From noreply at r-forge.r-project.org  Wed Oct  2 05:04:38 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  2 Oct 2013 05:04:38 +0200 (CEST)
Subject: [Rcpp-commits] r4553 - in pkg/Rcpp: . inst
	inst/include/Rcpp/api/meat
Message-ID: <20131002030438.99A08185C26@r-forge.r-project.org>

Author: edd
Date: 2013-10-02 05:04:36 +0200 (Wed, 02 Oct 2013)
New Revision: 4553

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/DESCRIPTION
   pkg/Rcpp/inst/NEWS.Rd
   pkg/Rcpp/inst/THANKS
   pkg/Rcpp/inst/include/Rcpp/api/meat/is.h
Log:
applied patch by Thomas Tse to provide missing is<T>() for Character(Vector|Matrix)


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-09-30 01:05:25 UTC (rev 4552)
+++ pkg/Rcpp/ChangeLog	2013-10-02 03:04:36 UTC (rev 4553)
@@ -1,3 +1,10 @@
+2013-10-01  Dirk Eddelbuettel  <edd at debian.org>
+
+	* inst/include/Rcpp/api/meat/is.h: Applied patch by Thomas Tse to
+	provide missing Character(Vector|Matrix)
+
+        * DESCRIPTION: Bump to development release 0.10.5.1
+
 2013-09-28  Dirk Eddelbuettel  <edd at debian.org>
 
         * DESCRIPTION: Release 0.10.5

Modified: pkg/Rcpp/DESCRIPTION
===================================================================
--- pkg/Rcpp/DESCRIPTION	2013-09-30 01:05:25 UTC (rev 4552)
+++ pkg/Rcpp/DESCRIPTION	2013-10-02 03:04:36 UTC (rev 4553)
@@ -1,6 +1,6 @@
 Package: Rcpp
 Title: Seamless R and C++ Integration
-Version: 0.10.5
+Version: 0.10.5.1
 Date: $Date$
 Author: Dirk Eddelbuettel and Romain Francois, with contributions 
  by Douglas Bates, John Chambers and JJ Allaire

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-09-30 01:05:25 UTC (rev 4552)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-02 03:04:36 UTC (rev 4553)
@@ -2,6 +2,17 @@
 \title{News for Package 'Rcpp'}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
 
+\section{Changes in Rcpp version 0.10.5.1 (2013-10-01)}{
+  \itemize{
+    \item Changes in Rcpp API:
+    \itemize{
+      \item Two missing \code{is<>()} templates for
+      \code{CharacterVector} and \code{CharacterMatrix} have been added
+      thanks to Thomas Tse.  
+    }
+  }
+}
+
 \section{Changes in Rcpp version 0.10.5 (2013-09-28)}{
   \itemize{
     \item Changes in R code:

Modified: pkg/Rcpp/inst/THANKS
===================================================================
--- pkg/Rcpp/inst/THANKS	2013-09-30 01:05:25 UTC (rev 4552)
+++ pkg/Rcpp/inst/THANKS	2013-10-02 03:04:36 UTC (rev 4553)
@@ -25,6 +25,7 @@
 Oleg Sklyar             for the incredibly cool inline package
 Alexey Stukalov         for a support enabling Intel Compiler 12.0 support
 Luke Tierney            for helpful discussions on R internals
+Thomas Tse              for a patch filling in two missing is<T>() instances
 Simon Urbanek           for help on OS X build issues and with R internals
 Ken Williams            for additional OS X testing
 Jelmer Ypma             for contributing the Rcout iostreams class patch

Modified: pkg/Rcpp/inst/include/Rcpp/api/meat/is.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/api/meat/is.h	2013-09-30 01:05:25 UTC (rev 4552)
+++ pkg/Rcpp/inst/include/Rcpp/api/meat/is.h	2013-10-02 03:04:36 UTC (rev 4553)
@@ -50,7 +50,12 @@
     template <> inline bool is__simple<String>( SEXP x ){
         return is_atomic(x) && TYPEOF(x) == STRSXP ;
     }
-    
+    template <> inline bool is__simple<CharacterVector>(SEXP x) {
+        return TYPEOF(x) == STRSXP;
+    }
+    template <> inline bool is__simple<CharacterMatrix>(SEXP x) {
+        return TYPEOF(x) == STRSXP && is_matrix(x);
+    }
     template <> inline bool is__simple<RObject>( SEXP x ){
         return true ;
     }


From noreply at r-forge.r-project.org  Thu Oct  3 01:43:24 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  3 Oct 2013 01:43:24 +0200 (CEST)
Subject: [Rcpp-commits] r4554 - in pkg/Rcpp: . inst inst/include/Rcpp/traits
Message-ID: <20131002234325.09A14185EFA@r-forge.r-project.org>

Author: edd
Date: 2013-10-03 01:43:24 +0200 (Thu, 03 Oct 2013)
New Revision: 4554

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/inst/NEWS.Rd
   pkg/Rcpp/inst/THANKS
   pkg/Rcpp/inst/include/Rcpp/traits/is_na.h
Log:
some is.na() fixes also thanks to Thomas Tse


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-02 03:04:36 UTC (rev 4553)
+++ pkg/Rcpp/ChangeLog	2013-10-02 23:43:24 UTC (rev 4554)
@@ -1,3 +1,7 @@
+2013-10-02  Dirk Eddelbuettel  <edd at debian.org>
+
+	* inst/include/Rcpp/traits/is_na.h: More fixes thanks to Thomas Tse
+
 2013-10-01  Dirk Eddelbuettel  <edd at debian.org>
 
 	* inst/include/Rcpp/api/meat/is.h: Applied patch by Thomas Tse to

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-02 03:04:36 UTC (rev 4553)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-02 23:43:24 UTC (rev 4554)
@@ -2,13 +2,13 @@
 \title{News for Package 'Rcpp'}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
 
-\section{Changes in Rcpp version 0.10.5.1 (2013-10-01)}{
+\section{Changes in Rcpp version 0.10.5.1 (2013-10-02)}{
   \itemize{
     \item Changes in Rcpp API:
     \itemize{
       \item Two missing \code{is<>()} templates for
-      \code{CharacterVector} and \code{CharacterMatrix} have been added
-      thanks to Thomas Tse.  
+      \code{CharacterVector} and \code{CharacterMatrix} have been added,
+      and tests for \code{is.na()} have been corrected thanks to Thomas Tse.  
     }
   }
 }

Modified: pkg/Rcpp/inst/THANKS
===================================================================
--- pkg/Rcpp/inst/THANKS	2013-10-02 03:04:36 UTC (rev 4553)
+++ pkg/Rcpp/inst/THANKS	2013-10-02 23:43:24 UTC (rev 4554)
@@ -25,7 +25,7 @@
 Oleg Sklyar             for the incredibly cool inline package
 Alexey Stukalov         for a support enabling Intel Compiler 12.0 support
 Luke Tierney            for helpful discussions on R internals
-Thomas Tse              for a patch filling in two missing is<T>() instances
+Thomas Tse              for several patches with small corrections
 Simon Urbanek           for help on OS X build issues and with R internals
 Ken Williams            for additional OS X testing
 Jelmer Ypma             for contributing the Rcout iostreams class patch

Modified: pkg/Rcpp/inst/include/Rcpp/traits/is_na.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/traits/is_na.h	2013-10-02 03:04:36 UTC (rev 4553)
+++ pkg/Rcpp/inst/include/Rcpp/traits/is_na.h	2013-10-02 23:43:24 UTC (rev 4554)
@@ -1,4 +1,4 @@
-// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; indent-tabs-mode: nil; -*-
 //
 // is_na.h: Rcpp R/C++ interface class library -- vector operators
 //                                                                      
@@ -23,36 +23,41 @@
 #define Rcpp__traits_is_na_h
 
 namespace Rcpp{
-namespace traits{
-	
-	// default to always false, applies to VECSXP, EXPRSXP and RAWSXP
-	template <int RTYPE> 
-	bool is_na( typename storage_type<RTYPE>::type ){
-	    return false ;    
-	}
-	
-	template <> 
-	inline bool is_na<INTSXP>( int x ){
-		return x == NA_INTEGER ;
-	}
-	
-	template <> 
-	inline bool is_na<REALSXP>( double x ){
-		return R_IsNA(x) ;
-	}
-	
-	template <> 
-	inline bool is_na<CPLXSXP>( Rcomplex x ){
-		return R_IsNA(x.r) || R_IsNA(x.i) ;
-	}
-	
-	template <>
-	inline bool is_na<STRSXP>( SEXP x ){ return x == NA_STRING ; }
-	
-	template <>
-	inline bool is_na<LGLSXP>( int x ){ return x == NA_LOGICAL ; }
-	
+
+    namespace traits{
+        
+        // default to always false, applies to VECSXP, EXPRSXP and RAWSXP
+        template <int RTYPE> 
+        bool is_na(typename storage_type<RTYPE>::type) {
+            return false;    
+        }
+        
+        template <> 
+        inline bool is_na<INTSXP>(int x) {
+            return x == NA_INTEGER;
+        }
+        
+        template <> 
+        inline bool is_na<REALSXP>(double x) {
+            return R_IsNA(x) || R_IsNaN(x);
+        }
+        
+        template <> 
+        inline bool is_na<CPLXSXP>(Rcomplex x) {
+            return R_IsNA(x.r) || R_IsNA(x.i) || R_IsNaN(x.r) || R_IsNaN(x.i);
+        }
+        
+        template <>
+        inline bool is_na<STRSXP>(SEXP x) { 
+            return false; // see rcpp-devel on 2013-10-02; was:  x == NA_STRING; 
+        }
+        
+        template <>
+        inline bool is_na<LGLSXP>(int x) { 
+            return x == NA_LOGICAL; 
+        }
+        
+    }
 }
-}
 
 #endif


From noreply at r-forge.r-project.org  Thu Oct  3 14:00:23 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  3 Oct 2013 14:00:23 +0200 (CEST)
Subject: [Rcpp-commits] r4555 - in pkg/Rcpp/inst: . include/Rcpp/traits
Message-ID: <20131003120023.9B455185736@r-forge.r-project.org>

Author: edd
Date: 2013-10-03 14:00:23 +0200 (Thu, 03 Oct 2013)
New Revision: 4555

Modified:
   pkg/Rcpp/inst/NEWS.Rd
   pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h
   pkg/Rcpp/inst/include/Rcpp/traits/is_na.h
Log:
corrected where Thomas's small patch is applied


Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-02 23:43:24 UTC (rev 4554)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-03 12:00:23 UTC (rev 4555)
@@ -8,7 +8,8 @@
     \itemize{
       \item Two missing \code{is<>()} templates for
       \code{CharacterVector} and \code{CharacterMatrix} have been added,
-      and tests for \code{is.na()} have been corrected thanks to Thomas Tse.  
+      and some tests for \code{is_na()} and \code{is_finite()} have been
+      corrected thanks to Thomas Tse.   
     }
   }
 }

Modified: pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h	2013-10-02 23:43:24 UTC (rev 4554)
+++ pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h	2013-10-03 12:00:23 UTC (rev 4555)
@@ -1,4 +1,4 @@
-// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; tab-width: 8 -*-
+// -*- mode: C++; c-indent-level: 4; c-basic-offset: 4; indent-tabs-mode: nil; -*-
 //
 // is_finite.h: Rcpp R/C++ interface class library -- is finite
 //                                                                      
@@ -23,33 +23,38 @@
 #define Rcpp__traits_is_finite_h
 
 namespace Rcpp{
-namespace traits{
-	
-	// default for complex, 
-	template <int RTYPE> 
-	bool is_finite( typename storage_type<RTYPE>::type) ;
-	
-	template <> 
-	inline bool is_finite<INTSXP>( int x ){
-		return x != NA_INTEGER ;
-	}
-	
-	template <> 
-	inline bool is_finite<REALSXP>( double x ){
-		return R_finite(x) ;
-	}
-	
-	template <> 
-	inline bool is_finite<CPLXSXP>( Rcomplex x ){
-		return !( !R_finite(x.r) || !R_finite(x.i) );
-	}
-	
-	template <>
-	inline bool is_finite<STRSXP>( SEXP x ){ return x != NA_STRING ; }
-	
-	template <>
-	inline bool is_finite<LGLSXP>( int x ){ return x != NA_LOGICAL ; }
-	
+
+    namespace traits{
+        
+        // default for complex, 
+        template <int RTYPE> 
+        bool is_finite( typename storage_type<RTYPE>::type);
+        
+        template <> 
+        inline bool is_finite<INTSXP>(int x){
+            return x != NA_INTEGER;
+        }
+        
+        template <> 
+        inline bool is_finite<REALSXP>(double x) {
+            return R_finite(x);
+        }
+        
+        template <> 
+        inline bool is_finite<CPLXSXP>(Rcomplex x) {
+            return !( !R_finite(x.r) || !R_finite(x.i) );
+        }
+        
+        template <>
+        inline bool is_finite<STRSXP>(SEXP x) { 
+            return false; // see rcpp-devel on 2013-10-02; was:  x != NA_STRING; 
+        }
+        
+        template <>
+        inline bool is_finite<LGLSXP>(int x) { 
+            return x != NA_LOGICAL; 
+        }
+        
 }
 }
 

Modified: pkg/Rcpp/inst/include/Rcpp/traits/is_na.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/traits/is_na.h	2013-10-02 23:43:24 UTC (rev 4554)
+++ pkg/Rcpp/inst/include/Rcpp/traits/is_na.h	2013-10-03 12:00:23 UTC (rev 4555)
@@ -49,7 +49,7 @@
         
         template <>
         inline bool is_na<STRSXP>(SEXP x) { 
-            return false; // see rcpp-devel on 2013-10-02; was:  x == NA_STRING; 
+            return x == NA_STRING; 
         }
         
         template <>


From noreply at r-forge.r-project.org  Thu Oct  3 18:34:50 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu,  3 Oct 2013 18:34:50 +0200 (CEST)
Subject: [Rcpp-commits] r4556 - in pkg/Rcpp: . R man
Message-ID: <20131003163450.6BC421851A3@r-forge.r-project.org>

Author: jmc
Date: 2013-10-03 18:34:49 +0200 (Thu, 03 Oct 2013)
New Revision: 4556

Added:
   pkg/Rcpp/R/classModule.R
   pkg/Rcpp/man/classModule.Rd
Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/NAMESPACE
   pkg/Rcpp/R/RcppClass.R
   pkg/Rcpp/R/loadModule.R
   pkg/Rcpp/man/setRcppClass.Rd
Log:
New classModule() function, its documentation and small related changes
to setRcppClass and loadModule


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-03 12:00:23 UTC (rev 4555)
+++ pkg/Rcpp/ChangeLog	2013-10-03 16:34:49 UTC (rev 4556)
@@ -1,3 +1,12 @@
+2013-10-03  John M Chambers  <jmc at r-project.org>
+
+	* R/classModule.R: new function to write module file for class
+	* man/classModule.Rd: documentation for new function classModule()
+	* NAMESPACE: export classModule
+	* R/loadModule.R: clean up an error message
+	* R/RcppClass.R: defaults for module consistent w. classModule()
+	* man/setRcppClass.Rd: add defaults, explain need for saveAs
+
 2013-10-02  Dirk Eddelbuettel  <edd at debian.org>
 
 	* inst/include/Rcpp/traits/is_na.h: More fixes thanks to Thomas Tse

Modified: pkg/Rcpp/NAMESPACE
===================================================================
--- pkg/Rcpp/NAMESPACE	2013-10-03 12:00:23 UTC (rev 4555)
+++ pkg/Rcpp/NAMESPACE	2013-10-03 16:34:49 UTC (rev 4556)
@@ -20,6 +20,7 @@
        setRcppClass,
        loadRcppClass,
        loadModule,
+       classModule,
        cppFunction,
        evalCpp,
        sourceCpp,

Modified: pkg/Rcpp/R/RcppClass.R
===================================================================
--- pkg/Rcpp/R/RcppClass.R	2013-10-03 12:00:23 UTC (rev 4555)
+++ pkg/Rcpp/R/RcppClass.R	2013-10-03 16:34:49 UTC (rev 4556)
@@ -37,7 +37,7 @@
 }
 
 loadRcppClass <- function(Class, CppClass = Class,
-                         module,
+                         module = paste0("class_",Class),
                          fields = character(),
                          contains = character(),
                          methods = list(),
@@ -51,22 +51,15 @@
             assign(saveAs, value, envir = where)
         return(value)
     }
-    if(!missing(module)) {
-        mod <- loadModule(module, NULL, env = where, loadNow = TRUE)
-        storage <- get("storage", envir = as.environment(mod))
-        if(exists(CppClass, envir = storage, inherits = FALSE)) {
-            cppclassinfo <- get(CppClass, envir = storage)
-            if(!is(cppclassinfo, "C++Class"))
-                stop(gettextf("Object \"%s\" in module \"%s\" is not a C++ class description", CppClass, module))
-        }
-        else
-            stop(gettextf("No object \"%s\" in module \"%s\"", CppClass, module))
-    }
-    else {
+    mod <- loadModule(module, NULL, env = where, loadNow = TRUE)
+    storage <- get("storage", envir = as.environment(mod))
+    if(exists(CppClass, envir = storage, inherits = FALSE)) {
+        cppclassinfo <- get(CppClass, envir = storage)
         if(!is(cppclassinfo, "C++Class"))
-            stop("If argument \"module\" is missing, CppClass must be a \"C++Class\" object")
-        CppClass <- .CppClassName(cppclassinfo)
+            stop(gettextf("Object \"%s\" in module \"%s\" is not a C++ class description", CppClass, module))
     }
+    else
+        stop(gettextf("No object \"%s\" in module \"%s\"", CppClass, module))
     allmethods <- .makeCppMethods(methods, cppclassinfo, where)
     allfields <- .makeCppFields(fields, cppclassinfo, where)
     value <- setRefClass(Class, fields = allfields,
@@ -155,9 +148,10 @@
                        cat("Field \"", fi, "\":\n", sep = "")
                        methods::show(field(fi))
                    }
-               }
-                   )
+               },
+    objectPointer = function()
+           .CppObject$.pointer
+    )
 
 
-## </Temporary:>
 

Added: pkg/Rcpp/R/classModule.R
===================================================================
--- pkg/Rcpp/R/classModule.R	                        (rev 0)
+++ pkg/Rcpp/R/classModule.R	2013-10-03 16:34:49 UTC (rev 4556)
@@ -0,0 +1,197 @@
+.stdHeader <- c(
+    "#include <Rcpp.h>",
+    "using namespace Rcpp ;"
+    )
+
+.asString <- function(what) if(is.character(what)) what else deparse(what)
+
+.strings <- function(expr) {
+    if(is.call(expr) && ! identical(expr[[1]], quote(`::`)))
+        lapply(as.list(expr)[-1], .strings)
+    else
+        .asString(expr)
+}
+
+.specifyItems <- function(what) {
+    what <- as.list(what)
+    wn <- allNames(what)
+    simple <- !nzchar(wn)
+    ## todo:  error checking here that unnamed elements are single strings
+    wn[simple] <- as.character(what[simple])
+    names(what) <- wn
+    what[simple] <- list(character())
+    what
+}
+
+.writeFieldFunction <- function(fldi, typei, CppClass, readOnly, ns, con){
+    rootName <- paste0("field_", fldi)
+    writeLines(sprintf("    %s %s_get(%s *obj) { return obj->%s; }\n",
+                       typei, rootName, CppClass, fldi), con)
+    value <- "_get"
+    if(!readOnly) {
+        writeLines(sprintf("    void %s_set(%s *obj, %s value) { obj->%s = value; }\n",
+                           rootName, CppClass, typei, fldi), con)
+        value <- c(value, "_set")
+    }
+    paste0(ns, "::field_", fldi, value)
+}
+
+.writeMethodFunction <- function(mdi, sigi, CppClass, ns, con) {
+    mName <- paste0("method_", mdi)
+    if(length(sigi) < 1)
+        stop(gettextf("The type signature for method %s for class %s was of length 0: Must at least include the return type",
+                      mdi, CppClass))
+    rtnType <- sigi[[1]]
+    sigi <- sigi[-1]
+    if(length(sigi)) {
+        argNames <- paste0("a", seq_along(sigi))
+        args <- paste(" ,", paste(sigi, argNames, collapse = ", "))
+    }
+    else argNames <- args <- ""
+    writeLines(sprintf("    %s %s(%s *obj%s){ return obj->%s(%s); }\n",
+                       rtnType, mName, CppClass, args, mdi, argNames), con)
+    paste0(ns, "::",mName)
+}
+
+classModule <- function(class, constructors, fields, methods,
+                        file = paste0(CppClass, "Module.cpp"),
+                        header = character(),
+                        module = paste0("class_",class), CppClass = class,
+                        readOnly = character(), rename = character(),
+                        Rfile = TRUE) {
+    ## some argument checks
+    ## TODO:  checks on constructors, fields, methods
+    if(length(readOnly)) {
+        readOnly <- as.character(readOnly)
+        if(!all(nzchar(readOnly)))
+            stop("argument readOnly should be a vector of non-empty strings")
+    }
+    newnames <- allNames(rename)
+    if(length(rename)) {
+        if(!all(sapply(rename, function(x) is.character(x) && length(x) == 1 && nzchar(x))))
+            stop("argument rename should be a vector of single, non-empty strings")
+        if(!all(nzchar(newnames)))
+            stop("all the elements of argument rename should be non-empty strings")
+    }
+    if(is.character(file)) {
+        ## are we in a package directory?  Writable, searchable src subdirectory:
+        if(file.access("src",3)==0)
+            cfile <- file.path("src", file)
+        else
+            cfile <- file
+        con <- file(cfile, "w")
+        on.exit({message(sprintf("Wrote C++ file \"%s\"", cfile)); close(con)})
+    }
+    else
+        con <- file
+    ## and for the R code:
+    if(identical(Rfile, FALSE)) {}
+    else {
+        if(identical(Rfile, TRUE))
+            Rfile <- sprintf("%sClass.R",class)
+        if(is.character(Rfile)) {
+            if(file.access("R",3)==0) # in a package directory
+                Rfile <- file.path("R", Rfile)
+            Rcon <- file(Rfile, "w")
+            msg <- sprintf("Wrote R file \"%s\"",Rfile)
+            on.exit({message(msg); close(Rcon)}, add = TRUE)
+        }
+        else
+            Rcon <- Rfile
+        Rfile <- TRUE
+    }
+    temp <- tempfile()
+    mcon <- file(temp, "w")
+    writeLines(.stdHeader, con)
+    if(length(header))
+        writeLines(header, con)
+    writeLines(c("", sprintf("RCPP_MODULE(%s) {\n",module), ""), mcon)
+    writeLines(sprintf("    class_<%s>(\"%s\")\n", CppClass, class), mcon)
+
+    ## the constructors argument defines a list of vectors of types
+    for( cons in constructors) {
+        if(length(cons) > 1 ||
+           (length(cons) == 1 && nzchar(cons) && !identical(cons, "void")))
+            cons <- paste0("<", paste(cons, collapse = ","),">")
+        else
+            cons = ""
+        writeLines(paste0("    .constructor",cons,"()"),mcon)
+    }
+    writeLines("", mcon)
+    flds <- .specifyItems(fields)
+    nm <- names(flds)
+    rdOnly <- nm %in% readOnly
+    macros <- ifelse(rdOnly, ".field_readonly", ".field")
+    test <- nm %in% rename
+    if(any(test))
+        nm[test] <- newnames[match(nm[test], newnames)]
+    ns <- NULL
+    for(i in seq_along(nm)) {
+        typei <- flds[[i]]
+        nmi <- fldi <- nm[[i]]
+        macroi <- macros[[i]]
+        if(!length(typei) || identical(typei, "")) ## direct field
+            writeLines(sprintf("    %s(\"%s\", &%s::%s)",
+                   macroi, nmi, CppClass, fldi), mcon)
+        else { # create a free function, e.g. for an inherited field
+            if(is.null(ns)) { # enclose in a namespace
+                ns <- paste("module",class,"NS", sep = "_")
+                writeLines(sprintf("\nnamespace %s {\n", ns),
+                           con)
+            }
+            fldFuns <- .writeFieldFunction(fldi, typei, CppClass, rdOnly[[i]], ns, con)
+            if(rdOnly[[i]])
+                ## NOTE:  string 3rd arg. required by problem w. module parsing 10/3/13
+                writeLines(sprintf("    .property(\"%s\", &%s, \"read-only field\")",
+                      nmi, fldFuns[[1]]), mcon)
+            else
+                writeLines(sprintf("    .property(\"%s\", &%s, &%s)",
+                      nmi, fldFuns[[1]], fldFuns[[2]]), mcon)
+        }
+    }
+    writeLines("", mcon)
+    sigs <- .specifyItems(methods)
+    nm <- mds <- names(sigs)
+    test <- nm %in% rename
+    if(any(test))
+        nm[test] <- newnames[match(nm[test], newnames)]
+    for(i in seq_along(nm)) {
+        sigi <- sigs[[i]]
+        nmi <-  nm[[i]]
+        mdi <- mds[[i]]
+        if(!length(sigi) || identical(sigi, "")) # direct method
+            writeLines(sprintf("    .method(\"%s\", &%s::%s)",
+                   nmi, CppClass, mdi), mcon)
+        else { # create a free function, e.g. for an inherited method
+            if(is.null(ns)) { # enclose in a namespace
+                ns <- paste("module",class,"NS", sep = "_")
+                writeLines(sprintf("\nnamespace %s {\n", ns),
+                           con)
+            }
+            mFun <- .writeMethodFunction(mdi, sigi, CppClass, ns, con)
+            writeLines(sprintf("    .method(\"%s\", &%s)",
+                  nmi, mFun), mcon)
+        }
+    }
+
+    writeLines("    ;\n}", mcon)
+    close(mcon)
+    if(!is.null(ns))
+        writeLines(sprintf("} // %s", ns), con) # close namespace
+    writeLines(readLines(file(temp, "r")), con)
+    if(Rfile) {
+        if(missing(CppClass))
+            CppString <- ""
+        else
+            CppString <- paste(",",dQuote(CppClass))
+        if(missing(module))
+            ModString <- ""
+        else
+            ModString <- paste(", module =", dQuote(module))
+        writeLines(sprintf("%s <- setRcppClass(\"%s\"%s%s)",
+                               class, class, CppString,ModString), Rcon)
+    }
+}
+
+
+

