Message:
-----------
as.mcmc.list.bugs method implemented (contributed by Mike Meredith)

Modified Paths:
--------------
    trunk/R2WinBUGS/NAMESPACE
    trunk/R2WinBUGS/R/bugs.sims.R
    trunk/R2WinBUGS/man/bugs.Rd

Added Paths:
-----------
    trunk/R2WinBUGS/R/as.mcmc.list.bugs.R

Modified: trunk/R2WinBUGS/NAMESPACE
===================================================================
--- trunk/R2WinBUGS/NAMESPACE	2009-02-12 11:17:21 UTC (rev 100)
+++ trunk/R2WinBUGS/NAMESPACE	2009-02-12 12:26:22 UTC (rev 101)
@@ -15,4 +15,4 @@
 
 S3method(print, bugs)
 S3method(plot, bugs)
-
+S3method(as.mcmc.list, bugs)

Added: trunk/R2WinBUGS/R/as.mcmc.list.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/as.mcmc.list.bugs.R	                        (rev 0)
+++ trunk/R2WinBUGS/R/as.mcmc.list.bugs.R	2009-02-12 12:26:22 UTC (rev 101)
@@ -0,0 +1,18 @@
+## Function as.mcmc.list.bugs contributed by Mike Meredith, 12 Feb 2009:
+as.mcmc.list.bugs <- function(x, ...) {
+    if(!inherits(x, "bugs")) 
+        stop("Method as.mcmc.list.bugs() is only intended for bugs objects.")
+    if(dim(x$sims.array)[2] != x$n.chains)
+        stop("Inconsistancy in bug object regarding the number of chains.")
+    mclis <- vector("list", x$n.chains)
+    strt <- x$n.burnin%/%x$n.thin + 1
+    end <- x$n.iter%/%x$n.thin
+    ord <- order(dimnames(x$sims.array)[[3]])
+    if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
+    for(i in 1:x$n.chains) {
+        tmp1 <- x$sims.array[,i,ord]
+        rownames(tmp1) <- strt:end
+        mclis[[i]] <- mcmc(tmp1, strt, end, 1)
+    }
+    as.mcmc.list(mclis)
+} 

Modified: trunk/R2WinBUGS/R/bugs.sims.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.sims.R	2009-02-12 11:17:21 UTC (rev 100)
+++ trunk/R2WinBUGS/R/bugs.sims.R	2009-02-12 12:26:22 UTC (rev 101)
@@ -123,7 +123,7 @@
   if(DIC) {
      ## Read DIC from BUGS log
      LOG <- bugs.log("log.txt")$DIC
-     if(any(is.na(LOG))) { ## Something went wrong --> Use Gelmans tweak
+     if(any(is.na(LOG))) { ## Something went wrong --> Use Gelman's tweak
         deviance <- all$sims.array[, , dim(sims.array)[3], drop = FALSE]
         if(!is.R()) dimnames(deviance) <- NULL
         dim(deviance) <- dim(deviance)[1:2]

Modified: trunk/R2WinBUGS/man/bugs.Rd
===================================================================
--- trunk/R2WinBUGS/man/bugs.Rd	2009-02-12 11:17:21 UTC (rev 100)
+++ trunk/R2WinBUGS/man/bugs.Rd	2009-02-12 12:26:22 UTC (rev 101)
@@ -71,7 +71,10 @@
   \item{codaPkg}{logical; if \code{FALSE} (default) a \code{bugs} object
     is returned, if \code{TRUE} file names of \pkg{WinBUGS} output are
     returned for easy access by the \pkg{coda} package through function
-    \code{\link{read.bugs}} (not used if \code{program="OpenBUGS"}).}
+    \code{\link{read.bugs}} (not used if \code{program="OpenBUGS"}).
+    A \code{bugs} object can be converted to an \code{mcmc.list} object as 
+    used by the \pkg{coda} package with the method \code{\link[coda]{as.mcmc.list}} 
+    (for which a method is provided by R2WinBUGS).}
   \item{bugs.directory}{directory that contains the \pkg{WinBUGS} executable.
     If the global option \code{R2WinBUGS.bugs.directory} is not \code{NULL}, 
     it will be used as the default.}


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[Bugs-r-devel] SF.net SVN: bugs-r:[100] trunk/R2WinBUGS

[<li...@us...>]

