[Bugs-r-devel] SF.net SVN: bugs-r: [20] trunk/R2WinBUGS

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

Revision: 20
          http://svn.sourceforge.net/bugs-r/?rev=20&view=rev
Author:   ligges
Date:     2007-05-20 08:45:39 -0700 (Sun, 20 May 2007)

Log Message:
-----------
Reverted some former changes:
- Added some tricks (defining no-op-functions) to make codetools calm.
- we do depend on coda now and we are importing parts of its Namespace now, in order to make codetools calm (S-PLUS does not like the "::" operator).

Modified Paths:
--------------
    trunk/R2WinBUGS/Changes
    trunk/R2WinBUGS/DESCRIPTION
    trunk/R2WinBUGS/NAMESPACE
    trunk/R2WinBUGS/R/attach.all.R
    trunk/R2WinBUGS/R/bugs.data.R
    trunk/R2WinBUGS/R/read.bugs.R

Modified: trunk/R2WinBUGS/Changes
===================================================================
--- trunk/R2WinBUGS/Changes	2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/Changes	2007-05-20 15:45:39 UTC (rev 20)
@@ -74,3 +74,7 @@
 - Ported to S-PLUS by Insightful Corp.
 - some fixes for codetools checks
 
+Update 2.1-4 (20 May 2007):
+- Depending on coda now (Namespace issues)
+- some more fixes for codetools checks
+- Vignette has been updated

Modified: trunk/R2WinBUGS/DESCRIPTION
===================================================================
--- trunk/R2WinBUGS/DESCRIPTION	2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/DESCRIPTION	2007-05-20 15:45:39 UTC (rev 20)
@@ -1,7 +1,7 @@
 Package: R2WinBUGS
 Title: Running WinBUGS and OpenBUGS from R / S-PLUS
-Date: 2007-05-13
-Version: 2.1-3
+Date: 2007-05-20
+Version: 2.1-4
 Author: originally written by Andrew Gelman <ge...@st...>;
  changes and packaged by Sibylle Sturtz <st...@st...>
  and Uwe Ligges <li...@st...>.
@@ -13,8 +13,8 @@
  convergence in a table and graph, and save the simulations in arrays for easy access
  in R / S-PLUS. In S-PLUS, the openbugs functionality and the windows emulation
  functionality is not yet available.
-Depends: R (>= 2.4.0)
-Suggests: coda (>= 0.9-0), BRugs (>= 0.3-0)
+Depends: R (>= 2.4.0), coda (>= 0.9-0)
+Suggests: BRugs (>= 0.3-0)
 SystemRequirements: WinBUGS 1.4
 URL: http://www.stat.columbia.edu/~gelman/bugsR/
 Maintainer: Sibylle Sturtz <st...@st...>

Modified: trunk/R2WinBUGS/NAMESPACE
===================================================================
--- trunk/R2WinBUGS/NAMESPACE	2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/NAMESPACE	2007-05-20 15:45:39 UTC (rev 20)
@@ -1,3 +1,5 @@
+importFrom(coda, mcmc.list, read.coda)
+
 export(bugs,
        attach.all,
        detach.all,
@@ -12,3 +14,4 @@
 
 S3method(print, bugs)
 S3method(plot, bugs)
+

Modified: trunk/R2WinBUGS/R/attach.all.R
===================================================================
--- trunk/R2WinBUGS/R/attach.all.R	2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/R/attach.all.R	2007-05-20 15:45:39 UTC (rev 20)
@@ -18,6 +18,9 @@
     if(overwrite) remove(list=rem, envir=.GlobalEnv)
     attach(x, name=name)
   } else {
+    ## next line is a dirty trick for R'd codetools check in R-2.5.0
+    ## (should be removed after codetoold have been improved):
+    attach.default <- get("attach.default") 
     attach.default(x, name = name)
   }
 }

Modified: trunk/R2WinBUGS/R/bugs.data.R
===================================================================
--- trunk/R2WinBUGS/R/bugs.data.R	2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/R/bugs.data.R	2007-05-20 15:45:39 UTC (rev 20)
@@ -24,6 +24,15 @@
 }
 
 
+if(is.R()){
+    ## need some fake functions for codetools
+    "writeDatafileS4" <- toSingleS4 <- function(...)
+        stop("This function is not intended to be called in R!")
+} else {
+
+### The rest of this file is for S-PLUS only...
+
+
 "writeDatafileS4" <- 
 #
 # Writes to file "towhere" text defining a list containing "DATA" in a form compatable with WinBUGS.
@@ -224,3 +233,5 @@
     }
     x
 }
+
+}

Modified: trunk/R2WinBUGS/R/read.bugs.R
===================================================================
--- trunk/R2WinBUGS/R/read.bugs.R	2007-05-20 15:42:40 UTC (rev 19)
+++ trunk/R2WinBUGS/R/read.bugs.R	2007-05-20 15:45:39 UTC (rev 20)
@@ -1,13 +1,7 @@
 read.bugs <- function(codafiles, ...){
-    if(!require(coda))
+    if(!is.R() && !require("coda"))
         stop("package 'coda' is required to use this function")
-    if (is.R()){
-      coda::mcmc.list(lapply(codafiles, coda::read.coda, 
-                      index.file = file.path(dirname(codafiles[1]), "codaIndex.txt"), 
-                      ...))
-    }else{
-      mcmc.list(lapply(codafiles, read.coda, 
-                       index.file = file.path(dirname(codafiles[1]), "codaIndex.txt"), 
-                       ...))
-    }
+    mcmc.list(lapply(codafiles, read.coda, 
+                     index.file = file.path(dirname(codafiles[1]), "codaIndex.txt"), 
+                     ...))
 }


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