bugs-r-devel

[Bugs-r-devel] SF.net SVN: bugs-r:[98] trunk/BRugs/man/model.save.state.Rd

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

Revision: 98
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=98&view=rev
Author:   ligges
Date:     2009-01-20 17:17:55 +0000 (Tue, 20 Jan 2009)

Log Message:
-----------
note by install process, hence empty value removed

Modified Paths:
--------------
    trunk/BRugs/man/model.save.state.Rd

Modified: trunk/BRugs/man/model.save.state.Rd
===================================================================
--- trunk/BRugs/man/model.save.state.Rd	2009-01-20 17:15:40 UTC (rev 97)
+++ trunk/BRugs/man/model.save.state.Rd	2009-01-20 17:17:55 UTC (rev 98)
@@ -8,8 +8,6 @@
 \arguments{
   \item{stem}{?????.}
 }
-\value{
-}
 \note{This function can be executed once a model has been successfully checked 
   ????? 
 (see \code{\link{modelCheck}}).


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[Bugs-r-devel] SF.net SVN: bugs-r:[97] trunk/BRugs

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

Revision: 97
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=97&view=rev
Author:   ligges
Date:     2009-01-20 17:15:40 +0000 (Tue, 20 Jan 2009)

Log Message:
-----------
bugfix release: 
- a device has been opened even if plot=FALSE in samples*()
- tests incorrect (OpenBUGS version)

Modified Paths:
--------------
    trunk/BRugs/DESCRIPTION
    trunk/BRugs/R/samples.autoC.R
    trunk/BRugs/R/samples.bgr.R
    trunk/BRugs/R/samples.density.R
    trunk/BRugs/R/samples.history.R
    trunk/BRugs/tests/BRugs.Rout.save

Modified: trunk/BRugs/DESCRIPTION
===================================================================
--- trunk/BRugs/DESCRIPTION	2009-01-20 15:28:01 UTC (rev 96)
+++ trunk/BRugs/DESCRIPTION	2009-01-20 17:15:40 UTC (rev 97)
@@ -1,7 +1,7 @@
 Package: BRugs
 Title: OpenBUGS and its R / S-PLUS interface BRugs
-Version: 0.4-2
-Date: 2007-09-20
+Version: 0.4-3
+Date: 2009-01-20
 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/R/samples.autoC.R
===================================================================
--- trunk/BRugs/R/samples.autoC.R	2009-01-20 15:28:01 UTC (rev 96)
+++ trunk/BRugs/R/samples.autoC.R	2009-01-20 17:15:40 UTC (rev 97)
@@ -3,7 +3,7 @@
 thin = samplesGetThin(), plot = TRUE, mfrow = c(3, 2), ask = NULL, ann = TRUE, ...)
 #   Plot auto correlation function
 {
-    if(is.null(ask)) {
+    if(plot && is.null(ask)) {
       if (is.R())
         ask <- !((dev.cur() > 1) && !dev.interactive())
       else
@@ -31,10 +31,12 @@
     thin <- max(c(thin, 1))
     samplesSetThin(thin)
     mons <- samplesMonitors(node)
-    if (is.R())
-      par(mfrow = mfrow, ask = ask, ann = ann)
-    else
-      par(mfrow = mfrow, ask = ask)
+    if(plot){
+        if (is.R())
+        par(mfrow = mfrow, ask = ask, ann = ann)
+        else
+        par(mfrow = mfrow, ask = ask)
+    }
     result <- lapply(mons, plotAutoC, plot = plot, ...)
     names(result) <- mons
     if(plot) invisible(result)

Modified: trunk/BRugs/R/samples.bgr.R
===================================================================
--- trunk/BRugs/R/samples.bgr.R	2009-01-20 15:28:01 UTC (rev 96)
+++ trunk/BRugs/R/samples.bgr.R	2009-01-20 17:15:40 UTC (rev 97)
@@ -5,7 +5,7 @@
     ask = NULL, ann = TRUE, ...)
 #   Plot bgr statistic                  
 {
-    if(is.null(ask)) {
+    if(plot && is.null(ask)) {
       if (is.R())
         ask <- !((dev.cur() > 1) && !dev.interactive())
       else
@@ -31,10 +31,12 @@
     thin <- max(c(thin, 1))
     samplesSetThin(thin)
     mons <- samplesMonitors(node)
-    if (is.R())
-      par(mfrow = mfrow, ask = ask, ann = ann)
-    else
-      par(mfrow = mfrow, ask = ask)
+    if(plot){
+        if (is.R())
+        par(mfrow = mfrow, ask = ask, ann = ann)
+        else
+        par(mfrow = mfrow, ask = ask)
+    }
     result <- lapply(mons, plotBgr, bins = bins, plot = plot, ...)
     names(result) <- mons
     if(plot) invisible(result)

Modified: trunk/BRugs/R/samples.density.R
===================================================================
--- trunk/BRugs/R/samples.density.R	2009-01-20 15:28:01 UTC (rev 96)
+++ trunk/BRugs/R/samples.density.R	2009-01-20 17:15:40 UTC (rev 97)
@@ -30,11 +30,11 @@
     thin <- max(c(thin, 1))
     samplesSetThin(thin)
     mons <- samplesMonitors(node)
-		if (is.R())
-      par(mfrow = mfrow, ask = ask, ann = ann)
+    if (is.R())
+        par(mfrow = mfrow, ask = ask, ann = ann)
     else
-      par(mfrow = mfrow, ask = ask)
+        par(mfrow = mfrow, ask = ask)
     junk <- sapply(mons, plotDensity, ...)
     if (!is.R())
-    	invisible()
+        invisible()
 }

Modified: trunk/BRugs/R/samples.history.R
===================================================================
--- trunk/BRugs/R/samples.history.R	2009-01-20 15:28:01 UTC (rev 96)
+++ trunk/BRugs/R/samples.history.R	2009-01-20 17:15:40 UTC (rev 97)
@@ -4,7 +4,7 @@
 thin = samplesGetThin(), plot = TRUE, mfrow = c(3, 1), ask = NULL, ann = TRUE, ...)
 #   Plot history                    
 {
-    if(is.null(ask)) {
+    if(plot && is.null(ask)) {
       if (is.R())
         ask <- !((dev.cur() > 1) && !dev.interactive())
       else
@@ -29,10 +29,12 @@
     thin <- max(c(thin, 1))
     samplesSetThin(thin)
     mons <- samplesMonitors(node)
-    if (is.R())
-      par(mfrow = mfrow, ask = ask, ann = ann)
-    else 
-      par(mfrow = mfrow, ask = ask)
+    if(plot){
+        if (is.R())
+        par(mfrow = mfrow, ask = ask, ann = ann)
+        else 
+        par(mfrow = mfrow, ask = ask)
+    }
     result <- lapply(mons, plotHistory, plot = plot, ...)
     names(result) <- mons
     if(plot) invisible(result)