Modified: pkg/Rcpp/R/loadModule.R
===================================================================
--- pkg/Rcpp/R/loadModule.R	2013-10-03 12:00:23 UTC (rev 4555)
+++ pkg/Rcpp/R/loadModule.R	2013-10-03 16:34:49 UTC (rev 4556)
@@ -74,7 +74,7 @@
         if(is(loadM, "error")) {
             if(.botched)
                return(.DummyModule(module, what))
-            stop(gettextf("Unable to load module \"%s\": %s (and not botched session)",
+            stop(gettextf("Unable to load module \"%s\": %s",
                 as(module, "character"), loadM$message))
         }
         if(!exists(metaName, envir = env, inherits =FALSE))

Added: pkg/Rcpp/man/classModule.Rd
===================================================================
--- pkg/Rcpp/man/classModule.Rd	                        (rev 0)
+++ pkg/Rcpp/man/classModule.Rd	2013-10-03 16:34:49 UTC (rev 4556)
@@ -0,0 +1,205 @@
+\name{classModule}
+\alias{classModule}
+\title{
+Create an Rcpp Module to Expose a C++ Class in R
+}
+\description{
+The arguments specify a C++ class and some combination of
+constructors, fields and methods to be shared with \R by creating a
+corresponding reference class in \R.
+The information needed in the call to \code{classModule()} is the
+simplest possible in order to create a C++ module for the class; for
+example, fields and methods in this class need only be identified by
+their name.
+Inherited fields and methods can also be included, but more
+information is needed.
+The function writes a C++ source file,
+containing a module definition to expose the class to
+\R, plus one line of \R source to create the corresponding reference
+class.
+}
+
+\usage{
+classModule(class, constructors = , fields = , methods = , file = ,
+    header = , module = , CppClass = class, readOnly = , rename = ,
+    Rfile = TRUE)
+}
+
+\arguments{
+  \item{class}{
+The name of the class in \R.  By default, this will be the same as the
+name of the class in C++, unless argument \code{CppClass} is supplied.
+}
+  \item{constructors}{
+A list of the signatures for any of the class constructors to be
+called from \R.  Each element of the list gives the data types in C++
+for the arguments to the corresponding constructor.  See Details and
+the example.
+}
+  \item{fields, methods}{
+The vector of names for the fields and for the methods to be exposed
+in \R.  For inherited fields and methods, type information needs to be
+supplied; see the section \dQuote{Inherited Fields and Methods}.
+}
+  \item{file}{
+Usually, the name for the file on which to write the C++ code,  by default
+\code{paste0(CppClass, "Module.cpp")}.
+If the current working directory in \R is the top-level
+directory for a package, the function writes the file in the
+\code{"src"} subdirectory.
+Otherwise the file is written in the working directory.
+
+The argument may also be a connection, already open for writing.
+
+}
+  \item{header}{
+Whatever lines of C++ header information are needed to include the
+definition of the class.  Typically this includes a file from the
+package where we are writing the module definition, as in the example below.
+}
+  \item{module}{
+The name for the Rcpp module,   by default
+\code{paste0("class_",CppClass)}.
+}
+  \item{CppClass}{
+The name for the class in C++.  By default and usually, the intended
+class name in \R.
+}
+  \item{readOnly}{
+Optional vector of field names.  These fields will be created as
+read-only in the interface.
+}
+  \item{rename}{
+Optional named character vector, used to name fields or methods
+differently in \R from their C++ name.  The elements of the vector are
+the C++ names and the corresponding elements of \code{names(rename)}
+the desired names in \R.  So \code{c(.age = "age")} renames the C++
+field or method \code{age} as \code{.age}.
+}
+  \item{Rfile}{
+Controls the writing of a one-line \R command to create the reference
+class corresponding to the C++ module information.  By default, this
+will be a file \code{paste0(class, "Class.R")}.
+If the working directory is an \R package source
+directory, the file will be written in the \code{R} subdirectory, otherwise in the working directory itself.
+
+Supplying a character string substitutes that file name for the
+default.
+
+The argument may also be a connection  open for
+writing or \code{FALSE} to suppress writing the \R source altogether.
+}
+}
+
+\details{
+The file created by the call to these functions only depends on the
+information in the C++ class supplied.  This file is intended to be
+part of the C++ source for an \R package.  The file only needs to
+modified when the information changes, either because the class has
+changed or because you want to expose different information to \R.  In
+that case you can either recall \code{classModule()} or edit the C++
+file created.
+
+The Rcpp Module mechanism has a number of other optional techniques,
+not covered by \code{classModule()}.  These should be entered into the
+C++ file created.  See the \dQuote{rcpp-modules} vignette with the
+package for current possibilities.
+
+For fields and methods specified directly in the C++ class,
+the fields and method arguments to \code{classModule()} are character vectors naming the
+corresponding members of the class.  For module construction, the
+data types of directly specified fields and of the arguments for the methods are not
+needed.
+
+For \emph{inherited} fields or methods, data type information is
+needed.  See the section \dQuote{Inherited Fields and Methods}.
+
+For exposing class constructors, the module needs to know the
+signatures of the constructors to be exposed; each signature is a
+character vector of the corresponding C++ data types.
+
+}
+
+\section{Inherited Fields and Methods}{
+If the C++ class inherits from one or more other classes, the standard
+Rcpp \code{Module} mechanism can not be used to expose inherited
+fields or methods.
+An indirect mechanism is used, generating free functions in C++ to
+expose the inherited members in \R.
+
+This mechanism requires data type information in the call to
+\code{classModule()}.
+This is provided by naming the corresponding element of the
+\code{fields} or \code{methods} argument with the name of the member.
+The actual element of the \code{fields} argument is then the single
+data type of the field.
+
+For the \code{methods} argument the argument will generally need to be
+a named list.
+The corresponding element of the list is the vector of data types for
+the return value and for the arguments, if any, to the method.
+For example, if C++ method \code{foo()} took a single argument of type
+\code{NumericVector} and returned a value of type \code{long}, the
+\code{methods} argument would be \code{list(foo = c("long",
+  "NumericVector"))}.
+
+See the second example below.
+}
+\value{
+Nothing, called for its side effect.
+}
+\author{
+  John Chambers
+}
+\seealso{
+\code{\link{setRcppClass}}, which must be called from some \R source
+in the package.
+}
+\examples{
+\dontrun{
+### Given the following C++ class, defined in file PopBD.h,
+### the call to classModule() shown below will write a file
+### src/PopBDModule.cpp containing a corresponding module definition.
+###   class PopBD {
+###     public:
+###       PopBD(void);
+###       PopBD(NumericVector initBirth, NumericVector initDeath);
+###   
+###       std::vector<double> birth;
+###       std::vector<double> death;
+###       std::vector<int> lineage;
+###       std::vector<long> size;
+###       void evolve(int);
+###   
+###   };
+### A file R/PopBDClass.R will be written containing the one line:
+###   PopBD <- setRcppClass("PopBD")
+###
+### The call below exposes the lineage and size fields, read-only,
+### and the evolve() method.
+
+classModule("PopBD",
+      constructors =
+        list("", c("NumericVector", "NumericVector")),
+      fields = c("lineage", "size"),
+      methods = "evolve",
+      header = '#include "PopBD.h"',
+      readOnly = c("lineage", "size"))
+
+### Example with inheritance:  the class PopCount inherits from 
+### the previous class, and adds a method table().  It has the same
+### constructors as the previous class.
+### To expose the table() method, and the inherited evolve() method and size field:
+
+classModule("PopCount",
+      constructors =
+        list("", c("NumericVector", "NumericVector")),
+      fields = c(size = "std::vector<long>"),
+      methods = list("table", evolve = c("void", "int")),
+      header = '#include "PopCount.h"',
+      readOnly = "size")
+}
+}
+
+\keyword{ programming }
+\keyword{ classes }

Modified: pkg/Rcpp/man/setRcppClass.Rd
===================================================================
--- pkg/Rcpp/man/setRcppClass.Rd	2013-10-03 12:00:23 UTC (rev 4555)
+++ pkg/Rcpp/man/setRcppClass.Rd	2013-10-03 16:34:49 UTC (rev 4556)
@@ -7,14 +7,15 @@
 }
 \description{
 A class is defined that includes the fields and methods of a C++ class
-defined, usually in this package.  The \R{} class can include new
-methods and fields, such as for prototyping new computations for the
-C++ class.
+defined, usually in this package.  For most applications, it is
+recommended to call
+\code{\link{classModule}()} to write files in the package with a call to \code{setRcppClass()} and the
+C++ module code required.  See Details.
 }
 \usage{
-setRcppClass(Class, CppClass, module, fields = list(), contains = ,
+setRcppClass(Class, CppClass = , module = , fields = list(), contains = ,
              methods = , saveAs = Class, where = , ...)
-loadRcppClass(Class, CppClass, module, fields = character(),
+loadRcppClass(Class, CppClass = , module = , fields = character(),
               contains = character(),
               methods = , saveAs = Class, where = , ...)
 }
@@ -30,19 +31,30 @@
   \item{module}{
 The Rcpp module in which the class is defined.  The module does not
 have to be loaded separately; \code{setRcppClass()} will arrange to
-load the module.
+load the module. By default, \code{"class_"} followed by the C++ class
+name.
 }
   \item{fields, contains, methods}{
 Additional fields, superclasses and method definitions in \R{} that
 extend the C++ class.  These arguments are passed on to
 \code{\link{setRefClass}()}.
-See Details for the implementation of methods.
+See Details for recommendations.
 }
   \item{saveAs}{
 Save a generator object for the class in the package's namespace under
 this name.  By default, the generator object has the name of the
 class.  To avoid saving any generator object, supply this argument as
 \code{NULL}.
+
+(This argument is currently needed because the actual class definition
+must take place at package load time, to include C++ pointer
+information.
+Therefore the
+value returned by \code{setRcppClass()} when called during package
+installation is not the generator object returned by
+\code{setRefClass()}.
+We may be able to hack
+around this problem in the future.)
 }
   \item{where}{
 The environment in which to save the class definition.  By default,


From noreply at r-forge.r-project.org  Fri Oct  4 04:28:56 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri,  4 Oct 2013 04:28:56 +0200 (CEST)
Subject: [Rcpp-commits] r4557 - pkg/Rcpp/inst
Message-ID: <20131004022856.3BA681854BC@r-forge.r-project.org>

Author: edd
Date: 2013-10-04 04:28:55 +0200 (Fri, 04 Oct 2013)
New Revision: 4557

Modified:
   pkg/Rcpp/inst/NEWS.Rd
Log:
NEWS entry for John's new commit


Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-03 16:34:49 UTC (rev 4556)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-04 02:28:55 UTC (rev 4557)
@@ -4,6 +4,12 @@
 
 \section{Changes in Rcpp version 0.10.5.1 (2013-10-02)}{
   \itemize{
+    \item Changes in Modules:
+    \itemize{
+      \item New function \code{classModule} which creates a C++ module
+      for a C++ class, which then results in a corresponding Reference
+      Class made available at the R level.
+    }
     \item Changes in Rcpp API:
     \itemize{
       \item Two missing \code{is<>()} templates for


From noreply at r-forge.r-project.org  Sun Oct  6 23:54:18 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun,  6 Oct 2013 23:54:18 +0200 (CEST)
Subject: [Rcpp-commits] r4558 - in pkg/Rcpp: . R man
Message-ID: <20131006215419.069EE185668@r-forge.r-project.org>

Author: jmc
Date: 2013-10-06 23:54:18 +0200 (Sun, 06 Oct 2013)
New Revision: 4558

Added:
   pkg/Rcpp/R/exposeClass.R
   pkg/Rcpp/man/exposeClass.Rd
Removed:
   pkg/Rcpp/R/classModule.R
   pkg/Rcpp/man/classModule.Rd
Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/NAMESPACE
   pkg/Rcpp/man/setRcppClass.Rd
Log:
Rename classModule to exposeClass; recommend it from setRcppClass.Rd


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-04 02:28:55 UTC (rev 4557)
+++ pkg/Rcpp/ChangeLog	2013-10-06 21:54:18 UTC (rev 4558)
@@ -1,3 +1,12 @@
+2013-10-06  John M Chambers  <jmc at r-project.org>
+
+	* NAMESPACE: change classModule to expose Class
+	* R/classModule.R: delete
+	* man/classModule.Rd: delete
+	* R/exposeClass.R: add
+	* man/exposeClass.Rd: add
+	* man/setRcppClass.Rd: update, clarify, recommend exposeClass()
+
 2013-10-03  John M Chambers  <jmc at r-project.org>
 
 	* R/classModule.R: new function to write module file for class

Modified: pkg/Rcpp/NAMESPACE
===================================================================
--- pkg/Rcpp/NAMESPACE	2013-10-04 02:28:55 UTC (rev 4557)
+++ pkg/Rcpp/NAMESPACE	2013-10-06 21:54:18 UTC (rev 4558)
@@ -20,8 +20,8 @@
        setRcppClass,
        loadRcppClass,
        loadModule,
-       classModule,
        cppFunction,
+       exposeClass,
        evalCpp,
        sourceCpp,
        compileAttributes,

Deleted: pkg/Rcpp/R/classModule.R
===================================================================
--- pkg/Rcpp/R/classModule.R	2013-10-04 02:28:55 UTC (rev 4557)
+++ pkg/Rcpp/R/classModule.R	2013-10-06 21:54:18 UTC (rev 4558)
@@ -1,197 +0,0 @@
-.stdHeader <- c(
-    "#include <Rcpp.h>",
-    "using namespace Rcpp ;"
-    )
-
-.asString <- function(what) if(is.character(what)) what else deparse(what)
-
-.strings <- function(expr) {
-    if(is.call(expr) && ! identical(expr[[1]], quote(`::`)))
-        lapply(as.list(expr)[-1], .strings)
-    else
-        .asString(expr)
-}
-
-.specifyItems <- function(what) {
-    what <- as.list(what)
-    wn <- allNames(what)
-    simple <- !nzchar(wn)
-    ## todo:  error checking here that unnamed elements are single strings
-    wn[simple] <- as.character(what[simple])
-    names(what) <- wn
-    what[simple] <- list(character())
-    what
-}
-
-.writeFieldFunction <- function(fldi, typei, CppClass, readOnly, ns, con){
-    rootName <- paste0("field_", fldi)
-    writeLines(sprintf("    %s %s_get(%s *obj) { return obj->%s; }\n",
-                       typei, rootName, CppClass, fldi), con)
-    value <- "_get"
-    if(!readOnly) {
-        writeLines(sprintf("    void %s_set(%s *obj, %s value) { obj->%s = value; }\n",
-                           rootName, CppClass, typei, fldi), con)
-        value <- c(value, "_set")
-    }
-    paste0(ns, "::field_", fldi, value)
-}
-
-.writeMethodFunction <- function(mdi, sigi, CppClass, ns, con) {
-    mName <- paste0("method_", mdi)
-    if(length(sigi) < 1)
-        stop(gettextf("The type signature for method %s for class %s was of length 0: Must at least include the return type",
-                      mdi, CppClass))
-    rtnType <- sigi[[1]]
-    sigi <- sigi[-1]
-    if(length(sigi)) {
-        argNames <- paste0("a", seq_along(sigi))
-        args <- paste(" ,", paste(sigi, argNames, collapse = ", "))
-    }
-    else argNames <- args <- ""
-    writeLines(sprintf("    %s %s(%s *obj%s){ return obj->%s(%s); }\n",
-                       rtnType, mName, CppClass, args, mdi, argNames), con)
-    paste0(ns, "::",mName)
-}
-
-classModule <- function(class, constructors, fields, methods,
-                        file = paste0(CppClass, "Module.cpp"),
-                        header = character(),
-                        module = paste0("class_",class), CppClass = class,
-                        readOnly = character(), rename = character(),
-                        Rfile = TRUE) {
-    ## some argument checks
-    ## TODO:  checks on constructors, fields, methods
-    if(length(readOnly)) {
-        readOnly <- as.character(readOnly)
-        if(!all(nzchar(readOnly)))
-            stop("argument readOnly should be a vector of non-empty strings")
-    }
-    newnames <- allNames(rename)
-    if(length(rename)) {
-        if(!all(sapply(rename, function(x) is.character(x) && length(x) == 1 && nzchar(x))))
-            stop("argument rename should be a vector of single, non-empty strings")
-        if(!all(nzchar(newnames)))
-            stop("all the elements of argument rename should be non-empty strings")
-    }
-    if(is.character(file)) {
-        ## are we in a package directory?  Writable, searchable src subdirectory:
-        if(file.access("src",3)==0)
-            cfile <- file.path("src", file)
-        else
-            cfile <- file
-        con <- file(cfile, "w")
-        on.exit({message(sprintf("Wrote C++ file \"%s\"", cfile)); close(con)})
-    }
-    else
-        con <- file
-    ## and for the R code:
-    if(identical(Rfile, FALSE)) {}
-    else {
-        if(identical(Rfile, TRUE))
-            Rfile <- sprintf("%sClass.R",class)
-        if(is.character(Rfile)) {
-            if(file.access("R",3)==0) # in a package directory
-                Rfile <- file.path("R", Rfile)
-            Rcon <- file(Rfile, "w")
-            msg <- sprintf("Wrote R file \"%s\"",Rfile)
-            on.exit({message(msg); close(Rcon)}, add = TRUE)
-        }
-        else
-            Rcon <- Rfile
-        Rfile <- TRUE
-    }
-    temp <- tempfile()
-    mcon <- file(temp, "w")
-    writeLines(.stdHeader, con)
-    if(length(header))
-        writeLines(header, con)
-    writeLines(c("", sprintf("RCPP_MODULE(%s) {\n",module), ""), mcon)
-    writeLines(sprintf("    class_<%s>(\"%s\")\n", CppClass, class), mcon)
-
-    ## the constructors argument defines a list of vectors of types
-    for( cons in constructors) {
-        if(length(cons) > 1 ||
-           (length(cons) == 1 && nzchar(cons) && !identical(cons, "void")))
-            cons <- paste0("<", paste(cons, collapse = ","),">")
-        else
-            cons = ""
-        writeLines(paste0("    .constructor",cons,"()"),mcon)
-    }
-    writeLines("", mcon)
-    flds <- .specifyItems(fields)
-    nm <- names(flds)
-    rdOnly <- nm %in% readOnly
-    macros <- ifelse(rdOnly, ".field_readonly", ".field")
-    test <- nm %in% rename
-    if(any(test))
-        nm[test] <- newnames[match(nm[test], newnames)]
-    ns <- NULL
-    for(i in seq_along(nm)) {
-        typei <- flds[[i]]
-        nmi <- fldi <- nm[[i]]
-        macroi <- macros[[i]]
-        if(!length(typei) || identical(typei, "")) ## direct field
-            writeLines(sprintf("    %s(\"%s\", &%s::%s)",
-                   macroi, nmi, CppClass, fldi), mcon)
-        else { # create a free function, e.g. for an inherited field
-            if(is.null(ns)) { # enclose in a namespace
-                ns <- paste("module",class,"NS", sep = "_")
-                writeLines(sprintf("\nnamespace %s {\n", ns),
-                           con)
-            }
-            fldFuns <- .writeFieldFunction(fldi, typei, CppClass, rdOnly[[i]], ns, con)
-            if(rdOnly[[i]])
-                ## NOTE:  string 3rd arg. required by problem w. module parsing 10/3/13
-                writeLines(sprintf("    .property(\"%s\", &%s, \"read-only field\")",
-                      nmi, fldFuns[[1]]), mcon)
-            else
-                writeLines(sprintf("    .property(\"%s\", &%s, &%s)",
-                      nmi, fldFuns[[1]], fldFuns[[2]]), mcon)
-        }
-    }
-    writeLines("", mcon)
-    sigs <- .specifyItems(methods)
-    nm <- mds <- names(sigs)
-    test <- nm %in% rename
-    if(any(test))
-        nm[test] <- newnames[match(nm[test], newnames)]
-    for(i in seq_along(nm)) {
-        sigi <- sigs[[i]]
-        nmi <-  nm[[i]]
-        mdi <- mds[[i]]
-        if(!length(sigi) || identical(sigi, "")) # direct method
-            writeLines(sprintf("    .method(\"%s\", &%s::%s)",
-                   nmi, CppClass, mdi), mcon)
-        else { # create a free function, e.g. for an inherited method
-            if(is.null(ns)) { # enclose in a namespace
-                ns <- paste("module",class,"NS", sep = "_")
-                writeLines(sprintf("\nnamespace %s {\n", ns),
-                           con)
-            }
-            mFun <- .writeMethodFunction(mdi, sigi, CppClass, ns, con)
-            writeLines(sprintf("    .method(\"%s\", &%s)",
-                  nmi, mFun), mcon)
-        }
-    }
-
-    writeLines("    ;\n}", mcon)
-    close(mcon)
-    if(!is.null(ns))
-        writeLines(sprintf("} // %s", ns), con) # close namespace
-    writeLines(readLines(file(temp, "r")), con)
-    if(Rfile) {
-        if(missing(CppClass))
-            CppString <- ""
-        else
-            CppString <- paste(",",dQuote(CppClass))
-        if(missing(module))
-            ModString <- ""
-        else
-            ModString <- paste(", module =", dQuote(module))
-        writeLines(sprintf("%s <- setRcppClass(\"%s\"%s%s)",
-                               class, class, CppString,ModString), Rcon)
-    }
-}
-
-
-