Revision: 100
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=100&view=rev
Author:   ligges
Date:     2009-02-12 11:17:21 +0000 (Thu, 12 Feb 2009)

Log Message:
-----------
- bugfix: plot.bugs() did not reset par(mfrow)
- bugfix: adaptive phase stuff cannot be read anymore by openbugs(), files are no longer shipped, feature has been removed
- openbugs now displays messages before starting the sampling (essentially using flush.console())

Modified Paths:
--------------
    trunk/R2WinBUGS/DESCRIPTION
    trunk/R2WinBUGS/R/openbugs.R
    trunk/R2WinBUGS/R/plot.bugs.R
    trunk/R2WinBUGS/inst/NEWS

Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION	2009-02-02 14:30:50 UTC (rev 99)
+++ trunk/R2WinBUGS/DESCRIPTION	2009-02-12 11:17:21 UTC (rev 100)
@@ -1,7 +1,7 @@
 Package: R2WinBUGS
 Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2009-02-02
-Version: 2.1-11
+Date: 2009-02-11
+Version: 2.1-12
 Author: originally written by Andrew Gelman <ge...@st...>;
  changes and packaged by Sibylle Sturtz <st...@st...>
  and Uwe Ligges <li...@st...>.

Modified: trunk/R2WinBUGS/R/openbugs.R
===================================================================
--- trunk/R2WinBUGS/R/openbugs.R	2009-02-02 14:30:50 UTC (rev 99)
+++ trunk/R2WinBUGS/R/openbugs.R	2009-02-12 11:17:21 UTC (rev 100)
@@ -57,13 +57,18 @@
   }
   BRugs::samplesSetThin(nThin)
   ## set the adaptive phases
-  adaptivelines <- scan(system.file("OpenBUGS", "Bugs", "Rsrc",
-                                    "Registry.txt", package="BRugs"),
-                        what="character", quiet = TRUE)
-  factories <- sub(".adaptivePhase", "",
-                   adaptivelines[grep("adaptivePhase",adaptivelines)])
-  sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
 
+## We do no longer have any Registry.txt file availabe, 
+## hence not resetting the adaptive phase any more.
+## People should move to BRugs directly.
+#  adaptivelines <- scan(system.file("OpenBUGS", "Bugs", "Rsrc",
+#                                    "Registry.txt", package="BRugs"),
+#                        what="character", quiet = TRUE)
+#  factories <- sub(".adaptivePhase", "",
+#                   adaptivelines[grep("adaptivePhase",adaptivelines)])
+#  sapply(factories, BRugs::modelSetAP, max(0, nBurnin-1))
+  cat("Start to sample ...\n")
+  flush.console()
   BRugs::modelUpdate(nBurnin)
   ## BRugs::samplesSetThin(nThin)
   if(DIC) {

Modified: trunk/R2WinBUGS/R/plot.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/plot.bugs.R	2009-02-02 14:30:50 UTC (rev 99)
+++ trunk/R2WinBUGS/R/plot.bugs.R	2009-02-12 11:17:21 UTC (rev 100)
@@ -1,11 +1,12 @@
 plot.bugs <- function (x, display.parallel = FALSE, ...){
     mar.old <- par("mar")
     pty.old <- par(pty = "m")
+    mfrow.old <- par("mfrow")
     if (is.R())
-    	layout(matrix(c(1,2),1,2))
+        layout(matrix(c(1,2),1,2))
     else
-    	par(mfrow = c(1,2))
-    	
+        par(mfrow = c(1,2))
+        
     bugs.plot.summary (x, ...)
     bugs.plot.inferences (x, display.parallel, ...)
     header <- ""
@@ -16,8 +17,8 @@
     header <- paste(header, x$n.chains, " chains, each with ",
         x$n.iter, " iterations (first ", x$n.burnin, " discarded)", sep = "")
     mtext(header, outer = TRUE, line = -1, cex = 0.7)
-    if (is.R())  par(pty = pty.old[[1]], mar = mar.old)
-    else  invisible(par(pty = pty.old[[1]], mar = mar.old))
+    if (is.R())  par(pty = pty.old[[1]], mar = mar.old, mfrow = mfrow.old)
+    else  invisible(par(pty = pty.old[[1]], mar = mar.old, mfrow = mfrow.old))
 }
 
 if (!is.R()) {

Modified: trunk/R2WinBUGS/inst/NEWS
===================================================================
--- trunk/R2WinBUGS/inst/NEWS	2009-02-02 14:30:50 UTC (rev 99)
+++ trunk/R2WinBUGS/inst/NEWS	2009-02-12 11:17:21 UTC (rev 100)
@@ -1,6 +1,14 @@
 Changes to R2WinBUGS:
 =====================
 