Modified: trunk/BRugs/tests/BRugs.Rout.save
===================================================================
--- trunk/BRugs/tests/BRugs.Rout.save	2009-01-20 15:28:01 UTC (rev 96)
+++ trunk/BRugs/tests/BRugs.Rout.save	2009-01-20 17:15:40 UTC (rev 97)
@@ -18,7 +18,7 @@
 > library(BRugs)
 Loading required package: coda
 Loading required package: lattice
-Welcome to BRugs running on OpenBUGS version 3.0.1
+Welcome to BRugs running on OpenBUGS version 3.0.3
 > 
 > BRugsFit(data = "ratsdata.txt", inits = "ratsinits.txt", 
 +     para = c("alpha", "beta"), modelFile = "ratsmodel.txt", 


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[Bugs-r-devel] SF.net SVN: bugs-r:[96] trunk/R2WinBUGS

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

Revision: 96
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=96&view=rev
Author:   ligges
Date:     2009-01-20 15:28:01 +0000 (Tue, 20 Jan 2009)

Log Message:
-----------
- NEWS entries for R2WinBUGS >= 0.2-8
- bugfix - working.directory has not been resetted correctly

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

Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION	2009-01-08 17:07:19 UTC (rev 95)
+++ trunk/R2WinBUGS/DESCRIPTION	2009-01-20 15:28:01 UTC (rev 96)
@@ -1,7 +1,7 @@
 Package: R2WinBUGS
 Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2009-01-08
-Version: 2.1-9
+Date: 2009-01-20
+Version: 2.1-10
 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	2009-01-08 17:07:19 UTC (rev 95)
+++ trunk/R2WinBUGS/R/bugs.R	2009-01-20 15:28:01 UTC (rev 96)
@@ -48,12 +48,12 @@
         ## Some tweaks for wine (particularly required for Mac OS)
         working.directory <- gsub("//", "/", working.directory)
         Sys.chmod(working.directory, mode="750")
-        on.exit(Sys.chmod(working.directory, mode="700"))
+        on.exit(Sys.chmod(working.directory, mode="700"), add = TRUE)
     }
+    savedWD <- getwd()
+    setwd(working.directory)
+    on.exit(setwd(savedWD), add = TRUE)
   }
-  savedWD <- getwd()
-  setwd(working.directory)
-  on.exit(setwd(savedWD), add = TRUE)
 