Added: pkg/Rcpp/R/exposeClass.R
===================================================================
--- pkg/Rcpp/R/exposeClass.R	                        (rev 0)
+++ pkg/Rcpp/R/exposeClass.R	2013-10-06 21:54:18 UTC (rev 4558)
@@ -0,0 +1,197 @@
+.stdHeader <- c(
+    "#include <Rcpp.h>",
+    "using namespace Rcpp ;"
+    )
+
+.asString <- function(what) if(is.character(what)) what else deparse(what)
+
+.strings <- function(expr) {
+    if(is.call(expr) && ! identical(expr[[1]], quote(`::`)))
+        lapply(as.list(expr)[-1], .strings)
+    else
+        .asString(expr)
+}
+
+.specifyItems <- function(what) {
+    what <- as.list(what)
+    wn <- allNames(what)
+    simple <- !nzchar(wn)
+    ## todo:  error checking here that unnamed elements are single strings
+    wn[simple] <- as.character(what[simple])
+    names(what) <- wn
+    what[simple] <- list(character())
+    what
+}
+
+.writeFieldFunction <- function(fldi, typei, CppClass, readOnly, ns, con){
+    rootName <- paste0("field_", fldi)
+    writeLines(sprintf("    %s %s_get(%s *obj) { return obj->%s; }\n",
+                       typei, rootName, CppClass, fldi), con)
+    value <- "_get"
+    if(!readOnly) {
+        writeLines(sprintf("    void %s_set(%s *obj, %s value) { obj->%s = value; }\n",
+                           rootName, CppClass, typei, fldi), con)
+        value <- c(value, "_set")
+    }
+    paste0(ns, "::field_", fldi, value)
+}
+
+.writeMethodFunction <- function(mdi, sigi, CppClass, ns, con) {
+    mName <- paste0("method_", mdi)
+    if(length(sigi) < 1)
+        stop(gettextf("The type signature for method %s for class %s was of length 0: Must at least include the return type",
+                      mdi, CppClass))
+    rtnType <- sigi[[1]]
+    sigi <- sigi[-1]
+    if(length(sigi)) {
+        argNames <- paste0("a", seq_along(sigi))
+        args <- paste(" ,", paste(sigi, argNames, collapse = ", "))
+    }
+    else argNames <- args <- ""
+    writeLines(sprintf("    %s %s(%s *obj%s){ return obj->%s(%s); }\n",
+                       rtnType, mName, CppClass, args, mdi, argNames), con)
+    paste0(ns, "::",mName)
+}
+
+exposeClass <- function(class, constructors, fields, methods,
+                        file = paste0(CppClass, "Module.cpp"),
+                        header = character(),
+                        module = paste0("class_",class), CppClass = class,
+                        readOnly = character(), rename = character(),
+                        Rfile = TRUE) {
+    ## some argument checks
+    ## TODO:  checks on constructors, fields, methods
+    if(length(readOnly)) {
+        readOnly <- as.character(readOnly)
+        if(!all(nzchar(readOnly)))
+            stop("argument readOnly should be a vector of non-empty strings")
+    }
+    newnames <- allNames(rename)
+    if(length(rename)) {
+        if(!all(sapply(rename, function(x) is.character(x) && length(x) == 1 && nzchar(x))))
+            stop("argument rename should be a vector of single, non-empty strings")
+        if(!all(nzchar(newnames)))
+            stop("all the elements of argument rename should be non-empty strings")
+    }
+    if(is.character(file)) {
+        ## are we in a package directory?  Writable, searchable src subdirectory:
+        if(file.access("src",3)==0)
+            cfile <- file.path("src", file)
+        else
+            cfile <- file
+        con <- file(cfile, "w")
+        on.exit({message(sprintf("Wrote C++ file \"%s\"", cfile)); close(con)})
+    }
+    else
+        con <- file
+    ## and for the R code:
+    if(identical(Rfile, FALSE)) {}
+    else {
+        if(identical(Rfile, TRUE))
+            Rfile <- sprintf("%sClass.R",class)
+        if(is.character(Rfile)) {
+            if(file.access("R",3)==0) # in a package directory
+                Rfile <- file.path("R", Rfile)
+            Rcon <- file(Rfile, "w")
+            msg <- sprintf("Wrote R file \"%s\"",Rfile)
+            on.exit({message(msg); close(Rcon)}, add = TRUE)
+        }
+        else
+            Rcon <- Rfile
+        Rfile <- TRUE
+    }
+    temp <- tempfile()
+    mcon <- file(temp, "w")
+    writeLines(.stdHeader, con)
+    if(length(header))
+        writeLines(header, con)
+    writeLines(c("", sprintf("RCPP_MODULE(%s) {\n",module), ""), mcon)
+    writeLines(sprintf("    class_<%s>(\"%s\")\n", CppClass, class), mcon)
+
+    ## the constructors argument defines a list of vectors of types
+    for( cons in constructors) {
+        if(length(cons) > 1 ||
+           (length(cons) == 1 && nzchar(cons) && !identical(cons, "void")))
+            cons <- paste0("<", paste(cons, collapse = ","),">")
+        else
+            cons = ""
+        writeLines(paste0("    .constructor",cons,"()"),mcon)
+    }
+    writeLines("", mcon)
+    flds <- .specifyItems(fields)
+    nm <- names(flds)
+    rdOnly <- nm %in% readOnly
+    macros <- ifelse(rdOnly, ".field_readonly", ".field")
+    test <- nm %in% rename
+    if(any(test))
+        nm[test] <- newnames[match(nm[test], newnames)]
+    ns <- NULL
+    for(i in seq_along(nm)) {
+        typei <- flds[[i]]
+        nmi <- fldi <- nm[[i]]
+        macroi <- macros[[i]]
+        if(!length(typei) || identical(typei, "")) ## direct field
+            writeLines(sprintf("    %s(\"%s\", &%s::%s)",
+                   macroi, nmi, CppClass, fldi), mcon)
+        else { # create a free function, e.g. for an inherited field
+            if(is.null(ns)) { # enclose in a namespace
+                ns <- paste("module",class,"NS", sep = "_")
+                writeLines(sprintf("\nnamespace %s {\n", ns),
+                           con)
+            }
+            fldFuns <- .writeFieldFunction(fldi, typei, CppClass, rdOnly[[i]], ns, con)
+            if(rdOnly[[i]])
+                ## NOTE:  string 3rd arg. required by problem w. module parsing 10/3/13
+                writeLines(sprintf("    .property(\"%s\", &%s, \"read-only field\")",
+                      nmi, fldFuns[[1]]), mcon)
+            else
+                writeLines(sprintf("    .property(\"%s\", &%s, &%s)",
+                      nmi, fldFuns[[1]], fldFuns[[2]]), mcon)
+        }
+    }
+    writeLines("", mcon)
+    sigs <- .specifyItems(methods)
+    nm <- mds <- names(sigs)
+    test <- nm %in% rename
+    if(any(test))
+        nm[test] <- newnames[match(nm[test], newnames)]
+    for(i in seq_along(nm)) {
+        sigi <- sigs[[i]]
+        nmi <-  nm[[i]]
+        mdi <- mds[[i]]
+        if(!length(sigi) || identical(sigi, "")) # direct method
+            writeLines(sprintf("    .method(\"%s\", &%s::%s)",
+                   nmi, CppClass, mdi), mcon)
+        else { # create a free function, e.g. for an inherited method
+            if(is.null(ns)) { # enclose in a namespace
+                ns <- paste("module",class,"NS", sep = "_")
+                writeLines(sprintf("\nnamespace %s {\n", ns),
+                           con)
+            }
+            mFun <- .writeMethodFunction(mdi, sigi, CppClass, ns, con)
+            writeLines(sprintf("    .method(\"%s\", &%s)",
+                  nmi, mFun), mcon)
+        }
+    }
+
+    writeLines("    ;\n}", mcon)
+    close(mcon)
+    if(!is.null(ns))
+        writeLines(sprintf("} // %s", ns), con) # close namespace
+    writeLines(readLines(file(temp, "r")), con)
+    if(Rfile) {
+        if(missing(CppClass))
+            CppString <- ""
+        else
+            CppString <- paste(",",dQuote(CppClass))
+        if(missing(module))
+            ModString <- ""
+        else
+            ModString <- paste(", module =", dQuote(module))
+        writeLines(sprintf("%s <- setRcppClass(\"%s\"%s%s)",
+                               class, class, CppString,ModString), Rcon)
+    }
+}
+
+
+

Deleted: pkg/Rcpp/man/classModule.Rd
===================================================================
--- pkg/Rcpp/man/classModule.Rd	2013-10-04 02:28:55 UTC (rev 4557)
+++ pkg/Rcpp/man/classModule.Rd	2013-10-06 21:54:18 UTC (rev 4558)
@@ -1,205 +0,0 @@
-\name{classModule}
-\alias{classModule}
-\title{
-Create an Rcpp Module to Expose a C++ Class in R
-}
-\description{
-The arguments specify a C++ class and some combination of
-constructors, fields and methods to be shared with \R by creating a
-corresponding reference class in \R.
-The information needed in the call to \code{classModule()} is the
-simplest possible in order to create a C++ module for the class; for
-example, fields and methods in this class need only be identified by
-their name.
-Inherited fields and methods can also be included, but more
-information is needed.
-The function writes a C++ source file,
-containing a module definition to expose the class to
-\R, plus one line of \R source to create the corresponding reference
-class.
-}
-
-\usage{
-classModule(class, constructors = , fields = , methods = , file = ,
-    header = , module = , CppClass = class, readOnly = , rename = ,
-    Rfile = TRUE)
-}
-
-\arguments{
-  \item{class}{
-The name of the class in \R.  By default, this will be the same as the
-name of the class in C++, unless argument \code{CppClass} is supplied.
-}
-  \item{constructors}{
-A list of the signatures for any of the class constructors to be
-called from \R.  Each element of the list gives the data types in C++
-for the arguments to the corresponding constructor.  See Details and
-the example.
-}
-  \item{fields, methods}{
-The vector of names for the fields and for the methods to be exposed
-in \R.  For inherited fields and methods, type information needs to be
-supplied; see the section \dQuote{Inherited Fields and Methods}.
-}
-  \item{file}{
-Usually, the name for the file on which to write the C++ code,  by default
-\code{paste0(CppClass, "Module.cpp")}.
-If the current working directory in \R is the top-level
-directory for a package, the function writes the file in the
-\code{"src"} subdirectory.
-Otherwise the file is written in the working directory.
-
-The argument may also be a connection, already open for writing.
-
-}
-  \item{header}{
-Whatever lines of C++ header information are needed to include the
-definition of the class.  Typically this includes a file from the
-package where we are writing the module definition, as in the example below.
-}
-  \item{module}{
-The name for the Rcpp module,   by default
-\code{paste0("class_",CppClass)}.
-}
-  \item{CppClass}{
-The name for the class in C++.  By default and usually, the intended
-class name in \R.
-}
-  \item{readOnly}{
-Optional vector of field names.  These fields will be created as
-read-only in the interface.
-}
-  \item{rename}{
-Optional named character vector, used to name fields or methods
-differently in \R from their C++ name.  The elements of the vector are
-the C++ names and the corresponding elements of \code{names(rename)}
-the desired names in \R.  So \code{c(.age = "age")} renames the C++
-field or method \code{age} as \code{.age}.
-}
-  \item{Rfile}{
-Controls the writing of a one-line \R command to create the reference
-class corresponding to the C++ module information.  By default, this
-will be a file \code{paste0(class, "Class.R")}.
-If the working directory is an \R package source
-directory, the file will be written in the \code{R} subdirectory, otherwise in the working directory itself.
-
-Supplying a character string substitutes that file name for the
-default.
-
-The argument may also be a connection  open for
-writing or \code{FALSE} to suppress writing the \R source altogether.
-}
-}
-
-\details{
-The file created by the call to these functions only depends on the
-information in the C++ class supplied.  This file is intended to be
-part of the C++ source for an \R package.  The file only needs to
-modified when the information changes, either because the class has
-changed or because you want to expose different information to \R.  In
-that case you can either recall \code{classModule()} or edit the C++
-file created.
-
-The Rcpp Module mechanism has a number of other optional techniques,
-not covered by \code{classModule()}.  These should be entered into the
-C++ file created.  See the \dQuote{rcpp-modules} vignette with the
-package for current possibilities.
-
-For fields and methods specified directly in the C++ class,
-the fields and method arguments to \code{classModule()} are character vectors naming the
-corresponding members of the class.  For module construction, the
-data types of directly specified fields and of the arguments for the methods are not
-needed.
-
-For \emph{inherited} fields or methods, data type information is
-needed.  See the section \dQuote{Inherited Fields and Methods}.
-
-For exposing class constructors, the module needs to know the
-signatures of the constructors to be exposed; each signature is a
-character vector of the corresponding C++ data types.
-
-}
-
-\section{Inherited Fields and Methods}{
-If the C++ class inherits from one or more other classes, the standard
-Rcpp \code{Module} mechanism can not be used to expose inherited
-fields or methods.
-An indirect mechanism is used, generating free functions in C++ to
-expose the inherited members in \R.
-
-This mechanism requires data type information in the call to
-\code{classModule()}.
-This is provided by naming the corresponding element of the
-\code{fields} or \code{methods} argument with the name of the member.
-The actual element of the \code{fields} argument is then the single
-data type of the field.
-
-For the \code{methods} argument the argument will generally need to be
-a named list.
-The corresponding element of the list is the vector of data types for
-the return value and for the arguments, if any, to the method.
-For example, if C++ method \code{foo()} took a single argument of type
-\code{NumericVector} and returned a value of type \code{long}, the
-\code{methods} argument would be \code{list(foo = c("long",
-  "NumericVector"))}.
-
-See the second example below.
-}
-\value{
-Nothing, called for its side effect.
-}
-\author{
-  John Chambers
-}
-\seealso{
-\code{\link{setRcppClass}}, which must be called from some \R source
-in the package.
-}
-\examples{
-\dontrun{
-### Given the following C++ class, defined in file PopBD.h,
-### the call to classModule() shown below will write a file
-### src/PopBDModule.cpp containing a corresponding module definition.
-###   class PopBD {
-###     public:
-###       PopBD(void);
-###       PopBD(NumericVector initBirth, NumericVector initDeath);
-###   
-###       std::vector<double> birth;
-###       std::vector<double> death;
-###       std::vector<int> lineage;
-###       std::vector<long> size;
-###       void evolve(int);
-###   
-###   };
-### A file R/PopBDClass.R will be written containing the one line:
-###   PopBD <- setRcppClass("PopBD")
-###
-### The call below exposes the lineage and size fields, read-only,
-### and the evolve() method.
-
-classModule("PopBD",
-      constructors =
-        list("", c("NumericVector", "NumericVector")),
-      fields = c("lineage", "size"),
-      methods = "evolve",
-      header = '#include "PopBD.h"',
-      readOnly = c("lineage", "size"))
-
-### Example with inheritance:  the class PopCount inherits from 
-### the previous class, and adds a method table().  It has the same
-### constructors as the previous class.
-### To expose the table() method, and the inherited evolve() method and size field:
-
-classModule("PopCount",
-      constructors =
-        list("", c("NumericVector", "NumericVector")),
-      fields = c(size = "std::vector<long>"),
-      methods = list("table", evolve = c("void", "int")),
-      header = '#include "PopCount.h"',
-      readOnly = "size")
-}
-}
-
-\keyword{ programming }
-\keyword{ classes }

Added: pkg/Rcpp/man/exposeClass.Rd
===================================================================
--- pkg/Rcpp/man/exposeClass.Rd	                        (rev 0)
+++ pkg/Rcpp/man/exposeClass.Rd	2013-10-06 21:54:18 UTC (rev 4558)
@@ -0,0 +1,205 @@
+\name{exposeClass}
+\alias{exposeClass}
+\title{
+Create an Rcpp Module to Expose a C++ Class in R
+}
+\description{
+The arguments specify a C++ class and some combination of
+constructors, fields and methods to be shared with \R by creating a
+corresponding reference class in \R.
+The information needed in the call to \code{exposeClass()} is the
+simplest possible in order to create a C++ module for the class; for
+example, fields and methods in this class need only be identified by
+their name.
+Inherited fields and methods can also be included, but more
+information is needed.
+The function writes a C++ source file,
+containing a module definition to expose the class to
+\R, plus one line of \R source to create the corresponding reference
+class.
+}
+
+\usage{
+exposeClass(class, constructors = , fields = , methods = , file = ,
+    header = , module = , CppClass = class, readOnly = , rename = ,
+    Rfile = TRUE)
+}
+
+\arguments{
+  \item{class}{
+The name of the class in \R.  By default, this will be the same as the
+name of the class in C++, unless argument \code{CppClass} is supplied.
+}
+  \item{constructors}{
+A list of the signatures for any of the class constructors to be
+called from \R.  Each element of the list gives the data types in C++
+for the arguments to the corresponding constructor.  See Details and
+the example.
+}
+  \item{fields, methods}{
+The vector of names for the fields and for the methods to be exposed
+in \R.  For inherited fields and methods, type information needs to be
+supplied; see the section \dQuote{Inherited Fields and Methods}.
+}
+  \item{file}{
+Usually, the name for the file on which to write the C++ code,  by default
+\code{paste0(CppClass, "Module.cpp")}.
+If the current working directory in \R is the top-level
+directory for a package, the function writes the file in the
+\code{"src"} subdirectory.
+Otherwise the file is written in the working directory.
+
+The argument may also be a connection, already open for writing.
+
+}
+  \item{header}{
+Whatever lines of C++ header information are needed to include the
+definition of the class.  Typically this includes a file from the
+package where we are writing the module definition, as in the example below.
+}
+  \item{module}{
+The name for the Rcpp module,   by default
+\code{paste0("class_",CppClass)}.
+}
+  \item{CppClass}{
+The name for the class in C++.  By default and usually, the intended
+class name in \R.
+}
+  \item{readOnly}{
+Optional vector of field names.  These fields will be created as
+read-only in the interface.
+}
+  \item{rename}{
+Optional named character vector, used to name fields or methods
+differently in \R from their C++ name.  The elements of the vector are
+the C++ names and the corresponding elements of \code{names(rename)}
+the desired names in \R.  So \code{c(.age = "age")} renames the C++
+field or method \code{age} as \code{.age}.
+}
+  \item{Rfile}{
+Controls the writing of a one-line \R command to create the reference
+class corresponding to the C++ module information.  By default, this
+will be a file \code{paste0(class, "Class.R")}.
+If the working directory is an \R package source
+directory, the file will be written in the \code{R} subdirectory, otherwise in the working directory itself.
+
+Supplying a character string substitutes that file name for the
+default.
+
+The argument may also be a connection  open for
+writing or \code{FALSE} to suppress writing the \R source altogether.
+}
+}
+
+\details{
+The file created by the call to these functions only depends on the
+information in the C++ class supplied.  This file is intended to be
+part of the C++ source for an \R package.  The file only needs to
+modified when the information changes, either because the class has
+changed or because you want to expose different information to \R.  In
+that case you can either recall \code{exposeClass()} or edit the C++
+file created.
+
+The Rcpp Module mechanism has a number of other optional techniques,
+not covered by \code{exposeClass()}.  These should be entered into the
+C++ file created.  See the \dQuote{rcpp-modules} vignette with the
+package for current possibilities.
+
+For fields and methods specified directly in the C++ class,
+the fields and method arguments to \code{exposeClass()} are character vectors naming the
+corresponding members of the class.  For module construction, the
+data types of directly specified fields and of the arguments for the methods are not
+needed.
+
+For \emph{inherited} fields or methods, data type information is
+needed.  See the section \dQuote{Inherited Fields and Methods}.
+
+For exposing class constructors, the module needs to know the
+signatures of the constructors to be exposed; each signature is a
+character vector of the corresponding C++ data types.
+
+}
+
+\section{Inherited Fields and Methods}{
+If the C++ class inherits from one or more other classes, the standard
+Rcpp \code{Module} mechanism can not be used to expose inherited
+fields or methods.
+An indirect mechanism is used, generating free functions in C++ to
+expose the inherited members in \R.
+
+This mechanism requires data type information in the call to
+\code{exposeClass()}.
+This is provided by naming the corresponding element of the
+\code{fields} or \code{methods} argument with the name of the member.
+The actual element of the \code{fields} argument is then the single
+data type of the field.
+
+For the \code{methods} argument the argument will generally need to be
+a named list.
+The corresponding element of the list is the vector of data types for
+the return value and for the arguments, if any, to the method.
+For example, if C++ method \code{foo()} took a single argument of type
+\code{NumericVector} and returned a value of type \code{long}, the
+\code{methods} argument would be \code{list(foo = c("long",
+  "NumericVector"))}.
+
+See the second example below.
+}
+\value{
+Nothing, called for its side effect.
+}
+\author{
+  John Chambers
+}
+\seealso{
+\code{\link{setRcppClass}}, which must be called from some \R source
+in the package.
+}
+\examples{
+\dontrun{
+### Given the following C++ class, defined in file PopBD.h,
+### the call to exposeClass() shown below will write a file
+### src/PopBDModule.cpp containing a corresponding module definition.
+###   class PopBD {
+###     public:
+###       PopBD(void);
+###       PopBD(NumericVector initBirth, NumericVector initDeath);
+###   
+###       std::vector<double> birth;
+###       std::vector<double> death;
+###       std::vector<int> lineage;
+###       std::vector<long> size;
+###       void evolve(int);
+###   
+###   };
+### A file R/PopBDClass.R will be written containing the one line:
+###   PopBD <- setRcppClass("PopBD")
+###
+### The call below exposes the lineage and size fields, read-only,
+### and the evolve() method.
+
+exposeClass("PopBD",
+      constructors =
+        list("", c("NumericVector", "NumericVector")),
+      fields = c("lineage", "size"),
+      methods = "evolve",
+      header = '#include "PopBD.h"',
+      readOnly = c("lineage", "size"))
+
+### Example with inheritance:  the class PopCount inherits from 
+### the previous class, and adds a method table().  It has the same
+### constructors as the previous class.
+### To expose the table() method, and the inherited evolve() method and size field:
+
+exposeClass("PopCount",
+      constructors =
+        list("", c("NumericVector", "NumericVector")),
+      fields = c(size = "std::vector<long>"),
+      methods = list("table", evolve = c("void", "int")),
+      header = '#include "PopCount.h"',
+      readOnly = "size")
+}
+}
+
+\keyword{ programming }
+\keyword{ classes }