+Update 2.1-12
+- bugfix: plot.bugs() did not reset par(mfrow)
+- bugfix: adaptive phase stuff cannot read from files anymore by openbugs(),
+          feature has been removed
+- openbugs now displays messages before starting the sampling 
+  (essentially using flush.console())
+
+
 Update 2.1-11
 - bugfix: if working.directory was unset and files are assumed to be in R's 
   former wd, these are copied to the tempdir that is set as new working 


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[Bugs-r-devel] SF.net SVN: bugs-r:[99] trunk/R2WinBUGS

[<li...@us...>]

Revision: 99
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=99&view=rev
Author:   ligges
Date:     2009-02-02 14:30:50 +0000 (Mon, 02 Feb 2009)

Log Message:
-----------
yet another working directory issue

Modified Paths:
--------------
    trunk/R2WinBUGS/DESCRIPTION
    trunk/R2WinBUGS/R/bugs.R
    trunk/R2WinBUGS/inst/NEWS

Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION	2009-01-20 17:17:55 UTC (rev 98)
+++ trunk/R2WinBUGS/DESCRIPTION	2009-02-02 14:30:50 UTC (rev 99)
@@ -1,7 +1,7 @@
 Package: R2WinBUGS
 Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2009-01-20
-Version: 2.1-10
+Date: 2009-02-02
+Version: 2.1-11
 Author: originally written by Andrew Gelman <ge...@st...>;
  changes and packaged by Sibylle Sturtz <st...@st...>
  and Uwe Ligges <li...@st...>.

Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R	2009-01-20 17:17:55 UTC (rev 98)
+++ trunk/R2WinBUGS/R/bugs.R	2009-02-02 14:30:50 UTC (rev 99)
@@ -42,6 +42,7 @@
   }
 
   ## Move to working drirectory or temporary directory when NULL
+  inTempDir <- FALSE
   if(is.null(working.directory)) {
     working.directory <- tempdir()
     if(useWINE){
@@ -53,6 +54,7 @@
     savedWD <- getwd()
     setwd(working.directory)
     on.exit(setwd(savedWD), add = TRUE)
+    inTempDir <- TRUE
   }
 
   ## model.file is not a file name but a model function
@@ -68,6 +70,8 @@
       model.file <- gsub("\\\\", "/", temp)
       if(!is.R()) on.exit(file.remove(model.file), add=TRUE)
   }
+  if(inTempDir && basename(model.file) == model.file)
+    try(file.copy(file.path(savedWD, model.file), model.file, overwrite = TRUE))
   if(!file.exists(model.file))
     stop(paste(model.file, "does not exist."))
   if(file.info(model.file)$isdir)
@@ -76,13 +80,16 @@
        (regexpr("\\.txt$", data) > 0))) {
     bugs.data.file <- bugs.data(data, dir = getwd(), digits)
   } else {
+    if(inTempDir && basename(data) == data)
+        try(file.copy(file.path(savedWD, data), data, overwrite = TRUE))
     if(!file.exists(data))
         stop("File", data, "does not exist.")
     bugs.data.file <- data
   }
 
-
   if (is.character(inits)) {
+    if(inTempDir && all(basename(inits) == inits))
+        try(file.copy(file.path(savedWD, inits), inits, overwrite = TRUE))
     if (!all(file.exists(inits))) {
         stop("One or more inits files are missing")
     }

Modified: trunk/R2WinBUGS/inst/NEWS
===================================================================
--- trunk/R2WinBUGS/inst/NEWS	2009-01-20 17:17:55 UTC (rev 98)
+++ trunk/R2WinBUGS/inst/NEWS	2009-02-02 14:30:50 UTC (rev 99)
@@ -1,6 +1,11 @@
 Changes to R2WinBUGS:
 =====================
 
+Update 2.1-11
+- bugfix: if working.directory was unset and files are assumed to be in R's 
+  former wd, these are copied to the tempdir that is set as new working 
+  directory now.
+
 Update 2.1-10
 - bugfix: working.directory was not always reset when function terminated.
 


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