   ## model.file is not a file name but a model function
   if(is.function(model.file)){

Modified: trunk/R2WinBUGS/inst/NEWS
===================================================================
--- trunk/R2WinBUGS/inst/NEWS	2009-01-08 17:07:19 UTC (rev 95)
+++ trunk/R2WinBUGS/inst/NEWS	2009-01-20 15:28:01 UTC (rev 96)
@@ -1,252 +1,256 @@
-Changes to R2WinBUGS:
-=====================
-
-Update 2.1-8?
-- findUnixBinary now fails (with a meaningfull error message) always if the
-  binary file does not exist.
-- If working.directory=NULL (the default setting), then a temporary
-  directory is used as a working directory to prevent overwriting/removing
-  the existing files.
-- File script.txt is also removed when clearWD=TRUE.
-- If model.file does not have a "txt" extension, then it is temporarily
-  copied to a file with "txt" extension in the working directory and
-  removed at the end of WinBUGS run.
-
-Update 2.1-7
-- this file is now available as NEWS file in top folder of installed package
-
-Update 2.1-6 (23 August 2007):
-- reverting back to use thin.updater since it is faster, however CODA files
-  have "wrong" indexes - this needs to be fixed in BUGS program
-- WINE arguments are now set in such a way that defaults work on Windows
-  and Linux
-- minor formatting in the code and help files
-- added R2WinBUGS-package help page
-
-Update 2.1-5 (12 June 2007):
-- proper indexing of CODA files also in R version
-- fixed useWINE documentation in bugs help page
-- note on supported BUGS versions
-- as.bugs.array now returns info on used rule for pD i.e. var(deviance)/2
-    or Dbar-Dhat
-- some internal fixes related to handling of DIC
-- merging and reversing ChangeLog files
-
-Update 2.1-4 (20 May 2007):
-- Depending on coda now (Namespace issues)
-- some more fixes for codetools checks
-- Vignette has been updated
-
-Update 2.1-3 (13 May 2007):
-- Ported to S-PLUS by Insightful Corp.
-- some fixes for codetools checks
-
-Update 2.0-4 (01 November 2006):
-- print.bugs / plot.bugs documentation fixes
-- write.model() fix
-
-Update 2.0-3 (06 October 2006):
-- \\. -> [.] in regular expressions
-
-Update 2.0-2 (26 July 2006):
-- changes for DIC, making use of BUGS internal calculations
-- some doc fixes
-
-Update 2.0-1 (26 May 2006):
-- some wine patches for 2.2-0 by Gregor Gorjanc
-
-Update 2.0-0 (08 May 2006):
-- bugs() doc fix/updates on scrambling
-- bugs.run() has new arg useWINE (by Gregor Gorjanc)
-- bugs() and bugs.script() patched for WINEPATH issue
-- bugs.script() changed to save log file in ASCII
-- new function bugs.log() by Gregor Gorjanc
-- new functions as.bugs.array, openbugs and sort.name by
-  Jouni Kerman and Andrew Gelman
-- new function write.model() based on ideas from Jouni Kerman
-
-Update 1.1-1 (17 Feb 2006):
-- WINE tweaks (mainly by Gregor Gorjanc)
-
-Update 1.1-0 (14 Dec 2005):
-- Contribution by Ben Bolker and Yun Yan's rbugs package:
-  make R2WinBUGS work under WINE
-
-Update 1.0-1 (14 Nov 2005):
-- make inits=NULL work (again ?)
-
-Update 1.0-0 (05 Aug 2005):
-- attach.all(), detach.all(), attach.bugs() and detach.bugs() added/changed
-  more or less according to Andrew Gelman's current bugs.R
-
-Update 0.2-9 (26 July 2005):
-- bugs has new argument clearWD
-
-Update 0.2-8 (30 May 2005):
-- bugs passed DIC to bugs.script in order to be able to disable it
-
-Update 0.2-6 (18 May 2005):
-- bugs() changes in order to return a file names of coda output files
-- new read.bugs() returns a coda mcmc.list object, if codaPkg=TRUE.
-
-Update 0.2-5 (20 Oct 2004):
-- bugs() and bugs.script() have a new argument bin that allows to specify
-  a number of iterations. After each "bin" iterations the coda files are saved.
-
-Update 0.2-4 (05 Oct 2004):
-- bugs.script() did not work for large n.iter values in update step
-  (no scientific notation allowed)
-
-Update 0.2-3 (10 Sept 2004):
-- bugs.data.inits split to bugs.inits and bugs.data, the latter exported
-  from the Namespace.
-  Now we can use already written data files in bugs().
-
-Update 0.2-2 (28 Apr 2004):
-- schools data: original (see references) instead of the rounded data
-
-During the process of packaging R2WinBUGS_0.1 - R2WinBUGS_0.2-1,
-quite a lot of changes had been made. Those changes are not
-documented anywhere ...
-
-During the process of packaging R2WinBUGS_0.1, quite a lot of changes had
-been made. Those changes are not documented anywhere ...
-
-Changes prior to R2WinBUGS_0.1:
-===============================
-
-Update 30 Oct 2003:
-  1.  Minor change to a return() statement to be compatible with R 1.8
-  2.  Just a warning (from Ben Goodrich):  if you are running Bugs.R inside
-      a loop, you have to be careful with the data() and the inits()
-      functions since they will not necessarily recognize locally-defined
-      variables.  One workaround is to define the variables used in data()
-      and inits() using global assignments (<<-), but this can sometimes
-      make the program run slower.
-Update 29 Aug 2003:
-  1.  Fixed "bugs.data.inits" function so you can use data that have the
-      same names as R functions.
-  2.  Changed T and F to TRUE and FALSE everywhere in case the variables
-      T and F are used as data in the main program
-  3.  Caution:  if you are entering the data as a list of variable names
-      (see 10 Apr 2003 update, item 1), the data to be input into must
-      be global variables.  This can be relevant if you are running bugs()
-      inside an R function.
-  4.  Caution:  bugs() has difficulty processing ragged arrays.  It is
-      better to save a whole matrix (e.g., "theta") rather than parts
-      (e.g., "theta[1:10,1]", "theta[1:5,2]").  If you want to save
-      part of a vector, you should do it as "theta[1:2]", not "theta[1]",
-      "theta[2]".
-Update 30 Apr 2003:  added time monitoring
-Update 29 Apr 2003:
-  1.  The "attach.all" function (no longer called "attach2") overwrites
-      so that all components of a list or data frame get attached.
-  2.  Program now looks in the directory /winbug~1/ rather than /winbug~2/
-  3.  Graphics parameters for margins are returned to their original state
-      at the end of the program.
-  4.  Added "digits.summary" option to the numerical display.
-  5.  Added "last.values" output:  a list that can be input as "inits"
-      if you want to run the simulations longer.
-Update 13 Apr 2003:  fixed new bug in round.bugs().  Now all numbers are
-  saved in scientific notation.
-Update 10 Apr 2003:
-  1.  It is now possible to enter the data as a list of variable names.
-      For example, before you had to enter data as,
-        data <- list (n=8, y=c(28,8,-3,7,-1,1,18,12))
-      or
-        n <- 8
-        y <- c(28,8,-3,7,-1,1,18,12)
-        data <- list (n=n, y=y)
-      Now you can enter the data as,
-        n <- 8
-        y <- c(28,8,-3,7,-1,1,18,12)
-        data <- list ("n", "y")
-      The bugs() function will figure out which method you are using (based
-      on whether "data" is a list of numbers or a vector of character
-      strings).
-      This doesn't look like much, but it's convenient when you're entering
-      lots of data!
-  2.  It is now possible to enter the initial values as a function,
-      so as to automatically a random list of inits for each of the chains.
-      For example, in the 8-schools example below, we can do:
-        inits <- function()
-          list (theta=rnorm(J,0,1), mu.theta=rnorm(1,0,100), sigma.theta=runif(1,0,100))
-
-      to set up the inits as a function (rather than setting up n.chains
-      sets of specific initial values).  Then, the function call,
-        schools.sim <- bugs (data, inits, parameters, "schools.txt", n.chains=3, n.iter=1000)
-      automatically sets up 3 sets of initial values (each a list of
-      theta, mu.theta, sigma.theta).