Modified: pkg/Rcpp/man/setRcppClass.Rd
===================================================================
--- pkg/Rcpp/man/setRcppClass.Rd	2013-10-04 02:28:55 UTC (rev 4557)
+++ pkg/Rcpp/man/setRcppClass.Rd	2013-10-06 21:54:18 UTC (rev 4558)
@@ -6,11 +6,13 @@
 Create a Class Extending a C++ Class
 }
 \description{
-A class is defined that includes the fields and methods of a C++ class
-defined, usually in this package.  For most applications, it is
-recommended to call
-\code{\link{classModule}()} to write files in the package with a call to \code{setRcppClass()} and the
-C++ module code required.  See Details.
+These routines create a class definition in \R for an exposed C++
+class, setting up and executing a load action to incorporate the C++
+pointer information.
+Neither function should normally need to be called directly; for most applications,
+a call to
+\code{\link{exposeClass}()} will create both C++ and \R code files to
+expose the C++ class.
 }
 \usage{
 setRcppClass(Class, CppClass = , module = , fields = list(), contains = ,
@@ -33,12 +35,14 @@
 have to be loaded separately; \code{setRcppClass()} will arrange to
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/rcpp -r 4558

From noreply at r-forge.r-project.org  Sun Oct  6 23:54:52 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun,  6 Oct 2013 23:54:52 +0200 (CEST)
Subject: [Rcpp-commits] r4559 - pkg/Rcpp
Message-ID: <20131006215453.027F4185668@r-forge.r-project.org>

Author: jmc
Date: 2013-10-06 23:54:52 +0200 (Sun, 06 Oct 2013)
New Revision: 4559

Modified:
   pkg/Rcpp/ChangeLog
Log:
typo

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-06 21:54:18 UTC (rev 4558)
+++ pkg/Rcpp/ChangeLog	2013-10-06 21:54:52 UTC (rev 4559)
@@ -1,6 +1,6 @@
 2013-10-06  John M Chambers  <jmc at r-project.org>
 
-	* NAMESPACE: change classModule to expose Class
+	* NAMESPACE: change classModule to exposeClass
 	* R/classModule.R: delete
 	* man/classModule.Rd: delete
 	* R/exposeClass.R: add


From noreply at r-forge.r-project.org  Mon Oct  7 00:11:33 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  7 Oct 2013 00:11:33 +0200 (CEST)
Subject: [Rcpp-commits] r4560 - in pkg/Rcpp: . R
Message-ID: <20131006221133.B36F11845BE@r-forge.r-project.org>

Author: jmc
Date: 2013-10-07 00:11:32 +0200 (Mon, 07 Oct 2013)
New Revision: 4560

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/R/exposeClass.R
Log:
Avoid warning from unclosed file(temp, "r") in exposeClass()


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-06 21:54:52 UTC (rev 4559)
+++ pkg/Rcpp/ChangeLog	2013-10-06 22:11:32 UTC (rev 4560)
@@ -1,5 +1,10 @@
 2013-10-06  John M Chambers  <jmc at r-project.org>
 
+	* R/exposeClass.R: avoid warning from unclosed file()
+
+
+2013-10-06  John M Chambers  <jmc at r-project.org>
+
 	* NAMESPACE: change classModule to exposeClass
 	* R/classModule.R: delete
 	* man/classModule.Rd: delete

Modified: pkg/Rcpp/R/exposeClass.R
===================================================================
--- pkg/Rcpp/R/exposeClass.R	2013-10-06 21:54:52 UTC (rev 4559)
+++ pkg/Rcpp/R/exposeClass.R	2013-10-06 22:11:32 UTC (rev 4560)
@@ -100,8 +100,8 @@
             Rcon <- Rfile
         Rfile <- TRUE
     }
-    temp <- tempfile()
-    mcon <- file(temp, "w")
+    mfile <- tempfile()
+    mcon <- file(mfile, "w")
     writeLines(.stdHeader, con)
     if(length(header))
         writeLines(header, con)
@@ -178,7 +178,7 @@
     close(mcon)
     if(!is.null(ns))
         writeLines(sprintf("} // %s", ns), con) # close namespace
-    writeLines(readLines(file(temp, "r")), con)
+    writeLines(readLines(mfile), con)
     if(Rfile) {
         if(missing(CppClass))
             CppString <- ""


From noreply at r-forge.r-project.org  Mon Oct  7 17:23:02 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  7 Oct 2013 17:23:02 +0200 (CEST)
Subject: [Rcpp-commits] r4561 - in pkg/Rcpp: . inst
Message-ID: <20131007152302.4BE3B186006@r-forge.r-project.org>

Author: edd
Date: 2013-10-07 17:23:02 +0200 (Mon, 07 Oct 2013)
New Revision: 4561

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/inst/NEWS.Rd
Log:
keep NEWS.Rd current with changes made by John but documented only in ChangeLog


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-06 22:11:32 UTC (rev 4560)
+++ pkg/Rcpp/ChangeLog	2013-10-07 15:23:02 UTC (rev 4561)
@@ -2,7 +2,6 @@
 
 	* R/exposeClass.R: avoid warning from unclosed file()
 
-
 2013-10-06  John M Chambers  <jmc at r-project.org>
 
 	* NAMESPACE: change classModule to exposeClass

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-06 22:11:32 UTC (rev 4560)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-07 15:23:02 UTC (rev 4561)
@@ -2,11 +2,11 @@
 \title{News for Package 'Rcpp'}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
 
-\section{Changes in Rcpp version 0.10.5.1 (2013-10-02)}{
+\section{Changes in Rcpp version 0.10.5.1 (2013-10-07)}{
   \itemize{
     \item Changes in Modules:
     \itemize{
-      \item New function \code{classModule} which creates a C++ module
+      \item New function \code{exposeClass} which creates a C++ module
       for a C++ class, which then results in a corresponding Reference
       Class made available at the R level.
     }


From noreply at r-forge.r-project.org  Mon Oct  7 18:32:53 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon,  7 Oct 2013 18:32:53 +0200 (CEST)
Subject: [Rcpp-commits] r4562 - pkg/Rcpp/inst
Message-ID: <20131007163253.90ABE185F33@r-forge.r-project.org>

Author: jmc
Date: 2013-10-07 18:32:53 +0200 (Mon, 07 Oct 2013)
New Revision: 4562

Modified:
   pkg/Rcpp/inst/NEWS.Rd
Log:
Correct the announcement about exposeClass()


Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-07 15:23:02 UTC (rev 4561)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-07 16:32:53 UTC (rev 4562)
@@ -4,11 +4,13 @@
 
 \section{Changes in Rcpp version 0.10.5.1 (2013-10-07)}{
   \itemize{
-    \item Changes in Modules:
+    \item Exposing C++ classes from a package:
     \itemize{
-      \item New function \code{exposeClass} which creates a C++ module
-      for a C++ class, which then results in a corresponding Reference
-      Class made available at the R level.
+      \item The function \code{exposeClass} takes a description of the
+        constructors, fields and methods to be exposed from a C++
+        class, and writes C++ and R files in the package.  Inherited
+        classes can be dealt with, but require data type information.
+        This approach avoids hand-coding module files.
     }
     \item Changes in Rcpp API:
     \itemize{


From noreply at r-forge.r-project.org  Wed Oct  9 00:02:28 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  9 Oct 2013 00:02:28 +0200 (CEST)
Subject: [Rcpp-commits] r4563 - in pkg/Rcpp: . inst man
Message-ID: <20131008220228.D2578184CC5@r-forge.r-project.org>

Author: edd
Date: 2013-10-09 00:02:26 +0200 (Wed, 09 Oct 2013)
New Revision: 4563

Added:
   pkg/Rcpp/man/LdFlags.Rd
Removed:
   pkg/Rcpp/man/RcppLdFlags.Rd
Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/NAMESPACE
   pkg/Rcpp/inst/NEWS.Rd
Log:
Export LdFlags, not RcppLdFlags, from NAMESPACE
Also correct manual page


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-07 16:32:53 UTC (rev 4562)
+++ pkg/Rcpp/ChangeLog	2013-10-08 22:02:26 UTC (rev 4563)
@@ -1,3 +1,8 @@
+2013-10-08  Dirk Eddelbuettel  <edd at debian.org>
+
+	* NAMESPACE: Export LdFlags, not RcppLdFlags
+	* man/LdFlags.Rd: Renamed from RcppLdFlags, and changed
+
 2013-10-06  John M Chambers  <jmc at r-project.org>
 
 	* R/exposeClass.R: avoid warning from unclosed file()

Modified: pkg/Rcpp/NAMESPACE
===================================================================
--- pkg/Rcpp/NAMESPACE	2013-10-07 16:32:53 UTC (rev 4562)
+++ pkg/Rcpp/NAMESPACE	2013-10-08 22:02:26 UTC (rev 4563)
@@ -26,7 +26,7 @@
        sourceCpp,
        compileAttributes,
        registerPlugin,
-       RcppLdFlags,
+       LdFlags,
        demangle,
        sizeof,
        cpp_object_initializer,

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-07 16:32:53 UTC (rev 4562)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-08 22:02:26 UTC (rev 4563)
@@ -19,6 +19,10 @@
       and some tests for \code{is_na()} and \code{is_finite()} have been
       corrected thanks to Thomas Tse.   
     }
+    \item Changes in R code:
+    \itemize{
+      \item Export linking helper function \code{LdFlags}, not \code{RcppLdFlags}
+    }
   }
 }
 

Copied: pkg/Rcpp/man/LdFlags.Rd (from rev 4562, pkg/Rcpp/man/RcppLdFlags.Rd)
===================================================================
--- pkg/Rcpp/man/LdFlags.Rd	                        (rev 0)
+++ pkg/Rcpp/man/LdFlags.Rd	2013-10-08 22:02:26 UTC (rev 4563)
@@ -0,0 +1,41 @@
+\name{LdFlags}
+\alias{LdFlags}
+\title{Provide Rcpp Linker Flags}
+\description{
+  \code{LdFlags} returns the required flags and options for the the
+  system linker. This allows portable use of \pkg{Rcpp} as package
+  location as well as operating-system specific details are abstracted
+  away behind the interface of this function.
+
+  It is commonly called from the files \code{Makevars} (or
+  \code{Makevars.win}) rather than in an interactive session.
+}
+\usage{
+LdFlags(static=staticLinking())
+}
+\arguments{
+  \item{static}{A boolean determining use of static (as opposed to
+  dynamic) linking; defaults to using the \code{staticLinking()}
+  function which defaults to \code{FALSE} on Linux, and \code{TRUE}
+  if the operating system is different from Linux.}
+}
+\value{
+  A character vector suitable by use by the system linker in order to
+  create a library based on \pkg{Rcpp}.
+}
+\details{
+  This function is not meant to used interactively, and is intended
+  solely for use by the build tools.
+}
+\references{
+  Dirk Eddelbuettel and Romain Francois (2011). \pkg{Rcpp}: Seamless R
+  and C++ Integration. \emph{Journal of Statistical Software},
+  \bold{40(8)}, 1-18. URL http://www.jstatsoft.org/v40/i08/ and
+  available as \code{vignette("Rcpp-introduction")}.
+}
+\seealso{
+  The vignette \sQuote{Rcpp-package} has more details.
+}
+\author{Dirk Eddelbuettel and Romain Francois}
+\keyword{programming}
+\keyword{interface}

Deleted: pkg/Rcpp/man/RcppLdFlags.Rd
===================================================================
--- pkg/Rcpp/man/RcppLdFlags.Rd	2013-10-07 16:32:53 UTC (rev 4562)
+++ pkg/Rcpp/man/RcppLdFlags.Rd	2013-10-08 22:02:26 UTC (rev 4563)
@@ -1,41 +0,0 @@
-\name{RcppLdFlags}
-\alias{RcppLdFlags}
-\title{Provide Rcpp Linker Flags}
-\description{
-  \code{RcppLdFlags} returns the required flags and options for the the
-  system linker. This allows portable use of \pkg{Rcpp} as package
-  location as well as operating-system specific details are abstracted
-  away behind the interface of this function.
-
-  It is commonly called from the files \code{Makevars} (or
-  \code{Makevars.win}) rather than in an interactive session.
-}
-\usage{
-RcppLdFlags(static=staticLinking())
-}
-\arguments{
-  \item{static}{A boolean determining use of static (as opposed to
-  dynamic) linking; defaults to using the \code{staticLinking()}
-  function which defaults to \code{FALSE} on Linux, and \code{TRUE}
-  if the operating system is different from Linux.}
-}
-\value{
-  A character vector suitable by use by the system linker in order to
-  create a library based on \pkg{Rcpp}.
-}
-\details{
-  This function is not meant to used interactively, and is intended
-  solely for use by the build tools.
-}
-\references{
-  Dirk Eddelbuettel and Romain Francois (2011). \pkg{Rcpp}: Seamless R
-  and C++ Integration. \emph{Journal of Statistical Software},
-  \bold{40(8)}, 1-18. URL http://www.jstatsoft.org/v40/i08/ and
-  available as \code{vignette("Rcpp-introduction")}.
-}
-\seealso{
-  The vignette \sQuote{Rcpp-package} has more details.
-}
-\author{Dirk Eddelbuettel and Romain Francois}
-\keyword{programming}
-\keyword{interface}


From noreply at r-forge.r-project.org  Wed Oct  9 00:24:27 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  9 Oct 2013 00:24:27 +0200 (CEST)
Subject: [Rcpp-commits] r4564 - pkg/Rcpp/inst
Message-ID: <20131008222427.6187418499E@r-forge.r-project.org>

Author: jmc
Date: 2013-10-09 00:24:27 +0200 (Wed, 09 Oct 2013)
New Revision: 4564

Modified:
   pkg/Rcpp/inst/NEWS.Rd
Log:
Conform to standard for item heading


Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-08 22:02:26 UTC (rev 4563)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-08 22:24:27 UTC (rev 4564)
@@ -4,16 +4,14 @@
 
 \section{Changes in Rcpp version 0.10.5.1 (2013-10-07)}{
   \itemize{
-    \item Exposing C++ classes from a package:
+    \item Changes in Rcpp API:
     \itemize{
       \item The function \code{exposeClass} takes a description of the
         constructors, fields and methods to be exposed from a C++
         class, and writes C++ and R files in the package.  Inherited
         classes can be dealt with, but require data type information.
         This approach avoids hand-coding module files.
-    }
-    \item Changes in Rcpp API:
-    \itemize{
+
       \item Two missing \code{is<>()} templates for
       \code{CharacterVector} and \code{CharacterMatrix} have been added,
       and some tests for \code{is_na()} and \code{is_finite()} have been


From noreply at r-forge.r-project.org  Wed Oct  9 03:21:07 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  9 Oct 2013 03:21:07 +0200 (CEST)
Subject: [Rcpp-commits] r4565 - pkg/Rcpp
Message-ID: <20131009012107.777E0186393@r-forge.r-project.org>

Author: edd
Date: 2013-10-09 03:21:05 +0200 (Wed, 09 Oct 2013)
New Revision: 4565

Modified:
   pkg/Rcpp/DESCRIPTION
Log:
roll Version up a minor


Modified: pkg/Rcpp/DESCRIPTION
===================================================================
--- pkg/Rcpp/DESCRIPTION	2013-10-08 22:24:27 UTC (rev 4564)
+++ pkg/Rcpp/DESCRIPTION	2013-10-09 01:21:05 UTC (rev 4565)
@@ -1,6 +1,6 @@
 Package: Rcpp
 Title: Seamless R and C++ Integration
-Version: 0.10.5.1
+Version: 0.10.5.2
 Date: $Date$
 Author: Dirk Eddelbuettel and Romain Francois, with contributions 
  by Douglas Bates, John Chambers and JJ Allaire


From noreply at r-forge.r-project.org  Wed Oct  9 03:39:40 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed,  9 Oct 2013 03:39:40 +0200 (CEST)
Subject: [Rcpp-commits] r4566 - in pkg/Rcpp: . inst man
Message-ID: <20131009013940.B9489185F6D@r-forge.r-project.org>

Author: edd
Date: 2013-10-09 03:39:39 +0200 (Wed, 09 Oct 2013)
New Revision: 4566

Added:
   pkg/Rcpp/man/RcppLdFlags.Rd
Removed:
   pkg/Rcpp/man/LdFlags.Rd
Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/NAMESPACE
   pkg/Rcpp/inst/NEWS.Rd
Log:
turns out we RcppLdFlags and LdFlags -- so both exported and documented now


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-09 01:21:05 UTC (rev 4565)
+++ pkg/Rcpp/ChangeLog	2013-10-09 01:39:39 UTC (rev 4566)
@@ -1,7 +1,7 @@
 2013-10-08  Dirk Eddelbuettel  <edd at debian.org>
 
-	* NAMESPACE: Export LdFlags, not RcppLdFlags
-	* man/LdFlags.Rd: Renamed from RcppLdFlags, and changed
+	* NAMESPACE: Export LdFlags as well as RcppLdFlags
+	* man/RcppLdFlags.Rd: Updated
 
 2013-10-06  John M Chambers  <jmc at r-project.org>
 

Modified: pkg/Rcpp/NAMESPACE
===================================================================
--- pkg/Rcpp/NAMESPACE	2013-10-09 01:21:05 UTC (rev 4565)
+++ pkg/Rcpp/NAMESPACE	2013-10-09 01:39:39 UTC (rev 4566)
@@ -26,6 +26,7 @@
        sourceCpp,
        compileAttributes,
        registerPlugin,
+       RcppLdFlags,
        LdFlags,
        demangle,
        sizeof,

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-09 01:21:05 UTC (rev 4565)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-09 01:39:39 UTC (rev 4566)
@@ -2,7 +2,7 @@
 \title{News for Package 'Rcpp'}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
 
-\section{Changes in Rcpp version 0.10.5.1 (2013-10-07)}{
+\section{Changes in Rcpp version 0.10.5.2 (2013-10-08)}{
   \itemize{
     \item Changes in Rcpp API:
     \itemize{
@@ -11,15 +11,15 @@
         class, and writes C++ and R files in the package.  Inherited
         classes can be dealt with, but require data type information.
         This approach avoids hand-coding module files.
-
       \item Two missing \code{is<>()} templates for
-      \code{CharacterVector} and \code{CharacterMatrix} have been added,
-      and some tests for \code{is_na()} and \code{is_finite()} have been
-      corrected thanks to Thomas Tse.   
+        \code{CharacterVector} and \code{CharacterMatrix} have been added,
+        and some tests for \code{is_na()} and \code{is_finite()} have been
+        corrected thanks to Thomas Tse.   
     }
     \item Changes in R code:
     \itemize{
-      \item Export linking helper function \code{LdFlags}, not \code{RcppLdFlags}
+      \item Export linking helper function \code{LdFlags} as well as
+        \code{RcppLdFlags}.
     }
   }
 }

Deleted: pkg/Rcpp/man/LdFlags.Rd
===================================================================
--- pkg/Rcpp/man/LdFlags.Rd	2013-10-09 01:21:05 UTC (rev 4565)
+++ pkg/Rcpp/man/LdFlags.Rd	2013-10-09 01:39:39 UTC (rev 4566)
@@ -1,41 +0,0 @@
-\name{LdFlags}
-\alias{LdFlags}
-\title{Provide Rcpp Linker Flags}
-\description{
-  \code{LdFlags} returns the required flags and options for the the
-  system linker. This allows portable use of \pkg{Rcpp} as package
-  location as well as operating-system specific details are abstracted
-  away behind the interface of this function.
-
-  It is commonly called from the files \code{Makevars} (or
-  \code{Makevars.win}) rather than in an interactive session.
-}
-\usage{
-LdFlags(static=staticLinking())
-}
-\arguments{
-  \item{static}{A boolean determining use of static (as opposed to
-  dynamic) linking; defaults to using the \code{staticLinking()}
-  function which defaults to \code{FALSE} on Linux, and \code{TRUE}
-  if the operating system is different from Linux.}
-}
-\value{
-  A character vector suitable by use by the system linker in order to
-  create a library based on \pkg{Rcpp}.
-}
-\details{
-  This function is not meant to used interactively, and is intended
-  solely for use by the build tools.
-}
-\references{
-  Dirk Eddelbuettel and Romain Francois (2011). \pkg{Rcpp}: Seamless R
-  and C++ Integration. \emph{Journal of Statistical Software},
-  \bold{40(8)}, 1-18. URL http://www.jstatsoft.org/v40/i08/ and
-  available as \code{vignette("Rcpp-introduction")}.
-}
-\seealso{
-  The vignette \sQuote{Rcpp-package} has more details.
-}
-\author{Dirk Eddelbuettel and Romain Francois}
-\keyword{programming}
-\keyword{interface}

Copied: pkg/Rcpp/man/RcppLdFlags.Rd (from rev 4564, pkg/Rcpp/man/LdFlags.Rd)
===================================================================
--- pkg/Rcpp/man/RcppLdFlags.Rd	                        (rev 0)
+++ pkg/Rcpp/man/RcppLdFlags.Rd	2013-10-09 01:39:39 UTC (rev 4566)
@@ -0,0 +1,43 @@
+\name{LdFlags}
+\alias{LdFlags}
+\alias{RcppLdFlags}
+\title{Provide Rcpp Linker Flags}
+\description{
+  \code{LdFlags} and \code{RcppLdFlags} return the required flags and
+  options for the the system linker. This allows portable use of
+  \pkg{Rcpp} as package location as well as operating-system specific
+  details are abstracted away behind the interface of this function.
+
+  \code{LdFlags} is commonly called from the files \code{Makevars} (or
+  \code{Makevars.win}) rather than in an interactive session.
+}
+\usage{
+LdFlags(static=staticLinking())
+RcppLdFlags(static=staticLinking())
+}
+\arguments{
+  \item{static}{A boolean determining use of static (as opposed to
+  dynamic) linking; defaults to using the \code{staticLinking()}
+  function which defaults to \code{FALSE} on Linux, and \code{TRUE}
+  if the operating system is different from Linux.}
+}
+\value{
+  A character vector suitable by use by the system linker in order to
+  create a library based on \pkg{Rcpp}.
+}
+\details{
+  Thee functions are not meant to used interactively, and are intended
+  solely for use by the build tools.
+}
+\references{
+  Dirk Eddelbuettel and Romain Francois (2011). \pkg{Rcpp}: Seamless R
+  and C++ Integration. \emph{Journal of Statistical Software},
+  \bold{40(8)}, 1-18. URL http://www.jstatsoft.org/v40/i08/ and
+  available as \code{vignette("Rcpp-introduction")}.
+}
+\seealso{
+  The vignette \sQuote{Rcpp-package} has more details.
+}
+\author{Dirk Eddelbuettel and Romain Francois}
+\keyword{programming}
+\keyword{interface}


From noreply at r-forge.r-project.org  Thu Oct 10 00:45:17 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 10 Oct 2013 00:45:17 +0200 (CEST)
Subject: [Rcpp-commits] r4567 - pkg/RcppGSL
Message-ID: <20131009224517.41D7D185D8E@r-forge.r-project.org>

Author: edd
Date: 2013-10-10 00:45:15 +0200 (Thu, 10 Oct 2013)
New Revision: 4567

Modified:
   pkg/RcppGSL/ChangeLog
   pkg/RcppGSL/DESCRIPTION
   pkg/RcppGSL/NAMESPACE
Log:
Import LdFlags from Rcpp