-  3.  Bug in the initial rounding (the function round.bugs()) has been fixed.
-      Thanks for Mark Clements for finding the bug and fixing it!
-      Also, we have set the default rounding to 5 digits instead of 2.
-Update 01 Apr 2003:  use layout() rather than split.screen() for graphical
-  display
-Update 18 Mar 2003:
-  1.  Get the Bugs configuration information from the original file
-      (Registry_default.odc) rather than overwriting each time.  (Fixes a
-      bug that occurred when R was interrupted in the middle of a Bugs run.)
-  2.  Display different colored dots in the right panel of the graphical
-      display, to show the medians from each chain.
-Update 13 Mar 2003:  fix minor bug in monitor()
-Update 10 Mar 2003:  fix bug in pD and DIC calculations
-Update 7 Mar 2003:
-  1.  Fix display.parallel=T option by adding min.width so that very
-      intervals are still visible.
-  2.  Compute pD separately for each sequence (which gives much more
-      reasonable estimates before convergence).
-Update 8 Feb 2003:  minor fixes in graphical display
-Update 6 Feb 2003:
-  1.  Approximate "effective sample size" n.eff given for each parameter.
-  2.  More explanatory material displayed.
-  3.  Use bringToTop() to automatically bring up the graphics window.
-Update 4 Feb 2003:
-  1.  Automatically compute the deviance, DIC, and pD.  Bugs will not
-      always compute DIC and pD, so we do so using the definition,
-      DIC = E(deviance) + pD, using var(deviance)/2 as an estimate of pD.
-      (This is derived from the chi^2 distribution.  We can't use the
-      Spiegelhalter et al. definition of DIC because we don't have access
-      to the deviance function.)
-  2.  Set default for n.thin so that, after thinning, the total number
-      saved iterations, n.sims, is approximately 1000.
-Update 14 Jan 2003 to run with the new WinBugs1.4.  You may see an error
-  message and need to fix the dos.location assignment in bugs().
-Update 6 Jan 2003:
-  1.  Fix of bug that occurred with uppercase and lowercase variable names
-  2.  Set default for n.thin so that no more than about 500 iterations
-      will be saved from each sequence
-  3.  New option "display.parallel" added to show 80% inferences from
-      parallel sequences on the right panel of the graphical display.  This
-      can be useful to understand what is going on when there are
-      convergence problems.
-Update 26 Dec 2002:  fix of minwidth in bugs.plot.summary
-Update 11 Dec 2002:
-  1.  Automatic fixing of adaptive phases.  Now you no longer need to run
-      for thousands of iterations when slice or Metropolis sampling is used.
-  2.  Various minor fixes
-Update 10 Dec 2002:
-  1.  Cool graphical display of convergence and inferences!
-  2.  New "attach2" function that overwrites so that all components of
-      the list are attached
-Update 29 Nov 2002:
-  1.  Fix of bug in 24 Nov update.
-  2.  Fix of bug in 16 Nov update.
-  3.  Length of chains is now pecified in terms of "n.iter" rather than
-      "n.keep".
-Update 24 Nov 2002:  improved treatment of "parameters.to.save".  For
-  example, you can now use "alpha" to indicate an entire array of parameters,
-  whereas before you had to save "alpha[]" or "alpha[,]" or whatever.
-Update 16 Nov 2002:  mean, sd, median added to outputs
-Update 4 Nov 2002:  more error-flagging added
-Update 26 Oct 2002:
-  1.  Parameters saved in order of the "parameters.to.save" vector
-      (not alphabetical order).
-  2.  Output saved in both matrix and list form.
-  3.  With the attach.sims=T setting (which is the default), the simulations
-      for all the saved parameters are saved as R objects.  This is
-      convenient for later use of the simulations.
-Updates to 16 Oct 2002:  more error-flagging added, mean/sd added to summary,
-  fixing scientific notation so Bugs can always read data and inits
-Update 21 Sept 2002:  "quit=F" option changed to "debug=T"
-First version written 18 Sept 2002 by Andrew Gelman,
-  adapted from the EmBedBugs package by Kenneth Rice
+Changes to R2WinBUGS:
+=====================
+
+Update 2.1-10
+- bugfix: working.directory was not always reset when function terminated.
+
+Update 2.1-9
+- R2WinBUGS now works on OS X and Solaris (with suitable versions of wine)
+- findUnixBinary now fails (with a meaningfull error message) always if the
+  binary file does not exist.
+- If working.directory=NULL (the default setting), then a temporary
+  directory is used as a working directory to prevent overwriting/removing
+  the existing files.
+- File script.txt is also removed when clearWD=TRUE.
+- If model.file does not have a "txt" extension, then it is temporarily
+  copied to a file with "txt" extension in the working directory and
+  removed at the end of WinBUGS run.
+
+Update 2.1-7
+- this file is now available as NEWS file in top folder of installed package
+
+Update 2.1-6 (23 August 2007):
+- reverting back to use thin.updater since it is faster, however CODA files
+  have "wrong" indexes - this needs to be fixed in BUGS program
+- WINE arguments are now set in such a way that defaults work on Windows
+  and Linux
+- minor formatting in the code and help files
+- added R2WinBUGS-package help page
+
+Update 2.1-5 (12 June 2007):
+- proper indexing of CODA files also in R version
+- fixed useWINE documentation in bugs help page
+- note on supported BUGS versions
+- as.bugs.array now returns info on used rule for pD i.e. var(deviance)/2
+    or Dbar-Dhat
+- some internal fixes related to handling of DIC
+- merging and reversing ChangeLog files
+
+Update 2.1-4 (20 May 2007):
+- Depending on coda now (Namespace issues)
+- some more fixes for codetools checks
+- Vignette has been updated
+
+Update 2.1-3 (13 May 2007):
+- Ported to S-PLUS by Insightful Corp.
+- some fixes for codetools checks
+
+Update 2.0-4 (01 November 2006):
+- print.bugs / plot.bugs documentation fixes
+- write.model() fix
+
+Update 2.0-3 (06 October 2006):
+- \\. -> [.] in regular expressions
+
+Update 2.0-2 (26 July 2006):
+- changes for DIC, making use of BUGS internal calculations
+- some doc fixes
+
+Update 2.0-1 (26 May 2006):
+- some wine patches for 2.2-0 by Gregor Gorjanc
+
+Update 2.0-0 (08 May 2006):
+- bugs() doc fix/updates on scrambling
+- bugs.run() has new arg useWINE (by Gregor Gorjanc)
+- bugs() and bugs.script() patched for WINEPATH issue
+- bugs.script() changed to save log file in ASCII
+- new function bugs.log() by Gregor Gorjanc
+- new functions as.bugs.array, openbugs and sort.name by
+  Jouni Kerman and Andrew Gelman
+- new function write.model() based on ideas from Jouni Kerman
+
+Update 1.1-1 (17 Feb 2006):
+- WINE tweaks (mainly by Gregor Gorjanc)
+
+Update 1.1-0 (14 Dec 2005):
+- Contribution by Ben Bolker and Yun Yan's rbugs package:
+  make R2WinBUGS work under WINE
+
+Update 1.0-1 (14 Nov 2005):
+- make inits=NULL work (again ?)
+
+Update 1.0-0 (05 Aug 2005):
+- attach.all(), detach.all(), attach.bugs() and detach.bugs() added/changed
+  more or less according to Andrew Gelman's current bugs.R
+
+Update 0.2-9 (26 July 2005):
+- bugs has new argument clearWD
+
+Update 0.2-8 (30 May 2005):
+- bugs passed DIC to bugs.script in order to be able to disable it
+
+Update 0.2-6 (18 May 2005):
+- bugs() changes in order to return a file names of coda output files
+- new read.bugs() returns a coda mcmc.list object, if codaPkg=TRUE.
+
+Update 0.2-5 (20 Oct 2004):
+- bugs() and bugs.script() have a new argument bin that allows to specify
+  a number of iterations. After each "bin" iterations the coda files are saved.
+
+Update 0.2-4 (05 Oct 2004):
+- bugs.script() did not work for large n.iter values in update step
+  (no scientific notation allowed)
+
+Update 0.2-3 (10 Sept 2004):
+- bugs.data.inits split to bugs.inits and bugs.data, the latter exported
+  from the Namespace.
+  Now we can use already written data files in bugs().
+
+Update 0.2-2 (28 Apr 2004):
+- schools data: original (see references) instead of the rounded data
+
+During the process of packaging R2WinBUGS_0.1 - R2WinBUGS_0.2-1,
+quite a lot of changes had been made. Those changes are not
+documented anywhere ...
+
+During the process of packaging R2WinBUGS_0.1, quite a lot of changes had
+been made. Those changes are not documented anywhere ...
+
+Changes prior to R2WinBUGS_0.1:
+===============================
+
+Update 30 Oct 2003:
+  1.  Minor change to a return() statement to be compatible with R 1.8
+  2.  Just a warning (from Ben Goodrich):  if you are running Bugs.R inside
+      a loop, you have to be careful with the data() and the inits()
+      functions since they will not necessarily recognize locally-defined
+      variables.  One workaround is to define the variables used in data()
+      and inits() using global assignments (<<-), but this can sometimes
+      make the program run slower.
+Update 29 Aug 2003:
+  1.  Fixed "bugs.data.inits" function so you can use data that have the
+      same names as R functions.
+  2.  Changed T and F to TRUE and FALSE everywhere in case the variables
+      T and F are used as data in the main program
+  3.  Caution:  if you are entering the data as a list of variable names
+      (see 10 Apr 2003 update, item 1), the data to be input into must
+      be global variables.  This can be relevant if you are running bugs()
+      inside an R function.
+  4.  Caution:  bugs() has difficulty processing ragged arrays.  It is
+      better to save a whole matrix (e.g., "theta") rather than parts
+      (e.g., "theta[1:10,1]", "theta[1:5,2]").  If you want to save
+      part of a vector, you should do it as "theta[1:2]", not "theta[1]",
+      "theta[2]".
+Update 30 Apr 2003:  added time monitoring
+Update 29 Apr 2003:
+  1.  The "attach.all" function (no longer called "attach2") overwrites
+      so that all components of a list or data frame get attached.
+  2.  Program now looks in the directory /winbug~1/ rather than /winbug~2/
+  3.  Graphics parameters for margins are returned to their original state
+      at the end of the program.
+  4.  Added "digits.summary" option to the numerical display.
+  5.  Added "last.values" output:  a list that can be input as "inits"
+      if you want to run the simulations longer.
+Update 13 Apr 2003:  fixed new bug in round.bugs().  Now all numbers are
+  saved in scientific notation.
+Update 10 Apr 2003:
+  1.  It is now possible to enter the data as a list of variable names.
+      For example, before you had to enter data as,
+        data <- list (n=8, y=c(28,8,-3,7,-1,1,18,12))
+      or
+        n <- 8
+        y <- c(28,8,-3,7,-1,1,18,12)
+        data <- list (n=n, y=y)
+      Now you can enter the data as,
+        n <- 8
+        y <- c(28,8,-3,7,-1,1,18,12)
+        data <- list ("n", "y")
+      The bugs() function will figure out which method you are using (based
+      on whether "data" is a list of numbers or a vector of character
+      strings).
+      This doesn't look like much, but it's convenient when you're entering
+      lots of data!
+  2.  It is now possible to enter the initial values as a function,
+      so as to automatically a random list of inits for each of the chains.
+      For example, in the 8-schools example below, we can do:
+        inits <- function()
+          list (theta=rnorm(J,0,1), mu.theta=rnorm(1,0,100), sigma.theta=runif(1,0,100))
+
+      to set up the inits as a function (rather than setting up n.chains
+      sets of specific initial values).  Then, the function call,
+        schools.sim <- bugs (data, inits, parameters, "schools.txt", n.chains=3, n.iter=1000)
+      automatically sets up 3 sets of initial values (each a list of
+      theta, mu.theta, sigma.theta).
+  3.  Bug in the initial rounding (the function round.bugs()) has been fixed.
+      Thanks for Mark Clements for finding the bug and fixing it!
+      Also, we have set the default rounding to 5 digits instead of 2.
+Update 01 Apr 2003:  use layout() rather than split.screen() for graphical
+  display
+Update 18 Mar 2003:
+  1.  Get the Bugs configuration information from the original file
+      (Registry_default.odc) rather than overwriting each time.  (Fixes a
+      bug that occurred when R was interrupted in the middle of a Bugs run.)
+  2.  Display different colored dots in the right panel of the graphical
+      display, to show the medians from each chain.
+Update 13 Mar 2003:  fix minor bug in monitor()
+Update 10 Mar 2003:  fix bug in pD and DIC calculations
+Update 7 Mar 2003:
+  1.  Fix display.parallel=T option by adding min.width so that very
+      intervals are still visible.
+  2.  Compute pD separately for each sequence (which gives much more
+      reasonable estimates before convergence).
+Update 8 Feb 2003:  minor fixes in graphical display
+Update 6 Feb 2003:
+  1.  Approximate "effective sample size" n.eff given for each parameter.
+  2.  More explanatory material displayed.
+  3.  Use bringToTop() to automatically bring up the graphics window.
+Update 4 Feb 2003:
+  1.  Automatically compute the deviance, DIC, and pD.  Bugs will not
+      always compute DIC and pD, so we do so using the definition,
+      DIC = E(deviance) + pD, using var(deviance)/2 as an estimate of pD.
+      (This is derived from the chi^2 distribution.  We can't use the
+      Spiegelhalter et al. definition of DIC because we don't have access
+      to the deviance function.)
+  2.  Set default for n.thin so that, after thinning, the total number
+      saved iterations, n.sims, is approximately 1000.
+Update 14 Jan 2003 to run with the new WinBugs1.4.  You may see an error
+  message and need to fix the dos.location assignment in bugs().
+Update 6 Jan 2003:
+  1.  Fix of bug that occurred with uppercase and lowercase variable names
+  2.  Set default for n.thin so that no more than about 500 iterations
+      will be saved from each sequence
+  3.  New option "display.parallel" added to show 80% inferences from
+      parallel sequences on the right panel of the graphical display.  This
+      can be useful to understand what is going on when there are
+      convergence problems.
+Update 26 Dec 2002:  fix of minwidth in bugs.plot.summary
+Update 11 Dec 2002:
+  1.  Automatic fixing of adaptive phases.  Now you no longer need to run
+      for thousands of iterations when slice or Metropolis sampling is used.
+  2.  Various minor fixes
+Update 10 Dec 2002:
+  1.  Cool graphical display of convergence and inferences!
+  2.  New "attach2" function that overwrites so that all components of
+      the list are attached
+Update 29 Nov 2002:
+  1.  Fix of bug in 24 Nov update.
+  2.  Fix of bug in 16 Nov update.
+  3.  Length of chains is now pecified in terms of "n.iter" rather than
+      "n.keep".
+Update 24 Nov 2002:  improved treatment of "parameters.to.save".  For
+  example, you can now use "alpha" to indicate an entire array of parameters,
+  whereas before you had to save "alpha[]" or "alpha[,]" or whatever.
+Update 16 Nov 2002:  mean, sd, median added to outputs
+Update 4 Nov 2002:  more error-flagging added
+Update 26 Oct 2002:
+  1.  Parameters saved in order of the "parameters.to.save" vector
+      (not alphabetical order).
+  2.  Output saved in both matrix and list form.
+  3.  With the attach.sims=T setting (which is the default), the simulations
+      for all the saved parameters are saved as R objects.  This is
+      convenient for later use of the simulations.
+Updates to 16 Oct 2002:  more error-flagging added, mean/sd added to summary,
+  fixing scientific notation so Bugs can always read data and inits
+Update 21 Sept 2002:  "quit=F" option changed to "debug=T"
+First version written 18 Sept 2002 by Andrew Gelman,
+  adapted from the EmBedBugs package by Kenneth Rice