Modified: pkg/RcppGSL/ChangeLog
===================================================================
--- pkg/RcppGSL/ChangeLog	2013-10-09 01:39:39 UTC (rev 4566)
+++ pkg/RcppGSL/ChangeLog	2013-10-09 22:45:15 UTC (rev 4567)
@@ -1,3 +1,7 @@
+2013-10-09  Dirk Eddelbuettel  <edd at debian.org>
+
+	* NAMESPACE: Import LdFlags from Rcpp
+
 2013-09-10  Dirk Eddelbuettel  <edd at debian.org>
 
 	* DESCRIPTION (Imports): Now 'Imports: Rcpp' rather than Depends: to

Modified: pkg/RcppGSL/DESCRIPTION
===================================================================
--- pkg/RcppGSL/DESCRIPTION	2013-10-09 01:39:39 UTC (rev 4566)
+++ pkg/RcppGSL/DESCRIPTION	2013-10-09 22:45:15 UTC (rev 4567)
@@ -1,7 +1,7 @@
 Package: RcppGSL
 Type: Package
 Title: Rcpp integration for GNU GSL vectors and matrices
-Version: 0.2.0.2
+Version: 0.2.0.3
 Date: $Date$
 Author: Romain Francois and Dirk Eddelbuettel
 Maintainer: Dirk Eddelbuettel <edd at debian.org>
@@ -27,8 +27,8 @@
   write a similar package against another library.
 License: GPL (>= 2)
 LazyLoad: yes
-Imports: Rcpp (>= 0.9.8)
 Suggests: RUnit, inline, highlight
 LinkingTo: Rcpp
+Imports: Rcpp
 SystemRequirements: GNU GSL
 VignetteBuilder: highlight

Modified: pkg/RcppGSL/NAMESPACE
===================================================================
--- pkg/RcppGSL/NAMESPACE	2013-10-09 01:39:39 UTC (rev 4566)
+++ pkg/RcppGSL/NAMESPACE	2013-10-09 22:45:15 UTC (rev 4567)
@@ -1,6 +1,7 @@
 useDynLib(RcppGSL)
 
 importFrom(utils,assignInNamespace)
+importFrom(Rcpp,LdFlags)
 export(fastLmPure,
        fastLm)
 S3method(fastLm, default)


From noreply at r-forge.r-project.org  Thu Oct 10 02:53:10 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 10 Oct 2013 02:53:10 +0200 (CEST)
Subject: [Rcpp-commits] r4568 - in pkg/RcppGSL: . man
Message-ID: <20131010005310.F292118092D@r-forge.r-project.org>

Author: edd
Date: 2013-10-10 02:53:10 +0200 (Thu, 10 Oct 2013)
New Revision: 4568

Added:
   pkg/RcppGSL/man/LdFlags.Rd
Modified:
   pkg/RcppGSL/ChangeLog
   pkg/RcppGSL/NAMESPACE
Log:
Export LdFlags and CFlags, and added documentation for exported functions


Modified: pkg/RcppGSL/ChangeLog
===================================================================
--- pkg/RcppGSL/ChangeLog	2013-10-09 22:45:15 UTC (rev 4567)
+++ pkg/RcppGSL/ChangeLog	2013-10-10 00:53:10 UTC (rev 4568)
@@ -1,11 +1,12 @@
 2013-10-09  Dirk Eddelbuettel  <edd at debian.org>
 
-	* NAMESPACE: Import LdFlags from Rcpp
+	* NAMESPACE: Import LdFlags from Rcpp, and export LdFlags and CFlags
+	* man/LdFlags.Rd: Added documentation for exported functions
 
 2013-09-10  Dirk Eddelbuettel  <edd at debian.org>
 
 	* DESCRIPTION (Imports): Now 'Imports: Rcpp' rather than Depends: to
-	satisfy R CMD check for the R version under development 
+	satisfy R CMD check for the R version under development
 
 2013-08-24  Dirk Eddelbuettel  <edd at debian.org>
 

Modified: pkg/RcppGSL/NAMESPACE
===================================================================
--- pkg/RcppGSL/NAMESPACE	2013-10-09 22:45:15 UTC (rev 4567)
+++ pkg/RcppGSL/NAMESPACE	2013-10-10 00:53:10 UTC (rev 4568)
@@ -3,7 +3,9 @@
 importFrom(utils,assignInNamespace)
 importFrom(Rcpp,LdFlags)
 export(fastLmPure,
-       fastLm)
+       fastLm,
+       LdFlags,
+       CFlags)
 S3method(fastLm, default)
 S3method(fastLm, formula)
 S3method(predict, fastLm)

Added: pkg/RcppGSL/man/LdFlags.Rd
===================================================================
--- pkg/RcppGSL/man/LdFlags.Rd	                        (rev 0)
+++ pkg/RcppGSL/man/LdFlags.Rd	2013-10-10 00:53:10 UTC (rev 4568)
@@ -0,0 +1,47 @@
+\name{LdFlags}
+\alias{LdFlags}
+\alias{CFlags}
+\title{Provide RcppGSL Compiler and Linker Flags}
+\description{
+  \code{LdFlags} and \code{CFlags} return the required flags and
+  options for the compiler and system linker in order to build against
+  GNU GSL. This allows portable use of \pkg{RcppGSL} (which needs the
+  GNU GSL) as package location as well as operating-system specific
+  details are abstracted away behind the interface of this function.
+
+  \code{LdFlags} and \code{CFlags} are commonly called from the files
+  \code{Makevars} (or \code{Makevars.win}) rather than in an interactive
+  session. 
+}
+\usage{
+LdFlags(print=TRUE)
+RcppLdFlags(print=TRUE)
+}
+\arguments{
+  \item{print}{A boolean determining whether the requested value is
+  returned on the standard output, or silenly as a value.}
+}
+\value{
+  A character vector suitable by use by the system compiler linker in order to
+  compile and/or link against the GNU GSK.
+}
+\details{
+  Thee functions are not meant to used interactively, and are intended
+  solely for use by the build tools.
+
+  The values that are returned are acquired by the package at load
+  time. On Linux and OS X, the \code{pkg-config} program is queried. On
+  Windows, environment variables used for GNU GSL builds with R are used.
+}
+\references{
+  Dirk Eddelbuettel and Romain Francois (2011). \pkg{Rcpp}: Seamless R
+  and C++ Integration. \emph{Journal of Statistical Software},
+  \bold{40(8)}, 1-18. URL http://www.jstatsoft.org/v40/i08/ and
+  available as \code{vignette("Rcpp-introduction")}.
+}
+\seealso{
+  The document of the \code{pkg-config} system tool.
+}
+\author{Dirk Eddelbuettel and Romain Francois}
+\keyword{programming}
+\keyword{interface}


From noreply at r-forge.r-project.org  Thu Oct 10 03:23:33 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 10 Oct 2013 03:23:33 +0200 (CEST)
Subject: [Rcpp-commits] r4569 - pkg/RcppGSL/man
Message-ID: <20131010012333.45CEF185FFC@r-forge.r-project.org>

Author: edd
Date: 2013-10-10 03:23:31 +0200 (Thu, 10 Oct 2013)
New Revision: 4569

Modified:
   pkg/RcppGSL/man/LdFlags.Rd
Log:
copy and paste error: CFlags() is the other one


Modified: pkg/RcppGSL/man/LdFlags.Rd
===================================================================
--- pkg/RcppGSL/man/LdFlags.Rd	2013-10-10 00:53:10 UTC (rev 4568)
+++ pkg/RcppGSL/man/LdFlags.Rd	2013-10-10 01:23:31 UTC (rev 4569)
@@ -15,7 +15,7 @@
 }
 \usage{
 LdFlags(print=TRUE)
-RcppLdFlags(print=TRUE)
+CFlags(print=TRUE)
 }
 \arguments{
   \item{print}{A boolean determining whether the requested value is


From noreply at r-forge.r-project.org  Sun Oct 13 00:41:58 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun, 13 Oct 2013 00:41:58 +0200 (CEST)
Subject: [Rcpp-commits] r4570 - in pkg/Rcpp: . inst man
Message-ID: <20131012224158.780081863B7@r-forge.r-project.org>

Author: edd
Date: 2013-10-13 00:41:57 +0200 (Sun, 13 Oct 2013)
New Revision: 4570

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/DESCRIPTION
   pkg/Rcpp/inst/NEWS.Rd
   pkg/Rcpp/man/RcppLdFlags.Rd
Log:
Rolled Depends: on R to "R (>= 3.0.0)" as required by the vignette building code (with thanks to Uwe Ligges)
Also fixed one typo / grammar error in Rd file


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-10 01:23:31 UTC (rev 4569)
+++ pkg/Rcpp/ChangeLog	2013-10-12 22:41:57 UTC (rev 4570)
@@ -1,3 +1,8 @@
+2013-10-12  Dirk Eddelbuettel  <edd at debian.org>
+
+	* DESCRIPTION (Depends): Rolled Depends: on R to "R (>= 3.0.0)" as
+	required by the vignette building code (with thanks to Uwe Ligges)
+
 2013-10-08  Dirk Eddelbuettel  <edd at debian.org>
 
 	* NAMESPACE: Export LdFlags as well as RcppLdFlags

Modified: pkg/Rcpp/DESCRIPTION
===================================================================
--- pkg/Rcpp/DESCRIPTION	2013-10-10 01:23:31 UTC (rev 4569)
+++ pkg/Rcpp/DESCRIPTION	2013-10-12 22:41:57 UTC (rev 4570)
@@ -49,7 +49,7 @@
  Additional documentation is available via the paper by Eddelbuettel and
  Francois (2011, JSS) paper and the book by Eddelbuettel (2013, Springer); 
  see 'citation("Rcpp")' for details.
-Depends: R (>= 2.15.1)
+Depends: R (>= 3.0.0)
 Imports: methods
 Suggests: RUnit, inline, rbenchmark, highlight
 VignetteBuilder: highlight

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-10 01:23:31 UTC (rev 4569)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-12 22:41:57 UTC (rev 4570)
@@ -21,6 +21,11 @@
       \item Export linking helper function \code{LdFlags} as well as
         \code{RcppLdFlags}.
     }
+    \item Changes in R setup:
+    \itemize{
+      \item Raise requirement for R itself to be version 3.0.0 or later
+      as needed by the vignette processing
+    }
   }
 }
 

Modified: pkg/Rcpp/man/RcppLdFlags.Rd
===================================================================
--- pkg/Rcpp/man/RcppLdFlags.Rd	2013-10-10 01:23:31 UTC (rev 4569)
+++ pkg/Rcpp/man/RcppLdFlags.Rd	2013-10-12 22:41:57 UTC (rev 4570)
@@ -4,7 +4,7 @@
 \title{Provide Rcpp Linker Flags}
 \description{
   \code{LdFlags} and \code{RcppLdFlags} return the required flags and
-  options for the the system linker. This allows portable use of
+  options for the system linker. This allows portable use of
   \pkg{Rcpp} as package location as well as operating-system specific
   details are abstracted away behind the interface of this function.
 


From noreply at r-forge.r-project.org  Mon Oct 14 19:50:40 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 14 Oct 2013 19:50:40 +0200 (CEST)
Subject: [Rcpp-commits] r4571 - in pkg/RcppEigen: . inst/include vignettes
Message-ID: <20131014175040.922E2184AD5@r-forge.r-project.org>

Author: dmbates
Date: 2013-10-14 19:50:40 +0200 (Mon, 14 Oct 2013)
New Revision: 4571

Modified:
   pkg/RcppEigen/.Rbuildignore
   pkg/RcppEigen/DESCRIPTION
   pkg/RcppEigen/NEWS
   pkg/RcppEigen/NEWS.org
   pkg/RcppEigen/inst/include/RcppEigenCholmod.h
   pkg/RcppEigen/vignettes/RcppEigen-Introduction.Rnw
Log:
Create a version compatible with updates cholmod_factor struct in Matrix package.


Modified: pkg/RcppEigen/.Rbuildignore
===================================================================
--- pkg/RcppEigen/.Rbuildignore	2013-10-12 22:41:57 UTC (rev 4570)
+++ pkg/RcppEigen/.Rbuildignore	2013-10-14 17:50:40 UTC (rev 4571)
@@ -1 +1,4 @@
 vignettes/jss835/
+vignettes/RcppEigen-intro-nojss.*
+NEWS.org
+vignettes/jss.bst
\ No newline at end of file

Modified: pkg/RcppEigen/DESCRIPTION
===================================================================
--- pkg/RcppEigen/DESCRIPTION	2013-10-12 22:41:57 UTC (rev 4570)
+++ pkg/RcppEigen/DESCRIPTION	2013-10-14 17:50:40 UTC (rev 4571)
@@ -1,8 +1,8 @@
 Package: RcppEigen
 Type: Package
 Title: Rcpp integration for the Eigen templated linear algebra library.
-Version: 0.3.1.2.1
-Date: 2013-01-14
+Version: 0.3.1.2.3
+Date: 2013-10-14
 Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel
 Maintainer: Douglas Bates <bates at stat.wisc.edu>
 Description: R and Eigen integration using Rcpp.
@@ -23,9 +23,9 @@
  bindings/bridge to Eigen) is licensed under the GNU GPL version 2 or
  later, as is the rest of Rcpp.
 License: GPL (>= 2)
-Depends: Rcpp (>= 0.10.1), Matrix (>= 1.0-1), R(>= 2.14.0)
+Depends: R(>= 3.0.2)
 LazyLoad: yes
-LinkingTo: Rcpp
-Imports: Matrix
+LinkingTo: Rcpp (>= 0.10.5)
+Imports: Matrix (>= 1.0-16), Rcpp
 Suggests: inline, RUnit, testthat
 URL: http://eigen.tuxfamily.org

Modified: pkg/RcppEigen/NEWS
===================================================================
--- pkg/RcppEigen/NEWS	2013-10-12 22:41:57 UTC (rev 4570)
+++ pkg/RcppEigen/NEWS	2013-10-14 17:50:40 UTC (rev 4571)
@@ -1,20 +1,28 @@
-                       NEWS for RcppEigen-0.3.0
-                       ========================
+                     NEWS for RcppEigen-0.3.1.2.3
+                     ============================
 
 Author: Douglas Bates
-Date: 2013-02-02 Sun
+Date: 2013-10-14 Mon
 
 
 Table of Contents
 =================
-1 New features visible to users in RcppEigen-0.3.1.2
-2 New features visible to users in RcppEigen-0.3.1
-3 New features visible to users in RcppEigen-0.2.0
-4 New features not visible to users in RcppEigen-0.2.0
+1 New features visible to users in RcppEigen-0.3.1.2.3
+2 New features visible to users in RcppEigen-0.3.1.2
+3 New features visible to users in RcppEigen-0.3.1
+4 New features visible to users in RcppEigen-0.2.0
+5 New features not visible to users in RcppEigen-0.2.0
 
 
-1 New features visible to users in RcppEigen-0.3.1.2 
------------------------------------------------------
+1 New features visible to users in RcppEigen-0.3.1.2.3 
+=======================================================
+  + Fix to RcppEigenCholmod.h to incorporate changes in the
+    cholmod_factor struct. These changes are necessary if code
+    compiled against RcppEigen that uses CHOLMOD factors is to be run
+    with versions of the Matrix package >= 1.1-0
+
+2 New features visible to users in RcppEigen-0.3.1.2 
+=====================================================
   + Upgraded to Eigen 3.1.2
   + Fixes to RcppEigenWrap.h and adjustment of tests accordingly.
     The changes allow RowMajor matrices to be wrapped (thanks to Gael
@@ -27,8 +35,8 @@
     Makefiles
   + Fixes related to Rcpp 0.10.*
 
-2 New features visible to users in RcppEigen-0.3.1 
----------------------------------------------------
+3 New features visible to users in RcppEigen-0.3.1 
+===================================================
   + Upgraded to Eigen 3.1.0
   + Removed the "unsupported" Eigen module AutoDiff which defined a
     macro "sign" that conflicted with a function in the R API (which
@@ -39,8 +47,8 @@
     conflicting definitions in the std:: namespace and the R API and
     Eigen, which I don't have time to investigate.
 
-3 New features visible to users in RcppEigen-0.2.0 
----------------------------------------------------
+4 New features visible to users in RcppEigen-0.2.0 
+===================================================
   + Upgraded the version of Eigen to 3.1.0-alpha2, in which the sparse
     matrix modules are now in the "supported" tree.
   + Added several "unsupported" Eigen modules including
@@ -66,8 +74,8 @@
   + The ability to wrap RowMajor sparse matrices and to use
     as<Eigen::ArrayXd> etc.
 
-4 New features not visible to users in RcppEigen-0.2.0 
--------------------------------------------------------
+5 New features not visible to users in RcppEigen-0.2.0 
+=======================================================
   + Migrated some tests to the testthat package.  Currently there is
     some difficulty with combining testthat, inline and R CMD check.
     These checks are available as

Modified: pkg/RcppEigen/NEWS.org
===================================================================
--- pkg/RcppEigen/NEWS.org	2013-10-12 22:41:57 UTC (rev 4570)
+++ pkg/RcppEigen/NEWS.org	2013-10-14 17:50:40 UTC (rev 4571)
@@ -1,11 +1,17 @@
-#+TITLE:     NEWS for RcppEigen-0.3.0
+#+TITLE:     NEWS for RcppEigen-0.3.1.2.3
 #+AUTHOR:    Douglas Bates
 #+EMAIL:     bates at stat.wisc.edu
-#+DATE:      2013-02-02 Sun
+#+DATE:      2013-10-14 Mon
 #+DESCRIPTION: News regarding the latest version of RcppEigen
 #+KEYWORDS:
 #+LANGUAGE:  en
 
+* New features visible to users in RcppEigen-0.3.1.2.3
+  + Fix to RcppEigenCholmod.h to incorporate changes in the
+    cholmod_factor struct. These changes are necessary if code
+    compiled against RcppEigen that uses CHOLMOD factors is to be run
+    with versions of the Matrix package >= 1.1-0
+
 * New features visible to users in RcppEigen-0.3.1.2
   + Upgraded to Eigen 3.1.2
   + Fixes to RcppEigenWrap.h and adjustment of tests accordingly.

Modified: pkg/RcppEigen/inst/include/RcppEigenCholmod.h
===================================================================
--- pkg/RcppEigen/inst/include/RcppEigenCholmod.h	2013-10-12 22:41:57 UTC (rev 4570)
+++ pkg/RcppEigen/inst/include/RcppEigenCholmod.h	2013-10-14 17:50:40 UTC (rev 4571)
@@ -26,26 +26,43 @@
 extern "C" {
 #endif
 
-// from ../../src/UFconfig/UFconfig.h - line 51 :
-#ifndef UF_long
+// from Matrix/src/SuiteSparse_config/SuiteSparse_config.h - line 51 :
+#ifndef SuiteSparse_long
 
 #ifdef _WIN64
 
-#define UF_long __int64
-#define UF_long_max _I64_MAX
-#define UF_long_idd "I64d"
+#define SuiteSparse_long __int64
+#define SuiteSparse_long_max _I64_MAX
+#define SuiteSparse_long_idd "I64d"
 
 #else
 
-#define UF_long long
-#define UF_long_max LONG_MAX
-#define UF_long_idd "ld"
+#define SuiteSparse_long long
+#define SuiteSparse_long_max LONG_MAX
+#define SuiteSparse_long_idd "ld"
 
 #endif
-#define UF_long_id "%" UF_long_idd
+#define SuiteSparse_long_id "%" SuiteSparse_long_idd
 #endif
 
-#define CHOLMOD_DATE "Jan 25, 2011"
+/* For backward compatibility with prior versions of SuiteSparse.  The UF_*
+ * macros are deprecated and will be removed in a future version. */
+#ifndef UF_long
+#define UF_long     SuiteSparse_long
+#define UF_long_max SuiteSparse_long_max
+#define UF_long_idd SuiteSparse_long_idd
+#define UF_long_id  SuiteSparse_long_id
+#endif
+
+#define CHOLMOD_HAS_VERSION_FUNCTION
+
+#define CHOLMOD_DATE "April 25, 2013"
+#define CHOLMOD_VER_CODE(main,sub) ((main) * 1000 + (sub))
+#define CHOLMOD_MAIN_VERSION 2
+#define CHOLMOD_SUB_VERSION 1
+#define CHOLMOD_SUBSUB_VERSION 2
+#define CHOLMOD_VERSION \
+    CHOLMOD_VER_CODE(CHOLMOD_MAIN_VERSION,CHOLMOD_SUB_VERSION)
 // from ../../src/CHOLMOD/Include/cholmod_core.h - line 275 :
 /* Each CHOLMOD object has its own type code. */
 
@@ -61,9 +78,13 @@
 
 /* itype defines the types of integer used: */
 #define CHOLMOD_INT 0		/* all integer arrays are int */
-#define CHOLMOD_INTLONG 1	/* most are int, some are UF_long */
-#define CHOLMOD_LONG 2		/* all integer arrays are UF_long */
+#define CHOLMOD_INTLONG 1	/* most are int, some are SuiteSparse_long */
+#define CHOLMOD_LONG 2		/* all integer arrays are SuiteSparse_long */
 
+/* The itype of all parameters for all CHOLMOD routines must match.
+ * FUTURE WORK: CHOLMOD_INTLONG is not yet supported.
+ */
+
 /* dtype defines what the numerical type is (double or float): */
 #define CHOLMOD_DOUBLE 0	/* all numerical values are double */
 #define CHOLMOD_SINGLE 1	/* all numerical values are float */
@@ -92,6 +113,7 @@
 #define CHOLMOD_OUT_OF_MEMORY (-2)	/* failure: out of memory */
 #define CHOLMOD_TOO_LARGE (-3)		/* failure: integer overflow occured */
 #define CHOLMOD_INVALID (-4)		/* failure: invalid input */
+#define CHOLMOD_GPU_PROBLEM (-5)        /* failure: GPU fatal error */
 #define CHOLMOD_NOT_POSDEF (1)		/* warning: matrix not pos. def. */
 #define CHOLMOD_DSMALL (2)		/* warning: D for LDL'  or diag(L) or */
 					/* LL' has tiny absolute value */
@@ -731,7 +753,7 @@
 
 } cholmod_sparse ;
 
-// in ../../src/CHOLMOD/Include/cholmod_core.h  skip forward to - line 1495 :
+// in ../../src/CHOLMOD/Include/cholmod_core.h  skip forward to - line 1554 :
 /* A symbolic and numeric factorization, either simplicial or supernodal.
  * In all cases, the row indices in the columns of L are kept sorted. */
 
@@ -755,6 +777,9 @@
     void *Perm ;	/* size n, permutation used */
     void *ColCount ;	/* size n, column counts for simplicial L */
 
+    void *IPerm ;       /* size n, inverse permutation.  Only created by
+                         * cholmod_solve2 if Bset is used. */
+
     /* ---------------------------------------------------------------------- */
     /* simplicial factorization */
     /* ---------------------------------------------------------------------- */
@@ -846,17 +871,17 @@
      *	    except for the numerical values (x and z).
      */
 
-    int itype ;		/* The integer arrays are Perm, ColCount, p, i, nz,
-			 * next, prev, super, pi, px, and s.  If itype is
-			 * CHOLMOD_INT, all of these are int arrays.
-			 * CHOLMOD_INTLONG: p, pi, px are UF_long, others int.
-			 * CHOLMOD_LONG:    all integer arrays are UF_long. */
-    int xtype ;		/* pattern, real, complex, or zomplex */
-    int dtype ;		/* x and z double or float */
+    int itype ; /* The integer arrays are Perm, ColCount, p, i, nz,
+                 * next, prev, super, pi, px, and s.  If itype is
+		 * CHOLMOD_INT, all of these are int arrays.
+		 * CHOLMOD_INTLONG: p, pi, px are SuiteSparse_long, others int.
+		 * CHOLMOD_LONG:    all integer arrays are SuiteSparse_long. */
+    int xtype ; /* pattern, real, complex, or zomplex */
+    int dtype ; /* x and z double or float */
 