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Re: [Bugs-r-devel] Latest version of R2WinBUGS

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

Rodney Sparapani wrote:
> Hi Gang:
> 
> I see that you have posted the new version of R2WinBUGS.  Great!
> However, the NEWS file appears to be for the prior version.  I
> was hoping that this could be fixed.  It would be better IMHO
> if it advertised that R2WinBUGS now works on OS X and Solaris.
> Of course, I'm sure that are alot of other great new features
> and bug-fixes in there as well.  Thanks.
> 

Done in the sources and new bugfix release upcoming today...


Best,
uwe

[Bugs-r-devel] Latest version of R2WinBUGS

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

Hi Gang:

I see that you have posted the new version of R2WinBUGS.  Great!
However, the NEWS file appears to be for the prior version.  I
was hoping that this could be fixed.  It would be better IMHO
if it advertised that R2WinBUGS now works on OS X and Solaris.
Of course, I'm sure that are alot of other great new features
and bug-fixes in there as well.  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] Bayesian Disease Mapping conference

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

Rodney Sparapani wrote:
> Rodney Sparapani wrote:
>> Hi Guys:
>>
>> I just got back from the Bayesian Disease Mapping conference in
>> Charleston, SC, 12/10-11 by Andrew Lawson.  This was the conference 
>> that said
>> bring a laptop with R and WinBUGS installed.  So, I get there and Andrew
>> says that we are going to demo R2WinBUGS!  I couldn't believe the luck
>> since I had just worked with you guys on getting it going on OS X (and
>> also recently Solaris 10).  It worked flawlessly!  And, I found myself
>> helping other users install and run R2WinBUGS.  Kudos to you all!  You
>> now have 40 new users of R2WinBUGS.  Happy Holidays!
>>
> By the way, there were some Mac and Solaris users at the
> conference as well (slumming it with a Windows laptop).  So, I was
> wondering, are you guys going to release a new version
> of R2WinBUGS with all of those Mac and Solaris fixes that
> you kindly made for me?  Thanks.
> 


Thanks for the reminder.
I will send the recent version to CRAN in a minute.

Uwe

[Bugs-r-devel] SF.net SVN: bugs-r:[95] trunk/R2WinBUGS/DESCRIPTION

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

Revision: 95
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=95&view=rev
Author:   ligges
Date:     2009-01-08 17:07:19 +0000 (Thu, 08 Jan 2009)

Log Message:
-----------
new release

Modified Paths:
--------------
    trunk/R2WinBUGS/DESCRIPTION

Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION	2008-11-15 20:41:20 UTC (rev 94)
+++ trunk/R2WinBUGS/DESCRIPTION	2009-01-08 17:07:19 UTC (rev 95)
@@ -1,7 +1,7 @@
 Package: R2WinBUGS
 Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2008-02-01
-Version: 2.1-8
+Date: 2009-01-08
+Version: 2.1-9
 Author: originally written by Andrew Gelman <ge...@st...>;
  changes and packaged by Sibylle Sturtz <st...@st...>
  and Uwe Ligges <li...@st...>.


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Re: [Bugs-r-devel] Bayesian Disease Mapping conference

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

Rodney Sparapani wrote:
> Hi Guys:
>
> I just got back from the Bayesian Disease Mapping conference in
> Charleston, SC, 12/10-11 by Andrew Lawson.  This was the conference 
> that said
> bring a laptop with R and WinBUGS installed.  So, I get there and Andrew
> says that we are going to demo R2WinBUGS!  I couldn't believe the luck
> since I had just worked with you guys on getting it going on OS X (and
> also recently Solaris 10).  It worked flawlessly!  And, I found myself
> helping other users install and run R2WinBUGS.  Kudos to you all!  You
> now have 40 new users of R2WinBUGS.  Happy Holidays!
>
By the way, there were some Mac and Solaris users at the
conference as well (slumming it with a Windows laptop).  So, I was
wondering, are you guys going to release a new version
of R2WinBUGS with all of those Mac and Solaris fixes that
you kindly made for me?  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

[Bugs-r-devel] Bayesian Disease Mapping conference

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

Hi Guys:

I just got back from the Bayesian Disease Mapping conference in
Charleston, SC, 12/10-11 by Andrew Lawson.  This was the conference that 
said
bring a laptop with R and WinBUGS installed.  So, I get there and Andrew
says that we are going to demo R2WinBUGS!  I couldn't believe the luck
since I had just worked with you guys on getting it going on OS X (and
also recently Solaris 10).  It worked flawlessly!  And, I found myself
helping other users install and run R2WinBUGS.  Kudos to you all!  You
now have 40 new users of R2WinBUGS.  Happy Holidays!

-- 
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

[Bugs-r-devel] SF.net SVN: bugs-r:[94] trunk/R2WinBUGS/R/bugs.sims.R

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

Revision: 94
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=94&view=rev
Author:   ligges
Date:     2008-11-15 20:41:20 +0000 (Sat, 15 Nov 2008)

Log Message:
-----------
bugfix: partly constant and partly stochastic matrices were incorrectly captured by some too careful error checking

Modified Paths:
--------------
    trunk/R2WinBUGS/R/bugs.sims.R

Modified: trunk/R2WinBUGS/R/bugs.sims.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.sims.R	2008-10-26 19:26:30 UTC (rev 93)
+++ trunk/R2WinBUGS/R/bugs.sims.R	2008-11-15 20:41:20 UTC (rev 94)
@@ -48,8 +48,6 @@
       for (k in 1:dimension.short[j]) n.indexes.short[[j]][k] <- length (
         unique (unlist (lapply (indexes.long[long.short[[j]]], .subset, k))))
       length.short[j] <- prod(n.indexes.short[[j]])
-      if (length(long.short[[j]])!=length.short[j])
-        stop(paste("error in parameter", root.short[[j]], "in parameters.to.save"))
       indexes.short[[j]] <- as.list(numeric(length.short[j]))
       for (k in 1:length.short[j])
         indexes.short[[j]][[k]] <- indexes.long[[long.short[[j]][k]]]


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Re: [Bugs-r-devel] bugs help page - deafults

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

OK. Reasonable argument!

gg
________________________________________
From: Uwe Ligges [li...@st...]
Sent: Friday, October 31, 2008 2:48 PM
To: Gorjanc Gregor
Cc: bug...@li...
Subject: Re: [Bugs-r-devel] bugs help page - deafults

Gorjanc Gregor wrote:
> Hi,
>
> Uwe, I do not know if you have already rolled up the new version of R2WinBUGS.

I have not.

> I realized that there is no need to have bugs.directory="c:/Program Files/WinBUGS14/"
> in the example of bugs help page. This is the default already. I am away from the computer
> with devel stuff. Can you please "remove" that?

I am reluctant due to the following reason: People see in this example
that it might be relevant to set the director. Otherwise we will get
thousands of questions where we will have to answer that it is essential
to set that directory in case of non-English-default installations of
WinBUGS.
Note that a German installation will put it to "c:\Programme\..."

Best wishes,
Uwe


> Thanks!
>
> gg
>
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Bugs-r-devel mailing list
> Bug...@li...
> https://lists.sourceforge.net/lists/listinfo/bugs-r-devel

Re: [Bugs-r-devel] bugs help page - deafults

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

Gorjanc Gregor wrote:
> Hi,
> 
> Uwe, I do not know if you have already rolled up the new version of R2WinBUGS.

I have not.

> I realized that there is no need to have bugs.directory="c:/Program Files/WinBUGS14/"
> in the example of bugs help page. This is the default already. I am away from the computer
> with devel stuff. Can you please "remove" that?


I am reluctant due to the following reason: People see in this example 
that it might be relevant to set the director. Otherwise we will get 
thousands of questions where we will have to answer that it is essential 
to set that directory in case of non-English-default installations of 
WinBUGS.
Note that a German installation will put it to "c:\Programme\..."

Best wishes,
Uwe


> Thanks!
> 
> gg
> 
> -------------------------------------------------------------------------
> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
> Build the coolest Linux based applications with Moblin SDK & win great prizes
> Grand prize is a trip for two to an Open Source event anywhere in the world
> http://moblin-contest.org/redirect.php?banner_id=100&url=/
> _______________________________________________
> Bugs-r-devel mailing list
> Bug...@li...
> https://lists.sourceforge.net/lists/listinfo/bugs-r-devel

[Bugs-r-devel] bugs help page - deafults

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

Hi,

Uwe, I do not know if you have already rolled up the new version of R2WinBUGS.
I realized that there is no need to have bugs.directory="c:/Program Files/WinBUGS14/"
in the example of bugs help page. This is the default already. I am away from the computer
with devel stuff. Can you please "remove" that?

Thanks!

gg

Re: [Bugs-r-devel] Some Progress

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

Everyhting fine from my side.

gg
________________________________________
From: Uwe Ligges [li...@st...]
Sent: Wednesday, October 29, 2008 4:24 PM
To: Rodney Sparapani
Cc: bug...@li...
Subject: Re: [Bugs-r-devel] Some Progress

Rodney Sparapani wrote:
> Uwe Ligges wrote:
>> Rodney,
>>
>> I just committed `yet another workaround for wine under MacOS'. Can
>> you try again please? Otherwise, it would be very helpful if you could
>> debug.  We do not have a single Mac machine in our whole department,
>> just Linux and Windows.
>>
>> Best wishes,
>> Uwe
> Hi Uwe:
>
> That did it!!!  Thanks.


Great.

To ALL: Anything to do before a new release???

Uwe


-------------------------------------------------------------------------
This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
Build the coolest Linux based applications with Moblin SDK & win great prizes
Grand prize is a trip for two to an Open Source event anywhere in the world
http://moblin-contest.org/redirect.php?banner_id=100&url=/
_______________________________________________
Bugs-r-devel mailing list
Bug...@li...
https://lists.sourceforge.net/lists/listinfo/bugs-r-devel

Re: [Bugs-r-devel] Some Progress

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

Rodney Sparapani wrote:
> Uwe Ligges wrote:
>> Rodney,
>>
>> I just committed `yet another workaround for wine under MacOS'. Can 
>> you try again please? Otherwise, it would be very helpful if you could 
>> debug.  We do not have a single Mac machine in our whole department, 
>> just Linux and Windows.
>>
>> Best wishes,
>> Uwe
> Hi Uwe:
> 
> That did it!!!  Thanks.


Great.

To ALL: Anything to do before a new release???

Uwe

Re: [Bugs-r-devel] Some Progress

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

Uwe Ligges wrote:
> Rodney,
>
> I just committed `yet another workaround for wine under MacOS'. Can 
> you try again please? Otherwise, it would be very helpful if you could 
> debug.  We do not have a single Mac machine in our whole department, 
> just Linux and Windows.
>
> Best wishes,
> Uwe
Hi Uwe:

That did it!!!  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] Some Progress

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

Rodney,

I just committed `yet another workaround for wine under MacOS'. Can you 
try again please? Otherwise, it would be very helpful if you could 
debug.  We do not have a single Mac machine in our whole department, 
just Linux and Windows.

Best wishes,
Uwe




Rodney Sparapani wrote:
> Uwe Ligges wrote:
>>
>> You are looking for gsub(). I have committed the workaround:
>>   working.directory <- gsub("//", "/", working.directory)
>>
>> Uwe
> Ah, the AWK function gsub, I should have known!  But, the batch
> script still has // in working.directory so either the workaround
> is too late or too early.  Not sure which.
> 

[Bugs-r-devel] SF.net SVN: bugs-r:[93] trunk/R2WinBUGS/R/bugs.R

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

Revision: 93
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=93&view=rev
Author:   ligges
Date:     2008-10-26 19:26:30 +0000 (Sun, 26 Oct 2008)

Log Message:
-----------
yet another workaround for wine under MacOS

Modified Paths:
--------------
    trunk/R2WinBUGS/R/bugs.R

Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R	2008-10-16 08:59:34 UTC (rev 92)
+++ trunk/R2WinBUGS/R/bugs.R	2008-10-26 19:26:30 UTC (rev 93)
@@ -107,6 +107,10 @@
   } else {
     new.model.file <- model.file
   }
+  if(useWINE){
+        ## Some tweaks for wine (particularly required for Mac OS)
+        new.model.file <- gsub("//", "/", new.model.file)
+  }
   bugs.script(parameters.to.save, n.chains, n.iter, n.burnin, n.thin,
               new.model.file, debug=debug, is.inits=!is.null(inits),
               bin=bin, DIC=DIC, useWINE=useWINE, newWINE=newWINE,


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Re: [Bugs-r-devel] Some Progress

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

Uwe Ligges wrote:
>
>
> You are looking for gsub(). I have committed the workaround:
>   working.directory <- gsub("//", "/", working.directory)
>
> Uwe
Ah, the AWK function gsub, I should have known!  But, the batch
script still has // in working.directory so either the workaround
is too late or too early.  Not sure which.