 } cholmod_factor ;
 
-// in ../../src/CHOLMOD/Include/cholmod_core.h  skip forward to - line 1773 :
+// in ../../src/CHOLMOD/Include/cholmod_core.h  skip forward to - line 1836 :
 /* A dense matrix in column-oriented form.  It has no itype since it contains
  * no integers.  Entry in row i and column j is located in x [i+j*d].
  */
@@ -874,7 +899,7 @@
 
 } cholmod_dense ;
 
-// in ../../src/CHOLMOD/Include/cholmod_core.h  skip forward to - line 1952 :
+// in ../../src/CHOLMOD/Include/cholmod_core.h  skip forward to - line 2033 :
 /* A sparse matrix stored in triplet form. */
 
 typedef struct cholmod_triplet_struct
@@ -889,12 +914,55 @@
     void *x ;		/* size nzmax or 2*nzmax, if present */
     void *z ;		/* size nzmax, if present */
 
-    int stype ;		/* symmetry type */
-    //                  [................................]
-    int itype ;		/* CHOLMOD_LONG: i and j are UF_long.  Otherwise int. */
-    int xtype ;		/* pattern, real, complex, or zomplex */
-    int dtype ;		/* x and z are double or float */
+    int stype ;		/* Describes what parts of the matrix are considered:
+			 *
+	* 0:  matrix is "unsymmetric": use both upper and lower triangular parts
+	*     (the matrix may actually be symmetric in pattern and value, but
+	*     both parts are explicitly stored and used).  May be square or
+	*     rectangular.
+	* >0: matrix is square and symmetric.  Entries in the lower triangular
+	*     part are transposed and added to the upper triangular part when
+	*     the matrix is converted to cholmod_sparse form.
+	* <0: matrix is square and symmetric.  Entries in the upper triangular
+	*     part are transposed and added to the lower triangular part when
+	*     the matrix is converted to cholmod_sparse form.
+	*
+	* Note that stype>0 and stype<0 are different for cholmod_sparse and
+	* cholmod_triplet.  The reason is simple.  You can permute a symmetric
+	* triplet matrix by simply replacing a row and column index with their
+	* new row and column indices, via an inverse permutation.  Suppose
+	* P = L->Perm is your permutation, and Pinv is an array of size n.
+	* Suppose a symmetric matrix A is represent by a triplet matrix T, with
+	* entries only in the upper triangular part.  Then the following code:
+	*
+	*	Ti = T->i ;
+	*	Tj = T->j ;
+	*	for (k = 0 ; k < n  ; k++) Pinv [P [k]] = k ;
+	*	for (k = 0 ; k < nz ; k++) Ti [k] = Pinv [Ti [k]] ;
+	*	for (k = 0 ; k < nz ; k++) Tj [k] = Pinv [Tj [k]] ;
+	*
+	* creates the triplet form of C=P*A*P'.  However, if T initially
+	* contains just the upper triangular entries (T->stype = 1), after
+	* permutation it has entries in both the upper and lower triangular
+	* parts.  These entries should be transposed when constructing the
+	* cholmod_sparse form of A, which is what cholmod_triplet_to_sparse
+	* does.  Thus:
+	*
+	*	C = cholmod_triplet_to_sparse (T, 0, &Common) ;
+	*
+	* will return the matrix C = P*A*P'.
+	*
+	* Since the triplet matrix T is so simple to generate, it's quite easy
+	* to remove entries that you do not want, prior to converting T to the
+	* cholmod_sparse form.  So if you include these entries in T, CHOLMOD
+	* assumes that there must be a reason (such as the one above).  Thus,
+	* no entry in a triplet matrix is ever ignored.
+	*/
 
+    int itype ; /* CHOLMOD_LONG: i and j are SuiteSparse_long.  Otherwise int */
+    int xtype ; /* pattern, real, complex, or zomplex */
+    int dtype ; /* x and z are double or float */
+
 } cholmod_triplet ;
 
 // -------- our (Matrix)  short and const_ forms of of the pointers :

Modified: pkg/RcppEigen/vignettes/RcppEigen-Introduction.Rnw
===================================================================
--- pkg/RcppEigen/vignettes/RcppEigen-Introduction.Rnw	2013-10-12 22:41:57 UTC (rev 4570)
+++ pkg/RcppEigen/vignettes/RcppEigen-Introduction.Rnw	2013-10-14 17:50:40 UTC (rev 4571)
@@ -52,7 +52,7 @@
   URL: \url{http://dirk.eddelbuettel.com}\\
 }
 
-%% need no \usepackage{Sweave.sty}
+\usepackage{Sweave}
 
 \newcommand{\argmin}{\operatorname{argmin}\displaylimits}
 \newcommand{\rank}{\operatorname{rank}}


From noreply at r-forge.r-project.org  Mon Oct 14 19:58:23 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 14 Oct 2013 19:58:23 +0200 (CEST)
Subject: [Rcpp-commits] r4572 - in pkg/Rcpp: . inst/include
	inst/include/Rcpp inst/include/Rcpp/api/meat
	inst/include/Rcpp/protection inst/include/Rcpp/vector
Message-ID: <20131014175823.1F632184AD5@r-forge.r-project.org>

Author: romain
Date: 2013-10-14 19:58:22 +0200 (Mon, 14 Oct 2013)
New Revision: 4572

Added:
   pkg/Rcpp/inst/include/Rcpp/api/meat/protection.h
   pkg/Rcpp/inst/include/Rcpp/protection/
   pkg/Rcpp/inst/include/Rcpp/protection/Armor.h
   pkg/Rcpp/inst/include/Rcpp/protection/Shelter.h
   pkg/Rcpp/inst/include/Rcpp/protection/Shield.h
   pkg/Rcpp/inst/include/Rcpp/protection/protection.h
Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/DESCRIPTION
   pkg/Rcpp/inst/include/Rcpp/api/meat/meat.h
   pkg/Rcpp/inst/include/Rcpp/vector/Vector.h
   pkg/Rcpp/inst/include/RcppCommon.h
Log:
added Shield Armor and Shelter

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-14 17:50:40 UTC (rev 4571)
+++ pkg/Rcpp/ChangeLog	2013-10-14 17:58:22 UTC (rev 4572)
@@ -1,3 +1,8 @@
+2013-10-14 Romain Francois <romain at r-enthusiasts.com>
+	
+	* inst/include/Rcpp/protection/protection.h: added Shield/Shelter/Armor
+	* DESCRIPTION: bump to version 0.10.5.3
+
 2013-10-12  Dirk Eddelbuettel  <edd at debian.org>
 
 	* DESCRIPTION (Depends): Rolled Depends: on R to "R (>= 3.0.0)" as

Modified: pkg/Rcpp/DESCRIPTION
===================================================================
--- pkg/Rcpp/DESCRIPTION	2013-10-14 17:50:40 UTC (rev 4571)
+++ pkg/Rcpp/DESCRIPTION	2013-10-14 17:58:22 UTC (rev 4572)
@@ -1,6 +1,6 @@
 Package: Rcpp
 Title: Seamless R and C++ Integration
-Version: 0.10.5.2
+Version: 0.10.5.3
 Date: $Date$
 Author: Dirk Eddelbuettel and Romain Francois, with contributions 
  by Douglas Bates, John Chambers and JJ Allaire

Modified: pkg/Rcpp/inst/include/Rcpp/api/meat/meat.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/api/meat/meat.h	2013-10-14 17:50:40 UTC (rev 4571)
+++ pkg/Rcpp/inst/include/Rcpp/api/meat/meat.h	2013-10-14 17:58:22 UTC (rev 4572)
@@ -30,6 +30,7 @@
 #include <Rcpp/api/meat/Reference.h>
 #include <Rcpp/api/meat/is.h>
 #include <Rcpp/api/meat/export.h>
+#include <Rcpp/api/meat/protection.h>
 #include <Rcpp/api/meat/wrap.h>
 
 #endif

Added: pkg/Rcpp/inst/include/Rcpp/api/meat/protection.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/api/meat/protection.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/api/meat/protection.h	2013-10-14 17:58:22 UTC (rev 4572)
@@ -0,0 +1,43 @@
+// Copyright (C) 2013    Romain Francois
+//
+// This file is part of Rcpp.
+//
+// Rcpp is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// Rcpp is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Rcpp.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef Rcpp_protection_meat_H
+#define Rcpp_protection_meat_H
+      
+namespace Rcpp{
+
+    template <typename T>
+    template <typename U>
+    Armor<T>::Armor( U x ) : data() {
+        init( wrap(x) ) ;
+    }       
+        
+    template <typename T>
+    template <typename U>
+    inline Armor<T>& Armor<T>::operator=( U x ){
+        REPROTECT(data = wrap(x), index) ;
+        return *this ;
+    }
+         
+    template <typename T>
+    template <typename U>
+    inline Shield<T>::operator U() const { 
+        return as<U>(t) ; 
+    }
+}
+
+#endif

Added: pkg/Rcpp/inst/include/Rcpp/protection/Armor.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/protection/Armor.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/protection/Armor.h	2013-10-14 17:58:22 UTC (rev 4572)
@@ -0,0 +1,58 @@
+// Copyright (C) 2013    Romain Francois
+//
+// This file is part of Rcpp.
+//
+// Rcpp is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// Rcpp is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Rcpp.  If not, see <http://www.gnu.org/licenses/>.
+        
+#ifndef Rcpp_protection_Armor_H
+#define Rcpp_protection_Armor_H
+
+namespace Rcpp {
+    
+    template <typename T>
+    class Armor {
+    public:
+        
+        Armor() : data(){
+            init(R_NilValue) ;    
+        }
+        
+        template <typename U> Armor( U x );
+        
+        inline operator SEXP(){
+            return data ;
+        }
+              
+        template <typename U>
+        inline Armor& operator=( U x ) ;
+        
+        ~Armor(){
+            UNPROTECT(1) ;
+        }
+        
+    private:
+        void init(SEXP x){
+           PROTECT_WITH_INDEX( data = x, &index ) ;     
+        }
+        
+        SEXP data ;
+        PROTECT_INDEX index ;
+        
+        // not defined on purpose
+        Armor(const Armor&) ;
+        Armor& operator=(const Armor&) ; 
+    } ;
+}
+
+#endif

Added: pkg/Rcpp/inst/include/Rcpp/protection/Shelter.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/protection/Shelter.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/protection/Shelter.h	2013-10-14 17:58:22 UTC (rev 4572)
@@ -0,0 +1,47 @@
+// Copyright (C) 2013    Romain Francois
+//
+// This file is part of Rcpp.
+//
+// Rcpp is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// Rcpp is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Rcpp.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef Rcpp_protection_Shelter_H
+#define Rcpp_protection_Shelter_H
+
+namespace Rcpp {
+    
+    template <class T>
+    class Shelter {
+    public:
+        Shelter() : nprotected(0){}
+        
+        inline SEXP operator()(SEXP x){
+            nprotected++;             
+            return PROTECT(x) ;
+        }
+        
+        ~Shelter(){
+            UNPROTECT(nprotected) ;
+            nprotected = 0 ;
+        }
+        
+    private:
+        int nprotected ;
+          
+        // not defined on purpose
+        Shelter(const Shelter&) ;
+        Shelter& operator=(const Shelter&) ; 
+    } ;
+}
+
+#endif

Added: pkg/Rcpp/inst/include/Rcpp/protection/Shield.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/protection/Shield.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/protection/Shield.h	2013-10-14 17:58:22 UTC (rev 4572)
@@ -0,0 +1,44 @@
+// Copyright (C) 2013    Romain Francois
+//
+// This file is part of Rcpp.
+//
+// Rcpp is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// Rcpp is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Rcpp.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef Rcpp_protection_Shield_H
+#define Rcpp_protection_Shield_H
+
+namespace Rcpp {
+    
+    template <typename T>
+    class Shield{
+    public:
+        Shield( SEXP t_) : t(PROTECT(t_)){}
+        ~Shield(){
+            UNPROTECT(1) ;    
+        }
+        
+        template <typename U>
+        inline operator U() const  ;
+        
+    private:  
+        // not defined on purpose
+        Shield( const Shield& ) ;
+        Shield& operator=( const Shield& ) ;
+    
+        SEXP t ;
+    } ;
+    
+}
+
+#endif

Added: pkg/Rcpp/inst/include/Rcpp/protection/protection.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/protection/protection.h	                        (rev 0)
+++ pkg/Rcpp/inst/include/Rcpp/protection/protection.h	2013-10-14 17:58:22 UTC (rev 4572)
@@ -0,0 +1,25 @@
+// Copyright (C) 2013    Romain Francois
+//
+// This file is part of Rcpp.
+//
+// Rcpp is free software: you can redistribute it and/or modify it
+// under the terms of the GNU General Public License as published by
+// the Free Software Foundation, either version 2 of the License, or
+// (at your option) any later version.
+//
+// Rcpp is distributed in the hope that it will be useful, but
+// WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU General Public License
+// along with Rcpp.  If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef Rcpp_protection_protection_H
+#define Rcpp_protection_protection_H
+
+#include <Rcpp/protection/Shield.h>
+#include <Rcpp/protection/Shelter.h>
+#include <Rcpp/protection/Armor.h>
+
+#endif

Modified: pkg/Rcpp/inst/include/Rcpp/vector/Vector.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/vector/Vector.h	2013-10-14 17:50:40 UTC (rev 4571)
+++ pkg/Rcpp/inst/include/Rcpp/vector/Vector.h	2013-10-14 17:58:22 UTC (rev 4572)
@@ -88,7 +88,7 @@
         update_vector();
     }
     Vector( const char* st ) : RObject( internal::vector_from_string<RTYPE>(st) ){
-        RCPP_DEBUG_2( "Vector<%d>( const char* = %s )", RTYPE, st.c_str() )
+        RCPP_DEBUG_2( "Vector<%d>( const char* = %s )", RTYPE, st )
         update_vector();
     }
 	

Modified: pkg/Rcpp/inst/include/RcppCommon.h
===================================================================
--- pkg/Rcpp/inst/include/RcppCommon.h	2013-10-14 17:50:40 UTC (rev 4571)
+++ pkg/Rcpp/inst/include/RcppCommon.h	2013-10-14 17:58:22 UTC (rev 4572)
@@ -82,6 +82,7 @@
 #include <Rcpp/sprintf.h>
 
 
+#include <Rcpp/protection/protection.h>
 #include <Rcpp/lang.h>
 #include <Rcpp/complex.h>
 #include <Rcpp/barrier.h>


From noreply at r-forge.r-project.org  Tue Oct 15 16:19:37 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 15 Oct 2013 16:19:37 +0200 (CEST)
Subject: [Rcpp-commits] r4573 - pkg/RcppArmadillo
Message-ID: <20131015141937.1B98918346D@r-forge.r-project.org>

Author: mpacala
Date: 2013-10-15 16:19:36 +0200 (Tue, 15 Oct 2013)
New Revision: 4573

Added:
   pkg/RcppArmadillo/test
Log:
debug r-forge building process, testfile to trigger build


Added: pkg/RcppArmadillo/test
===================================================================

From noreply at r-forge.r-project.org  Wed Oct 16 11:57:44 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 16 Oct 2013 11:57:44 +0200 (CEST)
Subject: [Rcpp-commits] r4574 - in pkg/Rcpp: . inst/include/Rcpp/api/meat
Message-ID: <20131016095744.E565C1852C8@r-forge.r-project.org>

Author: romain
Date: 2013-10-16 11:57:44 +0200 (Wed, 16 Oct 2013)
New Revision: 4574

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/inst/include/Rcpp/api/meat/is.h
Log:
added missing is<Language> and is<DottedPair>

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-15 14:19:36 UTC (rev 4573)
+++ pkg/Rcpp/ChangeLog	2013-10-16 09:57:44 UTC (rev 4574)
@@ -1,3 +1,8 @@
+2013-10-16 Romain Francois <romain at r-enthusiasts.com>
+
+        * include/Rcpp/api/meat/is.h : added missing implementation for 
+        is<Language> and is<DottedPair>
+
 2013-10-14 Romain Francois <romain at r-enthusiasts.com>
 	
 	* inst/include/Rcpp/protection/protection.h: added Shield/Shelter/Armor

Modified: pkg/Rcpp/inst/include/Rcpp/api/meat/is.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/api/meat/is.h	2013-10-15 14:19:36 UTC (rev 4573)
+++ pkg/Rcpp/inst/include/Rcpp/api/meat/is.h	2013-10-16 09:57:44 UTC (rev 4574)
@@ -74,6 +74,12 @@
     template <> inline bool is__simple<LogicalVector>( SEXP x ){
         return TYPEOF(x) == LGLSXP ;
     }
+    template <> inline bool is__simple<Language>( SEXP x ){
+        return TYPEOF(x) == LANGSXP ;
+    }
+    template <> inline bool is__simple<DottedPair>( SEXP x ){
+        return TYPEOF(x) == LANGSXP ||?TYPEOF(x) == LISTSXP ;
+    }
     template <> inline bool is__simple<List>( SEXP x ){
         return TYPEOF(x) == VECSXP ;
     }


From noreply at r-forge.r-project.org  Wed Oct 16 23:00:56 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 16 Oct 2013 23:00:56 +0200 (CEST)
Subject: [Rcpp-commits] r4575 - pkg/Rcpp/inst/include/Rcpp/api/meat
Message-ID: <20131016210056.B20B4185044@r-forge.r-project.org>

Author: edd
Date: 2013-10-16 23:00:56 +0200 (Wed, 16 Oct 2013)
New Revision: 4575

Modified:
   pkg/Rcpp/inst/include/Rcpp/api/meat/is.h
Log:
fix a compile error due to non-ascii chars; minor whitespace edits too


Modified: pkg/Rcpp/inst/include/Rcpp/api/meat/is.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/api/meat/is.h	2013-10-16 09:57:44 UTC (rev 4574)
+++ pkg/Rcpp/inst/include/Rcpp/api/meat/is.h	2013-10-16 21:00:56 UTC (rev 4575)
@@ -30,23 +30,18 @@
         SEXP dim = Rf_getAttrib( x, R_DimSymbol) ;
         return dim != R_NilValue && Rf_length(dim) == 2 ;
     }
-    
     template <> inline bool is__simple<int>( SEXP x ){
         return is_atomic(x) && TYPEOF(x) == INTSXP ;
     }
-
     template <> inline bool is__simple<double>( SEXP x ){
         return is_atomic(x) && TYPEOF(x) == REALSXP ;
     }
-    
     template <> inline bool is__simple<bool>( SEXP x ){
         return is_atomic(x) && TYPEOF(x) == LGLSXP ;
     }
-    
     template <> inline bool is__simple<std::string>( SEXP x ){
         return is_atomic(x) && TYPEOF(x) == STRSXP ;
     }
-    
     template <> inline bool is__simple<String>( SEXP x ){
         return is_atomic(x) && TYPEOF(x) == STRSXP ;
     }
@@ -78,7 +73,7 @@
         return TYPEOF(x) == LANGSXP ;
     }
     template <> inline bool is__simple<DottedPair>( SEXP x ){
-        return TYPEOF(x) == LANGSXP ||?TYPEOF(x) == LISTSXP ;
+        return (TYPEOF(x) == LANGSXP) || (TYPEOF(x) == LISTSXP);
     }
     template <> inline bool is__simple<List>( SEXP x ){
         return TYPEOF(x) == VECSXP ;


From noreply at r-forge.r-project.org  Wed Oct 16 23:20:08 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 16 Oct 2013 23:20:08 +0200 (CEST)
Subject: [Rcpp-commits] r4576 - in pkg/Rcpp: . R inst man
Message-ID: <20131016212008.D64B018603C@r-forge.r-project.org>

Author: edd
Date: 2013-10-16 23:20:08 +0200 (Wed, 16 Oct 2013)
New Revision: 4576

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/R/Rcpp.package.skeleton.R
   pkg/Rcpp/inst/NEWS.Rd
   pkg/Rcpp/man/Rcpp.package.skeleton.Rd
Log:
deprecate namespace argument in Rcpp.package.skeleton


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-16 21:00:56 UTC (rev 4575)
+++ pkg/Rcpp/ChangeLog	2013-10-16 21:20:08 UTC (rev 4576)
@@ -1,3 +1,9 @@
+2013-10-16  Dirk Eddelbuettel  <edd at debian.org>
+
+	* R/Rcpp.package.skeleton.R (Rcpp.package.skeleton): Deprecate
+	namespace argument which package.skeleton() no longer uses
+	* man/Rcpp.package.skeleton.Rd: Updated documentation accordingly
+
 2013-10-16 Romain Francois <romain at r-enthusiasts.com>
 
         * include/Rcpp/api/meat/is.h : added missing implementation for 

Modified: pkg/Rcpp/R/Rcpp.package.skeleton.R
===================================================================
--- pkg/Rcpp/R/Rcpp.package.skeleton.R	2013-10-16 21:00:56 UTC (rev 4575)
+++ pkg/Rcpp/R/Rcpp.package.skeleton.R	2013-10-16 21:20:08 UTC (rev 4576)
@@ -1,6 +1,6 @@
 # -*- tab-width: 4; -*-
 
-# Copyright (C) 2009 - 2012  Dirk Eddelbuettel and Romain Francois
+# Copyright (C) 2009 - 2013  Dirk Eddelbuettel and Romain Francois
 #
 # This file is part of Rcpp.
 #
@@ -17,20 +17,17 @@
 # You should have received a copy of the GNU General Public License
 # along with Rcpp.  If not, see <http://www.gnu.org/licenses/>.
 