-- 
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

[Bugs-r-devel] SF.net SVN: bugs-r:[92] trunk/R2WinBUGS/R/bugs.R

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

Revision: 92
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=92&view=rev
Author:   ligges
Date:     2008-10-16 08:59:34 +0000 (Thu, 16 Oct 2008)

Log Message:
-----------
workaround: Mac's wine does not accept double slashes in pathnames

Modified Paths:
--------------
    trunk/R2WinBUGS/R/bugs.R

Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R	2008-10-11 19:31:56 UTC (rev 91)
+++ trunk/R2WinBUGS/R/bugs.R	2008-10-16 08:59:34 UTC (rev 92)
@@ -46,6 +46,7 @@
     working.directory <- tempdir()
     if(useWINE){
         ## Some tweaks for wine (particularly required for Mac OS)
+        working.directory <- gsub("//", "/", working.directory)
         Sys.chmod(working.directory, mode="750")
         on.exit(Sys.chmod(working.directory, mode="700"))
     }


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Re: [Bugs-r-devel] Some Progress

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

Rodney Sparapani wrote:
> Hi Guys:
> 
> Unfortunately, the patch did not fix the problem.  But, maybe it helped
> since now I'm getting an error message that I didn't have before:
> 
> fixme:shell:StrRetToStrNW unknown type!
> 
> Looking at the Wine sources, this function is on line 83 of 
> dlls/shell32/shellstring.c
> 
> This is one of the undocumented functions so I'm not clear
> and exactly it's purpose.  Based on the type of src, do something?
> However, the type of src is not one of the 3 types handled and 
> nothing is returned!  
> 
> Looking at the value of tempdir() gave me an idea why that might be:
> 
>> tempdir()
> [1] "/var/folders/z4/z4O5IqhPED0pjZUVP7s0mE+++TI/-Tmp-//RtmphdzhHo"
> 
> There appears to be an R bug here.  Two slashes in a row is not
> what is wanted. 


No, but we do not know any OS where it matters (not even Windows) ;-).
Hence again also a bug in wine.

> Of course, on Unix, this makes no difference since
> the extra slash is ignored.   But, we are not dealing with Unix, we
> are dealing with Wine's implementation of the Windows API.  So, after
> setting working.directory=tempdir() can we substitute single slashes
> for double slashes in working.directory
 >
> so that we get the following instead:
> 
> "/var/folders/z4/z4O5IqhPED0pjZUVP7s0mE+++TI/-Tmp-/RtmphdzhHo"


You are looking for gsub(). I have committed the workaround:
   working.directory <- gsub("//", "/", working.directory)

Uwe



> I spent some time looking through my S manual trying to find the
> function to do this, but I couldn't figure it out.  Do S and R
> support AWK functions since they were both invented at Bell Labs
> (if memory serves)?
> 

[Bugs-r-devel] Some Progress

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

Hi Guys:

Unfortunately, the patch did not fix the problem.  But, maybe it helped
since now I'm getting an error message that I didn't have before:

fixme:shell:StrRetToStrNW unknown type!

Looking at the Wine sources, this function is on line 83 of 
dlls/shell32/shellstring.c

This is one of the undocumented functions so I'm not clear
and exactly it's purpose.  Based on the type of src, do something?
However, the type of src is not one of the 3 types handled and 
nothing is returned!  

Looking at the value of tempdir() gave me an idea why that might be:

> tempdir()
[1] "/var/folders/z4/z4O5IqhPED0pjZUVP7s0mE+++TI/-Tmp-//RtmphdzhHo"

There appears to be an R bug here.  Two slashes in a row is not
what is wanted.  Of course, on Unix, this makes no difference since
the extra slash is ignored.   But, we are not dealing with Unix, we
are dealing with Wine's implementation of the Windows API.  So, after
setting working.directory=tempdir() can we substitute single slashes
for double slashes in working.directory

so that we get the following instead:

"/var/folders/z4/z4O5IqhPED0pjZUVP7s0mE+++TI/-Tmp-/RtmphdzhHo"

I spent some time looking through my S manual trying to find the
function to do this, but I couldn't figure it out.  Do S and R
support AWK functions since they were both invented at Bell Labs
(if memory serves)?

-- 
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] Mac bug regressions

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

Hi!

> From: Uwe Ligges [li...@st...]
> I just made an update in the repository.
> Maybe you want to try it out.

Yes. Please try also the default example from bugs(). Latest changes
to findUnixBinary should now cause more meaningful error messages.

gg

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

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

Rodney Sparapani wrote:
> Uwe Ligges wrote:
>>
>>
>> Well, I do not want to make the tempdir insecure. It might be used by 
>> other packages as well and users might expect privacy of their data. 
>> Consider you have data from patients of a clinical trial. Everybody 
>> using the same machine could access and read temporary data in that 
>> case. We should not use dirty tricks. We have problems enough telling 
>> people that R *is* secure given no contributed packages are installed.
>>
>> Uwe
> No, not everybody.  That's why I suggested 750, rather than 755.  What if
> you changed it to 750, then changed it back to 700 after the model file
> is read in, but before the sampling begins?  That way, it would only be
> available as long as necessary.
> 

I just made an update in the repository.
Maybe you want to try it out.

Best,
Uwe

[Bugs-r-devel] SF.net SVN: bugs-r:[91] trunk/R2WinBUGS/R/bugs.R

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

Revision: 91
          http://bugs-r.svn.sourceforge.net/bugs-r/?rev=91&view=rev
Author:   ligges
Date:     2008-10-11 19:31:56 +0000 (Sat, 11 Oct 2008)

Log Message:
-----------
make tempdir() group-readable (750) if wine is used

Modified Paths:
--------------
    trunk/R2WinBUGS/R/bugs.R

Modified: trunk/R2WinBUGS/R/bugs.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.R	2008-10-11 17:47:53 UTC (rev 90)
+++ trunk/R2WinBUGS/R/bugs.R	2008-10-11 19:31:56 UTC (rev 91)
@@ -44,10 +44,15 @@
   ## Move to working drirectory or temporary directory when NULL
   if(is.null(working.directory)) {
     working.directory <- tempdir()
+    if(useWINE){
+        ## Some tweaks for wine (particularly required for Mac OS)
+        Sys.chmod(working.directory, mode="750")
+        on.exit(Sys.chmod(working.directory, mode="700"))
+    }
   }
   savedWD <- getwd()
   setwd(working.directory)
-  on.exit(setwd(savedWD))
+  on.exit(setwd(savedWD), add = TRUE)
 
   ## model.file is not a file name but a model function
   if(is.function(model.file)){


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