-Rcpp.package.skeleton <- function(
-	name = "anRpackage", list = character(), environment = .GlobalEnv,
-	path = ".", force = FALSE, namespace = TRUE,
-	code_files = character(), cpp_files = character(),
-	example_code = TRUE,
-	attributes = TRUE,
-	module = FALSE,
-	author = "Who wrote it",
-	maintainer = if(missing( author)) "Who to complain to" else author,
-	email = "yourfault at somewhere.net",
-	license = "What Licence is it under ?"
-	){
-	
-	if (!is.character(cpp_files)) 
+Rcpp.package.skeleton <- function(name = "anRpackage", list = character(),
+                                  environment = .GlobalEnv,
+                                  path = ".", force = FALSE,
+                                  code_files = character(), cpp_files = character(),
+                                  example_code = TRUE, attributes = TRUE, module = FALSE,
+                                  author = "Who wrote it",
+                                  maintainer = if(missing( author)) "Who to complain to" else author,
+                                  email = "yourfault at somewhere.net",
+                                  license = "What Licence is it under ?") {
+
+	if (!is.character(cpp_files))
 		stop("'cpp_files' must be a character vector")
 	# set example_code if attributes is set
 	if( isTRUE(attributes) )
@@ -40,7 +37,7 @@
 	if( !length(list) ){
 		fake <- TRUE
 		assign( "Rcpp.fake.fun", function(){}, envir = env )
-		if( example_code && !isTRUE(attributes)){ 
+		if( example_code && !isTRUE(attributes)){
 			assign( "rcpp_hello_world", function(){}, envir = env )
 			remove_hello_world <- TRUE
 		} else {
@@ -59,7 +56,6 @@
 	# first let the traditional version do its business
 	call <- match.call()
 	call[[1]] <- as.name("package.skeleton")
-	call[["namespace"]] <- namespace
 	# remove Rcpp specific arguments
 
 	call <- call[ c( 1L, which( names(call) %in% names(formals(package.skeleton)))) ]
@@ -117,15 +113,15 @@
 		}
 		close( ns )
 	}
-	
+
 	# update the package description help page
 	package_help_page <- file.path( root, "man", sprintf( "%s-package.Rd", name ) )
 	if( file.exists(package_help_page) ){
 	    lines <- readLines(package_help_page)
 	    lines <- gsub( "What license is it under?", license, lines, fixed = TRUE )
-	    lines <- gsub( "Who to complain to <yourfault at somewhere.net>", 
-	        sprintf( "%s <%s>", maintainer, email),  
-	        lines, 
+	    lines <- gsub( "Who to complain to <yourfault at somewhere.net>",
+	        sprintf( "%s <%s>", maintainer, email),
+	        lines,
 	        fixed = TRUE
 	        )
 	    lines <- gsub( "Who wrote it", author, lines, fixed = TRUE )
@@ -149,7 +145,7 @@
 		file.copy( file.path( skeleton, "Makevars.win" ), Makevars.win )
 		message( " >> added Makevars.win file with Rcpp settings" )
 	}
-	
+
 	if ( length(cpp_files) > 0L ) {
 		for (file in cpp_files) {
 			file.copy(file, src)
@@ -157,10 +153,10 @@
 		}
 		compileAttributes(root)
 	}
-	
+
 	if( example_code ){
 		if ( isTRUE( attributes ) ) {
-			file.copy( file.path( skeleton, "rcpp_hello_world_attributes.cpp" ), 
+			file.copy( file.path( skeleton, "rcpp_hello_world_attributes.cpp" ),
 								 file.path( src, "rcpp_hello_world.cpp" ) )
 			message( " >> added example src file using Rcpp attributes")
 			compileAttributes(root)
@@ -170,16 +166,16 @@
 			header <- gsub( "@PKG@", name, header, fixed = TRUE )
 			writeLines( header , file.path( src, "rcpp_hello_world.h" ) )
 			message( " >> added example header file using Rcpp classes")
-			
+
 			file.copy( file.path( skeleton, "rcpp_hello_world.cpp" ), src )
 			message( " >> added example src file using Rcpp classes")
-			
+
 			rcode <- readLines( file.path( skeleton, "rcpp_hello_world.R" ) )
 			rcode <- gsub( "@PKG@", name, rcode, fixed = TRUE )
 			writeLines( rcode , file.path( root, "R", "rcpp_hello_world.R" ) )
 			message( " >> added example R file calling the C++ example")
 		}
-		
+
 		hello.Rd <- file.path( root, "man", "rcpp_hello_world.Rd")
 		unlink( hello.Rd )
 		file.copy(

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-16 21:00:56 UTC (rev 4575)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-16 21:20:08 UTC (rev 4576)
@@ -20,6 +20,8 @@
     \itemize{
       \item Export linking helper function \code{LdFlags} as well as
         \code{RcppLdFlags}.
+      \item Function \code{Rcpp.package.skeleton()} no longer passes a
+        \code{namespace} argument on to \code{package.skeleton()}
     }
     \item Changes in R setup:
     \itemize{

Modified: pkg/Rcpp/man/Rcpp.package.skeleton.Rd
===================================================================
--- pkg/Rcpp/man/Rcpp.package.skeleton.Rd	2013-10-16 21:00:56 UTC (rev 4575)
+++ pkg/Rcpp/man/Rcpp.package.skeleton.Rd	2013-10-16 21:20:08 UTC (rev 4576)
@@ -13,7 +13,7 @@
 \usage{
 Rcpp.package.skeleton(name = "anRpackage", list = character(), 
 	environment = .GlobalEnv, path = ".", force = FALSE, 
-	namespace = TRUE, code_files = character(), cpp_files = character(),
+	code_files = character(), cpp_files = character(),
 	example_code = TRUE, attributes = TRUE, module = FALSE, 
 	author = "Who wrote it", 
 	maintainer = if(missing( author)) "Who to complain to" else author, 
@@ -27,7 +27,6 @@
 	\item{environment}{See \link[utils]{package.skeleton}}
 	\item{path}{See \link[utils]{package.skeleton}}
 	\item{force}{See \link[utils]{package.skeleton}}
-	\item{namespace}{See \link[utils]{package.skeleton}}
 	\item{code_files}{See \link[utils]{package.skeleton}}
 	\item{cpp_files}{A character vector with the paths to C++ source files to add to the package. }
 	\item{example_code}{If TRUE, example c++ code using Rcpp is added to the package. }


From noreply at r-forge.r-project.org  Thu Oct 17 16:47:18 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 17 Oct 2013 16:47:18 +0200 (CEST)
Subject: [Rcpp-commits] r4577 - in pkg/Rcpp: . R inst
Message-ID: <20131017144718.86927185D9B@r-forge.r-project.org>

Author: jjallaire
Date: 2013-10-17 16:47:18 +0200 (Thu, 17 Oct 2013)
New Revision: 4577

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/R/Attributes.R
   pkg/Rcpp/inst/NEWS.Rd
Log:
sourceCpp now correctly binds to Rtools 3.0 and 3.1

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-16 21:20:08 UTC (rev 4576)
+++ pkg/Rcpp/ChangeLog	2013-10-17 14:47:18 UTC (rev 4577)
@@ -1,3 +1,7 @@
+2013-10-17  JJ Allaire <jj at rstudio.org>
+
+        * R/Attributes.R: sourceCpp now correctly binds to Rtools 3.0 and 3.1
+
 2013-10-16  Dirk Eddelbuettel  <edd at debian.org>
 
 	* R/Rcpp.package.skeleton.R (Rcpp.package.skeleton): Deprecate

Modified: pkg/Rcpp/R/Attributes.R
===================================================================
--- pkg/Rcpp/R/Attributes.R	2013-10-16 21:20:08 UTC (rev 4576)
+++ pkg/Rcpp/R/Attributes.R	2013-10-17 14:47:18 UTC (rev 4577)
@@ -653,7 +653,8 @@
 
             # Check version -- we only support 2.15 and 2.16 right now
             ver <- key$`Current Version`
-            if (identical("2.15", ver) || identical("2.16", ver)) {
+            if (identical("2.15", ver) || identical("2.16", ver) ||
+                identical("3.0", ver) || identical("3.1", ver)) {
 
                 # See if the InstallPath leads to the expected directories
                 rToolsPath <- key$`InstallPath`

Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-16 21:20:08 UTC (rev 4576)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-17 14:47:18 UTC (rev 4577)
@@ -28,6 +28,10 @@
       \item Raise requirement for R itself to be version 3.0.0 or later
       as needed by the vignette processing
     }
+    \item Changes in Rcpp attributes: 
+    \itemize{
+      \item \code{sourceCpp} now correctly binds to Rtools 3.0 and 3.1
+    }
   }
 }
 


From noreply at r-forge.r-project.org  Fri Oct 18 14:55:12 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Fri, 18 Oct 2013 14:55:12 +0200 (CEST)
Subject: [Rcpp-commits] r4578 - pkg/RcppExamples
Message-ID: <20131018125513.04A38186025@r-forge.r-project.org>

Author: edd
Date: 2013-10-18 14:55:12 +0200 (Fri, 18 Oct 2013)
New Revision: 4578

Added:
   pkg/RcppExamples/deleteMe
Log:
empty change to trigger build at R-Forge

Added: pkg/RcppExamples/deleteMe
===================================================================

From noreply at r-forge.r-project.org  Mon Oct 21 01:10:59 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 21 Oct 2013 01:10:59 +0200 (CEST)
Subject: [Rcpp-commits] r4579 - pkg/RcppGSL/R
Message-ID: <20131020231059.9CD98185118@r-forge.r-project.org>

Author: edd
Date: 2013-10-21 01:10:59 +0200 (Mon, 21 Oct 2013)
New Revision: 4579

Modified:
   pkg/RcppGSL/R/inline.R
Log:
fix a copy-and-pasto error (and trigger an R-Forge rebuild as well)


Modified: pkg/RcppGSL/R/inline.R
===================================================================
--- pkg/RcppGSL/R/inline.R	2013-10-18 12:55:12 UTC (rev 4578)
+++ pkg/RcppGSL/R/inline.R	2013-10-20 23:10:59 UTC (rev 4579)
@@ -13,7 +13,7 @@
 ## GNU General Public License for more details.
 ##
 ## You should have received a copy of the GNU General Public License
-## along with RcppArmadillo.  If not, see <http://www.gnu.org/licenses/>.
+## along with RcppGSL.  If not, see <http://www.gnu.org/licenses/>.
 
 .pkgglobalenv <- new.env(parent=emptyenv())
 


From noreply at r-forge.r-project.org  Tue Oct 22 20:38:37 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 22 Oct 2013 20:38:37 +0200 (CEST)
Subject: [Rcpp-commits] r4580 - in pkg/RcppGSL: . inst
Message-ID: <20131022183837.E0F071852C9@r-forge.r-project.org>

Author: edd
Date: 2013-10-22 20:38:37 +0200 (Tue, 22 Oct 2013)
New Revision: 4580

Modified:
   pkg/RcppGSL/ChangeLog
   pkg/RcppGSL/DESCRIPTION
   pkg/RcppGSL/NAMESPACE
   pkg/RcppGSL/inst/NEWS.Rd
Log:
minor tweak of not importing LdPath from Rcpp (R-devel's R CMD check came to
its senses) but added Rcpp to Suggests: as the vignette uses the bibtex file
from Rcpp (via a call to Rcpp:::bib())


Modified: pkg/RcppGSL/ChangeLog
===================================================================
--- pkg/RcppGSL/ChangeLog	2013-10-20 23:10:59 UTC (rev 4579)
+++ pkg/RcppGSL/ChangeLog	2013-10-22 18:38:37 UTC (rev 4580)
@@ -1,6 +1,11 @@
+2013-10-22  Dirk Eddelbuettel  <edd at debian.org>
+
+	* DESCRIPTION: Added 'Suggests: Rcpp' to build vignette as we call
+	into Rcpp to get its bibtex file
+
 2013-10-09  Dirk Eddelbuettel  <edd at debian.org>
 
-	* NAMESPACE: Import LdFlags from Rcpp, and export LdFlags and CFlags
+	* NAMESPACE: Export LdFlags and CFlags
 	* man/LdFlags.Rd: Added documentation for exported functions
 
 2013-09-10  Dirk Eddelbuettel  <edd at debian.org>

Modified: pkg/RcppGSL/DESCRIPTION
===================================================================
--- pkg/RcppGSL/DESCRIPTION	2013-10-20 23:10:59 UTC (rev 4579)
+++ pkg/RcppGSL/DESCRIPTION	2013-10-22 18:38:37 UTC (rev 4580)
@@ -27,8 +27,7 @@
   write a similar package against another library.
 License: GPL (>= 2)
 LazyLoad: yes
-Suggests: RUnit, inline, highlight
+Suggests: Rcpp, RUnit, inline, highlight
 LinkingTo: Rcpp
-Imports: Rcpp
 SystemRequirements: GNU GSL
 VignetteBuilder: highlight

Modified: pkg/RcppGSL/NAMESPACE
===================================================================
--- pkg/RcppGSL/NAMESPACE	2013-10-20 23:10:59 UTC (rev 4579)
+++ pkg/RcppGSL/NAMESPACE	2013-10-22 18:38:37 UTC (rev 4580)
@@ -1,7 +1,6 @@
 useDynLib(RcppGSL)
 
 importFrom(utils,assignInNamespace)
-importFrom(Rcpp,LdFlags)
 export(fastLmPure,
        fastLm,
        LdFlags,

Modified: pkg/RcppGSL/inst/NEWS.Rd
===================================================================
--- pkg/RcppGSL/inst/NEWS.Rd	2013-10-20 23:10:59 UTC (rev 4579)
+++ pkg/RcppGSL/inst/NEWS.Rd	2013-10-22 18:38:37 UTC (rev 4580)
@@ -15,9 +15,8 @@
     also been added for command-line builds.
     \item Unit tests now use \code{sourceCpp()} instead of
     \code{cxxfunction()} from the \pkg{inline} package
-    \item The \code{DESCRIPTION} file now uses \code{Imports: Rcpp}
-    rather than \code{Depends: Rcpp} to satisfy \code{R CMD check} under
-    the R development version.
+    \item The \code{DESCRIPTION} file now uses \code{Suggests: Rcpp}
+    (instead of \code{Depends: Rcpp}) to permit building of the vignette
   }
 }
 


From noreply at r-forge.r-project.org  Wed Oct 23 02:56:45 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 23 Oct 2013 02:56:45 +0200 (CEST)
Subject: [Rcpp-commits] r4581 - in pkg/Rcpp/inst/include/Rcpp: api/meat
	traits
Message-ID: <20131023005645.17701185AC8@r-forge.r-project.org>

Author: edd
Date: 2013-10-23 02:56:44 +0200 (Wed, 23 Oct 2013)
New Revision: 4581

Modified:
   pkg/Rcpp/inst/include/Rcpp/api/meat/is.h
   pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h
Log:
suppress two "unused paramter 'x'" warnings


Modified: pkg/Rcpp/inst/include/Rcpp/api/meat/is.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/api/meat/is.h	2013-10-22 18:38:37 UTC (rev 4580)
+++ pkg/Rcpp/inst/include/Rcpp/api/meat/is.h	2013-10-23 00:56:44 UTC (rev 4581)
@@ -51,7 +51,7 @@
     template <> inline bool is__simple<CharacterMatrix>(SEXP x) {
         return TYPEOF(x) == STRSXP && is_matrix(x);
     }
-    template <> inline bool is__simple<RObject>( SEXP x ){
+    template <> inline bool is__simple<RObject>(SEXP) {
         return true ;
     }
     template <> inline bool is__simple<IntegerVector>( SEXP x ){

Modified: pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h	2013-10-22 18:38:37 UTC (rev 4580)
+++ pkg/Rcpp/inst/include/Rcpp/traits/is_finite.h	2013-10-23 00:56:44 UTC (rev 4581)
@@ -46,8 +46,8 @@
         }
         
         template <>
-        inline bool is_finite<STRSXP>(SEXP x) { 
-            return false; // see rcpp-devel on 2013-10-02; was:  x != NA_STRING; 
+        inline bool is_finite<STRSXP>(SEXP) { 
+            return false; 	// see rcpp-devel on 2013-10-02; was:  x != NA_STRING; 
         }
         
         template <>


From noreply at r-forge.r-project.org  Wed Oct 23 03:21:12 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Wed, 23 Oct 2013 03:21:12 +0200 (CEST)
Subject: [Rcpp-commits] r4582 - pkg/RcppXts
Message-ID: <20131023012112.AD8E0185C0A@r-forge.r-project.org>

Author: edd
Date: 2013-10-23 03:21:10 +0200 (Wed, 23 Oct 2013)
New Revision: 4582

Modified:
   pkg/RcppXts/ChangeLog
   pkg/RcppXts/DESCRIPTION
   pkg/RcppXts/NAMESPACE
Log:
minor cleanup in NAMESPACE and DESCRIPTION


Modified: pkg/RcppXts/ChangeLog
===================================================================
--- pkg/RcppXts/ChangeLog	2013-10-23 00:56:44 UTC (rev 4581)
+++ pkg/RcppXts/ChangeLog	2013-10-23 01:21:10 UTC (rev 4582)
@@ -1,3 +1,7 @@
+2013-10-22  Dirk Eddelbuettel  <edd at debian.org>
+
+	* NAMESPACE: Minor cleanup
+
 2013-07-12  Dirk Eddelbuettel  <edd at debian.org>
 
 	* man/RcppXts-package.Rd: Added some documentation for new functions

Modified: pkg/RcppXts/DESCRIPTION
===================================================================
--- pkg/RcppXts/DESCRIPTION	2013-10-23 00:56:44 UTC (rev 4581)
+++ pkg/RcppXts/DESCRIPTION	2013-10-23 01:21:10 UTC (rev 4582)
@@ -1,7 +1,7 @@
 Package: RcppXts
 Type: Package
 Title: Interface the xts API via Rcpp
-Version: 0.0.4.1
+Version: 0.0.4.2
 Date: $Date$
 Author: Dirk Eddelbuettel
 Maintainer: Dirk Eddelbuettel <edd at debian.org>
@@ -11,6 +11,7 @@
  In its current state, the package is mostly a proof-of-concept to support
  adding useful functions, and does not yet add any of its own.
 License: GPL (>= 2)
-Depends: methods, Rcpp (>= 0.10.2), xts (>= 0.9-6)
+Depends: xts (>= 0.9-6)
+Imports: methods, Rcpp (>= 0.10.2)
 LinkingTo: Rcpp, xts
 RcppModules: xts

Modified: pkg/RcppXts/NAMESPACE
===================================================================
--- pkg/RcppXts/NAMESPACE	2013-10-23 00:56:44 UTC (rev 4581)
+++ pkg/RcppXts/NAMESPACE	2013-10-23 01:21:10 UTC (rev 4582)
@@ -1,5 +1,6 @@
 useDynLib(RcppXts)
 exportPattern("^[[:alpha:]]+")
-import(Rcpp)
+import(methods)
+importFrom(Rcpp, loadModule)
 import(xts)
 


From noreply at r-forge.r-project.org  Thu Oct 24 17:57:12 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Thu, 24 Oct 2013 17:57:12 +0200 (CEST)
Subject: [Rcpp-commits] r4583 - pkg/RcppEigen
Message-ID: <20131024155712.B4DA8185011@r-forge.r-project.org>

Author: dmbates
Date: 2013-10-24 17:57:12 +0200 (Thu, 24 Oct 2013)
New Revision: 4583

Modified:
   pkg/RcppEigen/DESCRIPTION
Log:
Release date

Modified: pkg/RcppEigen/DESCRIPTION
===================================================================
--- pkg/RcppEigen/DESCRIPTION	2013-10-23 01:21:10 UTC (rev 4582)
+++ pkg/RcppEigen/DESCRIPTION	2013-10-24 15:57:12 UTC (rev 4583)
@@ -2,7 +2,7 @@
 Type: Package
 Title: Rcpp integration for the Eigen templated linear algebra library.
 Version: 0.3.1.2.3
-Date: 2013-10-14
+Date: 2013-10-24
 Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel
 Maintainer: Douglas Bates <bates at stat.wisc.edu>
 Description: R and Eigen integration using Rcpp.
@@ -26,6 +26,6 @@
 Depends: R(>= 3.0.2)
 LazyLoad: yes
 LinkingTo: Rcpp (>= 0.10.5)
-Imports: Matrix (>= 1.0-16), Rcpp
+Imports: Matrix (>= 1.1-0), Rcpp
 Suggests: inline, RUnit, testthat
 URL: http://eigen.tuxfamily.org


From noreply at r-forge.r-project.org  Sun Oct 27 02:00:06 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun, 27 Oct 2013 02:00:06 +0100 (CET)
Subject: [Rcpp-commits] r4584 - testlogs
Message-ID: <20131027010006.B3019185E5C@r-forge.r-project.org>

Author: edd
Date: 2013-10-27 02:00:06 +0100 (Sun, 27 Oct 2013)
New Revision: 4584

Added:
   testlogs/Rcpp-Summary-20131026.R
   testlogs/Rcpp-check-20131026-1602.txt
   testlogs/result-20131026-183339.RData
   testlogs/result-20131026-183339.txt
Log:
Rcpp release regression tests on 2013-10-26:  
115 pass, 
30 fail for missing,
1 fails as before for missing x11


Added: testlogs/Rcpp-Summary-20131026.R
===================================================================
--- testlogs/Rcpp-Summary-20131026.R	                        (rev 0)
+++ testlogs/Rcpp-Summary-20131026.R	2013-10-27 01:00:06 UTC (rev 4584)
@@ -0,0 +1,90 @@
+## results here are edited after a second run following manual
+## installation of a number of package missing in the first run
+
+## loads 'res'
+load("~/svn/rcpp/testlogs/result-20131026-183339.RData")
+
+## good <- as.character(subset(res, res==0)[,1])
+## dput(good)
+goodPkg <- c("accelerometry", "acer", "AdaptiveSparsity", "ALKr", "Amelia",
+             "apcluster", "BayesComm", "bcp", "bcpa", "bfa", "bfp", "bifactorial",
+             "blockcluster", "ccaPP", "cda", "cladoRcpp", "clogitL1", "clusteval",
+             "ConConPiWiFun", "coneproj", "Delaporte", "ecp", "EpiContactTrace",
+             "ExactNumCI", "fastGHQuad", "FastPCS", "FastRCS", "FBFsearch",
+             "fdaMixed", "forecast", "gRbase", "gRim", "growcurves", "GSE",
+             "GUTS", "GxM", "HLMdiag", "httpuv", "inarmix", "jaatha", "Kmisc",
+             "lm.br", "maxent", "minqa", "MPTinR", "msgl", "multmod", "mvabund",
+             "MVB", "NetSim", "NetworkAnalysis", "oem", "PedCNV", "phom",
+             "phylobase", "planar", "PReMiuM", "prospectr", "psgp", "Rankcluster",
+             "Rclusterpp", "RcppArmadillo", "RcppBDT", "rcppbugs", "RcppClassic",
+             "RcppClassicExamples", "RcppCNPy", "RcppDE", "RcppEigen", "RcppExamples",
+             "RcppGSL", "RcppOctave", "RcppProgress", "RcppRoll", "RcppSMC",
+             "RcppXts", "RcppZiggurat", "rexpokit", "rforensicbatwing", "rgam",
+             "RInside", "Rmalschains", "RMessenger", "rmgarch", "Rmixmod",
+             "robustgam", "robustHD", "rococo", "rotations", "RProtoBuf",
+             "RQuantLib", "RSNNS", "RSofia", "rugarch", "RVowpalWabbit", "SBSA",
+             "sdcMicro", "sequences", "simFrame", "sparseHessianFD", "sparseLTSEigen",
+             "SpatialTools", "stochvol", "survSNP", "tagcloud", "termstrc",
+             "tmg", "transmission", "trustOptim", "unmarked", "VIM", "waffect",
+             "WideLM", "wordcloud", "zic")
+
+
+## bad <- as.character(subset(res, res==1)[,1])
+## dput(bad)
+badPkg <- c("ALDqr", "CDM", "classify", "climdex.pcic", "disclapmix", "diversitree",
+            "fugeR", "Funclustering", "geiger", "GeneticTools", "gMWT", "GOsummaries",
+            "hsphase", "hypervolume", "KernSmoothIRT", "LaF", "lme4", "marked",
+            "mets", "mirt", "miscF", "ngspatial", "openair", "orQA",
+            "sdcTable", "sirt", "spacodiR", "surveillance", "TAM", "tbart",
+            "VIMGUI")
+
+bad4missing <- c("ALDqr",		# 'HyperbolicDist?
+                 "CDM",			# sirt, TAM
+                 "classify",		# ?R2WinBUGS? ?R2jags?
+		 "climdex.pcic",	# 'PCIct'
+                 "disclapmix",		# disclap
+                 "diversitree",		# ?deSolve? ?subplex?
+                 "fugeR",		# snowfall
+		 "Funclustering",	# fda
+                 "geiger",		# ?msm? ?subplex? ?deSolve? ?coda? ?ncbit?
+                 "GeneticTools",	# ?gMWT? ?snpStats?
+                 "gMWT",		# ?clinfun?
+                 "GOsummaries",		# ?gProfileR? ?limma?
+                 "hsphase",		# snowfall
+                 "hypervolume",		# raster, maps
+                 "LaF",			# 'yaml'
+                 "lme4",		# MEMSS
+                 "marked",		# ?optimx? ?coda? ?R2admb?
+                 "mets",		# ?lava? ?timereg? ?prodlim?
+                 "mirt",		# ?GPArotation?
+                 "miscF",		# ?MCMCpack?
+                 "ngspatial",		# ?batchmeans?
+                 "openair",		# ?latticeExtra? ?hexbin? ?RgoogleMaps? ?png? ?mapdata?
+                 "orQA",		# ?genefilter?
+                 "sdcTable",		# ?lpSolveAPI?
+                 "sirt",		# ?pbivnorm? ?sfsmisc?
+                 "spacodiR",		# ?picante?
+                 "surveillance",	# ?spatstat?
+                 "TAM",			# ?tensor? ?sfsmisc? ?GPArotation? ?psych?
+                 "tbart",		# ?GISTools?
+                 "VIMGUI")		# VIM, survey
+
+bad4rcpp <- c()				# Yay!
+
+## these fail initially but can all be run with some extra effort
+bad4notrcpp <-   c("KernSmoothIRT")	# rgl failed, needs full x11 session
+
+good <- length(goodPkg)
+bad  <- length(bad4missing) + length(bad4rcpp) + length(bad4notrcpp)
+stopifnot(all.equal(bad,length(badPkg)))  ## account for GeoBIO
+
+cat("Good       ", good, "\n")
+cat("Bad        ", bad, "\n")
+cat("  RcppErr  ", length(bad4rcpp), "\n")
+cat("  MissDep  ", length(bad4missing), "\n")
+cat("  NotRcpp  ", length(bad4notrcpp), "\n")
+cat("Total      ", good + bad, "\n")
+cat("Error Pct  ", length(bad4rcpp) / (good + bad), "\n")
+
+
+

Added: testlogs/Rcpp-check-20131026-1602.txt
===================================================================
--- testlogs/Rcpp-check-20131026-1602.txt	                        (rev 0)
+++ testlogs/Rcpp-check-20131026-1602.txt	2013-10-27 01:00:06 UTC (rev 4584)
@@ -0,0 +1,344 @@
+Started at  2013-10-26 16:02:56 
+  [1] "accelerometry"       "acer"                "AdaptiveSparsity"   
+  [4] "ALDqr"               "ALKr"                "Amelia"             
+  [7] "apcluster"           "BayesComm"           "bcp"                
+ [10] "bcpa"                "bfa"                 "bfp"                
+ [13] "bifactorial"         "blockcluster"        "ccaPP"              
+ [16] "cda"                 "CDM"                 "cladoRcpp"          
+ [19] "classify"            "climdex.pcic"        "clogitL1"           
+ [22] "clusteval"           "ConConPiWiFun"       "coneproj"           
+ [25] "Delaporte"           "disclapmix"          "diversitree"        
+ [28] "ecp"                 "EpiContactTrace"     "ExactNumCI"         
+ [31] "fastGHQuad"          "FastPCS"             "FastRCS"            
+ [34] "FBFsearch"           "fdaMixed"            "forecast"           
+ [37] "fugeR"               "Funclustering"       "geiger"             
+ [40] "GeneticTools"        "gMWT"                "GOsummaries"        
+ [43] "gRbase"              "gRim"                "growcurves"         
+ [46] "GSE"                 "GUTS"                "GxM"                
+ [49] "HLMdiag"             "hsphase"             "httpuv"             
+ [52] "hypervolume"         "inarmix"             "jaatha"             
+ [55] "KernSmoothIRT"       "Kmisc"               "LaF"                
+ [58] "lm.br"               "lme4"                "marked"             
+ [61] "maxent"              "mets"                "minqa"              
+ [64] "mirt"                "miscF"               "MPTinR"             
+ [67] "msgl"                "multmod"             "mvabund"            
+ [70] "MVB"                 "NetSim"              "NetworkAnalysis"    
+ [73] "ngspatial"           "oem"                 "openair"            
+ [76] "orQA"                "PedCNV"              "phom"               
+ [79] "phylobase"           "planar"              "PReMiuM"            
+ [82] "prospectr"           "psgp"                "Rankcluster"        
+ [85] "Rclusterpp"          "RcppArmadillo"       "RcppBDT"            
+ [88] "rcppbugs"            "RcppClassic"         "RcppClassicExamples"
+ [91] "RcppCNPy"            "RcppDE"              "RcppEigen"          
+ [94] "RcppExamples"        "RcppGSL"             "RcppOctave"         
+ [97] "RcppProgress"        "RcppRoll"            "RcppSMC"            
+[100] "RcppXts"             "RcppZiggurat"        "rexpokit"           
+[103] "rforensicbatwing"    "rgam"                "RInside"            
+[106] "Rmalschains"         "RMessenger"          "rmgarch"            
+[109] "Rmixmod"             "robustgam"           "robustHD"           
+[112] "rococo"              "rotations"           "RProtoBuf"          
+[115] "RQuantLib"           "RSNNS"               "RSofia"             
+[118] "rugarch"             "RVowpalWabbit"       "SBSA"               
+[121] "sdcMicro"            "sdcTable"            "sequences"          
+[124] "simFrame"            "sirt"                "spacodiR"           
+[127] "sparseHessianFD"     "sparseLTSEigen"      "SpatialTools"       
+[130] "stochvol"            "surveillance"        "survSNP"            
+[133] "tagcloud"            "TAM"                 "tbart"              
+[136] "termstrc"            "tmg"                 "transmission"       
+[139] "trustOptim"          "unmarked"            "VIM"                
+[142] "VIMGUI"              "waffect"             "WideLM"             
+[145] "wordcloud"           "zic"                
+0 : accelerometry_2.0.tar.gz 
+0 : acer_0.1.2.tar.gz 
+0 : AdaptiveSparsity_1.2.tar.gz 
+1 : ALDqr_0.2.tar.gz 
+0 : ALKr_0.5.3.tar.gz 
+0 : Amelia_1.7.2.tar.gz 
+0 : apcluster_1.3.2.tar.gz 
+0 : BayesComm_0.1-0.tar.gz 
+0 : bcp_3.0.1.tar.gz 
+0 : bcpa_1.0.tar.gz 
+0 : bfa_0.3.tar.gz 
+0 : bfp_0.0-25.tar.gz 
+0 : bifactorial_1.4.7.tar.gz 
+0 : blockcluster_3.0.tar.gz 
+0 : ccaPP_0.2.0.tar.gz 
+0 : cda_1.3.3.tar.gz 
+1 : CDM_2.4-9.tar.gz 
+0 : cladoRcpp_0.14.2.tar.gz 
+1 : classify_1.1.tar.gz 
+1 : climdex.pcic_0.7-4.tar.gz 
+0 : clogitL1_1.1.tar.gz 
+0 : clusteval_0.1.tar.gz 
+0 : ConConPiWiFun_0.4.1.tar.gz 
+0 : coneproj_1.2.tar.gz 
+0 : Delaporte_1.0-1.tar.gz 
+1 : disclapmix_1.2.tar.gz 
+1 : diversitree_0.9-6.tar.gz 
+0 : ecp_1.5.4.tar.gz 
+0 : EpiContactTrace_0.8.6.tar.gz 
+0 : ExactNumCI_1.0.0.tar.gz 
+0 : fastGHQuad_0.1-1.tar.gz 
+0 : FastPCS_0.0.6.tar.gz 
+0 : FastRCS_0.0.1.tar.gz 
+0 : FBFsearch_1.0.tar.gz 
+0 : fdaMixed_0.2.tar.gz 
+0 : forecast_4.8.tar.gz 
+1 : fugeR_0.1.2.tar.gz 
+1 : Funclustering_1.0.tar.gz 
+1 : geiger_1.99-3.tar.gz 
+1 : GeneticTools_0.2.1.tar.gz 
+1 : gMWT_0.3.tar.gz 
+1 : GOsummaries_1.0.tar.gz 
+0 : gRbase_1.6-12.tar.gz 
+0 : gRim_0.1-17.tar.gz 
+0 : growcurves_0.2.3.5.tar.gz 
+0 : GSE_3.0.tar.gz 
+0 : GUTS_0.2.8.tar.gz 
+0 : GxM_1.0.tar.gz 
+0 : HLMdiag_0.2.3.tar.gz 
+1 : hsphase_1.2.3.tar.gz 
+0 : httpuv_1.2.0.tar.gz 
+1 : hypervolume_0.9.9.tar.gz 
+0 : inarmix_0.2.tar.gz 
+0 : jaatha_2.1.tar.gz 
+1 : KernSmoothIRT_6.0.tar.gz 
+0 : Kmisc_0.4.0-1.tar.gz 
+1 : LaF_0.5.tar.gz 
+0 : lm.br_2.2.tar.gz 
+1 : lme4_1.0-5.tar.gz 
+1 : marked_1.1.2.tar.gz 
+0 : maxent_1.3.3.tar.gz 
+1 : mets_0.2.4.tar.gz 
+0 : minqa_1.2.1.tar.gz 
+1 : mirt_0.9.0.tar.gz 
+1 : miscF_0.1-2.tar.gz 
+0 : MPTinR_1.1.8.tar.gz 
+0 : msgl_0.1.4.tar.gz 
+0 : multmod_1.0.tar.gz 
+0 : mvabund_3.8.0.tar.gz 
+0 : MVB_1.1.tar.gz 
+0 : NetSim_0.9.tar.gz 
+0 : NetworkAnalysis_0.3-1.tar.gz 
+1 : ngspatial_1.0-1.tar.gz 
+0 : oem_1.02.tar.gz 
+1 : openair_0.8-5.tar.gz 
+1 : orQA_0.2.1.tar.gz 
+0 : PedCNV_0.1.tar.gz 
+0 : phom_1.0.2.tar.gz 
+0 : phylobase_0.6.5.2.tar.gz 
+0 : planar_1.2.4.tar.gz 
+0 : PReMiuM_3.0.21.tar.gz 
+0 : prospectr_0.1.tar.gz 
+0 : psgp_0.3-4.tar.gz 
+0 : Rankcluster_0.91.tar.gz 
+0 : Rclusterpp_0.2.2.tar.gz 
+0 : RcppArmadillo_0.3.920.1.tar.gz 
+0 : RcppBDT_0.2.1.tar.gz 
+0 : rcppbugs_0.1.4.tar.gz 
+0 : RcppClassic_0.9.4.tar.gz 
+0 : RcppClassicExamples_0.1.1.tar.gz 
+0 : RcppCNPy_0.2.0.tar.gz 
+0 : RcppDE_0.1.1.tar.gz 
+1 : RcppEigen_0.3.1.2.3.tar.gz 
+0 : RcppExamples_0.1.6.tar.gz 
+0 : RcppGSL_0.2.0.tar.gz 
+0 : RcppOctave_0.11.2.tar.gz 
+0 : RcppProgress_0.1.tar.gz 
+0 : RcppRoll_0.1.0.tar.gz 
+0 : RcppSMC_0.1.1.tar.gz 
+0 : RcppXts_0.0.4.tar.gz 
+0 : RcppZiggurat_0.0.1.tar.gz 
+0 : rexpokit_0.24.1.tar.gz 
+0 : rforensicbatwing_1.1.tar.gz 
+0 : rgam_0.6.1.tar.gz 
+0 : RInside_0.2.10.tar.gz 
+0 : Rmalschains_0.2-1.tar.gz 
+0 : RMessenger_0.1.3.tar.gz 
+0 : rmgarch_1.2-0.tar.gz 
+0 : Rmixmod_1.1.3.tar.gz 
+0 : robustgam_0.1.7.tar.gz 
+0 : robustHD_0.3.2.tar.gz 
+0 : rococo_1.1.0.tar.gz 
+0 : rotations_0.1.tar.gz 
+0 : RProtoBuf_0.3.1.tar.gz 
+0 : RQuantLib_0.3.10.tar.gz 
+0 : RSNNS_0.4-3.tar.gz 
+0 : RSofia_1.1.tar.gz 
+0 : rugarch_1.2-7.tar.gz 
+0 : RVowpalWabbit_0.0.5.tar.gz 
+0 : SBSA_0.2.0.tar.gz 
+0 : sdcMicro_4.0.3.tar.gz 
+1 : sdcTable_0.10.2.tar.gz 
+0 : sequences_0.5.7.tar.gz 
+0 : simFrame_0.5.0.tar.gz 
+1 : sirt_0.38-25.tar.gz 
+1 : spacodiR_0.13.0115.tar.gz 
+0 : sparseHessianFD_0.1.0.tar.gz 
+0 : sparseLTSEigen_0.1.3.tar.gz 
+0 : SpatialTools_0.5.4.tar.gz 
+0 : stochvol_0.7-1.tar.gz 
+1 : surveillance_1.6-0.tar.gz 
+0 : survSNP_0.21-5.tar.gz 
+0 : tagcloud_0.1.tar.gz 
+1 : TAM_0.9-9.tar.gz 
+1 : tbart_0.9.tar.gz 
+0 : termstrc_1.3.5.tar.gz 
+0 : tmg_0.1.tar.gz 
+0 : transmission_0.1.tar.gz 
+0 : trustOptim_0.8.1.tar.gz 
+0 : unmarked_0.10-2.tar.gz 
+0 : VIM_4.0.0.tar.gz 
+1 : VIMGUI_0.9.0.tar.gz 
+0 : waffect_1.2.tar.gz 
+0 : WideLM_0.1-1.tar.gz 
+0 : wordcloud_2.4.tar.gz 
+0 : zic_0.7.5.tar.gz 
+                    pkg res
+1         accelerometry   0
+2                  acer   0
+3      AdaptiveSparsity   0
+4                 ALDqr   1
+5                  ALKr   0
+6                Amelia   0
+7             apcluster   0
+8             BayesComm   0
+9                   bcp   0
+10                 bcpa   0
+11                  bfa   0
+12                  bfp   0
+13          bifactorial   0
+14         blockcluster   0
+15                ccaPP   0
+16                  cda   0
+17                  CDM   1
+18            cladoRcpp   0
+19             classify   1
+20         climdex.pcic   1
+21             clogitL1   0
+22            clusteval   0
+23        ConConPiWiFun   0
+24             coneproj   0
+25            Delaporte   0
+26           disclapmix   1
+27          diversitree   1
+28                  ecp   0
+29      EpiContactTrace   0
+30           ExactNumCI   0
+31           fastGHQuad   0
+32              FastPCS   0
+33              FastRCS   0
+34            FBFsearch   0
+35             fdaMixed   0
+36             forecast   0
+37                fugeR   1
+38        Funclustering   1
+39               geiger   1
+40         GeneticTools   1
+41                 gMWT   1
+42          GOsummaries   1
+43               gRbase   0
+44                 gRim   0
+45           growcurves   0
+46                  GSE   0
+47                 GUTS   0
+48                  GxM   0
+49              HLMdiag   0
+50              hsphase   1
+51               httpuv   0
+52          hypervolume   1
+53              inarmix   0
+54               jaatha   0
+55        KernSmoothIRT   1
+56                Kmisc   0
+57                  LaF   1
+58                lm.br   0
+59                 lme4   1
+60               marked   1
+61               maxent   0
+62                 mets   1
+63                minqa   0
+64                 mirt   1
+65                miscF   1
+66               MPTinR   0
+67                 msgl   0
+68              multmod   0
+69              mvabund   0
+70                  MVB   0
+71               NetSim   0
+72      NetworkAnalysis   0
+73            ngspatial   1
+74                  oem   0
+75              openair   1
+76                 orQA   1
+77               PedCNV   0
+78                 phom   0
+79            phylobase   0
+80               planar   0
+81              PReMiuM   0
+82            prospectr   0
+83                 psgp   0
+84          Rankcluster   0
+85           Rclusterpp   0
+86        RcppArmadillo   0
+87              RcppBDT   0
+88             rcppbugs   0
+89          RcppClassic   0
+90  RcppClassicExamples   0
+91             RcppCNPy   0
+92               RcppDE   0
+93            RcppEigen   1
+94         RcppExamples   0
+95              RcppGSL   0
+96           RcppOctave   0
+97         RcppProgress   0
+98             RcppRoll   0
+99              RcppSMC   0
+100             RcppXts   0
+101        RcppZiggurat   0
+102            rexpokit   0
+103    rforensicbatwing   0
+104                rgam   0
+105             RInside   0
+106         Rmalschains   0
+107          RMessenger   0
+108             rmgarch   0
+109             Rmixmod   0
+110           robustgam   0
+111            robustHD   0
+112              rococo   0
+113           rotations   0
+114           RProtoBuf   0
+115           RQuantLib   0
+116               RSNNS   0
+117              RSofia   0
+118             rugarch   0
+119       RVowpalWabbit   0
+120                SBSA   0
+121            sdcMicro   0
+122            sdcTable   1
+123           sequences   0
+124            simFrame   0
+125                sirt   1
+126            spacodiR   1
+127     sparseHessianFD   0
+128      sparseLTSEigen   0
+129        SpatialTools   0
+130            stochvol   0
+131        surveillance   1
+132             survSNP   0
+133            tagcloud   0
+134                 TAM   1
+135               tbart   1
+136            termstrc   0
+137                 tmg   0
+138        transmission   0
+139          trustOptim   0
+140            unmarked   0
+141                 VIM   0
+142              VIMGUI   1
+143             waffect   0
+144              WideLM   0
+145           wordcloud   0
+146                 zic   0
+Ended at  2013-10-26 18:33:39 

Added: testlogs/result-20131026-183339.RData
===================================================================
(Binary files differ)


Property changes on: testlogs/result-20131026-183339.RData
___________________________________________________________________
Added: svn:mime-type
   + application/octet-stream

Added: testlogs/result-20131026-183339.txt
===================================================================
--- testlogs/result-20131026-183339.txt	                        (rev 0)
+++ testlogs/result-20131026-183339.txt	2013-10-27 01:00:06 UTC (rev 4584)
@@ -0,0 +1,147 @@
+"pkg","res"
+"1","accelerometry",0
+"2","acer",0
+"3","AdaptiveSparsity",0
+"4","ALDqr",1
+"5","ALKr",0
+"6","Amelia",0
+"7","apcluster",0
+"8","BayesComm",0
+"9","bcp",0
+"10","bcpa",0
+"11","bfa",0
+"12","bfp",0
+"13","bifactorial",0
+"14","blockcluster",0
+"15","ccaPP",0
+"16","cda",0
+"17","CDM",1
+"18","cladoRcpp",0
+"19","classify",1
+"20","climdex.pcic",1
+"21","clogitL1",0
+"22","clusteval",0
+"23","ConConPiWiFun",0
+"24","coneproj",0
+"25","Delaporte",0
+"26","disclapmix",1
+"27","diversitree",1
+"28","ecp",0
+"29","EpiContactTrace",0
+"30","ExactNumCI",0
+"31","fastGHQuad",0
+"32","FastPCS",0
+"33","FastRCS",0
+"34","FBFsearch",0
+"35","fdaMixed",0
+"36","forecast",0
+"37","fugeR",1
+"38","Funclustering",1
+"39","geiger",1
+"40","GeneticTools",1
+"41","gMWT",1
+"42","GOsummaries",1
+"43","gRbase",0
+"44","gRim",0
+"45","growcurves",0
+"46","GSE",0
+"47","GUTS",0
+"48","GxM",0
+"49","HLMdiag",0
+"50","hsphase",1
+"51","httpuv",0
+"52","hypervolume",1
+"53","inarmix",0
+"54","jaatha",0
+"55","KernSmoothIRT",1
+"56","Kmisc",0
+"57","LaF",1
+"58","lm.br",0
+"59","lme4",1
+"60","marked",1
+"61","maxent",0
+"62","mets",1
+"63","minqa",0
+"64","mirt",1
+"65","miscF",1
+"66","MPTinR",0
+"67","msgl",0
+"68","multmod",0
+"69","mvabund",0
+"70","MVB",0
+"71","NetSim",0
+"72","NetworkAnalysis",0
+"73","ngspatial",1
+"74","oem",0
+"75","openair",1
+"76","orQA",1
+"77","PedCNV",0
+"78","phom",0
+"79","phylobase",0
+"80","planar",0
+"81","PReMiuM",0
+"82","prospectr",0
+"83","psgp",0
+"84","Rankcluster",0
+"85","Rclusterpp",0
+"86","RcppArmadillo",0
+"87","RcppBDT",0
+"88","rcppbugs",0
+"89","RcppClassic",0
+"90","RcppClassicExamples",0
+"91","RcppCNPy",0
+"92","RcppDE",0
+"93","RcppEigen",1
+"94","RcppExamples",0
+"95","RcppGSL",0
+"96","RcppOctave",0
+"97","RcppProgress",0
+"98","RcppRoll",0
+"99","RcppSMC",0
+"100","RcppXts",0
+"101","RcppZiggurat",0
+"102","rexpokit",0
+"103","rforensicbatwing",0
+"104","rgam",0
+"105","RInside",0
+"106","Rmalschains",0
+"107","RMessenger",0
+"108","rmgarch",0
+"109","Rmixmod",0
+"110","robustgam",0
+"111","robustHD",0
+"112","rococo",0
+"113","rotations",0
+"114","RProtoBuf",0
+"115","RQuantLib",0
+"116","RSNNS",0
+"117","RSofia",0
+"118","rugarch",0
+"119","RVowpalWabbit",0
+"120","SBSA",0
+"121","sdcMicro",0
+"122","sdcTable",1
+"123","sequences",0
+"124","simFrame",0
+"125","sirt",1
+"126","spacodiR",1
+"127","sparseHessianFD",0
+"128","sparseLTSEigen",0
+"129","SpatialTools",0
+"130","stochvol",0
+"131","surveillance",1
+"132","survSNP",0
+"133","tagcloud",0
+"134","TAM",1
+"135","tbart",1
+"136","termstrc",0
+"137","tmg",0
+"138","transmission",0
+"139","trustOptim",0
+"140","unmarked",0
+"141","VIM",0
+"142","VIMGUI",1
+"143","waffect",0
+"144","WideLM",0
+"145","wordcloud",0
+"146","zic",0


From noreply at r-forge.r-project.org  Sun Oct 27 23:19:22 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun, 27 Oct 2013 23:19:22 +0100 (CET)
Subject: [Rcpp-commits] r4585 - in pkg/Rcpp: . debian inst/include/Rcpp
Message-ID: <20131027221922.D69811862D4@r-forge.r-project.org>

Author: edd
Date: 2013-10-27 23:19:22 +0100 (Sun, 27 Oct 2013)
New Revision: 4585

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/DESCRIPTION
   pkg/Rcpp/debian/changelog
   pkg/Rcpp/debian/copyright
   pkg/Rcpp/debian/rules
   pkg/Rcpp/inst/include/Rcpp/config.h
Log:
Rcpp release 0.10.6


Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-27 01:00:06 UTC (rev 4584)
+++ pkg/Rcpp/ChangeLog	2013-10-27 22:19:22 UTC (rev 4585)
@@ -1,3 +1,10 @@
+2013-10-27  Dirk Eddelbuettel  <edd at debian.org>
+
+        * DESCRIPTION: Release 0.10.6
+        * inst/NEWS.Rd: Release 0.10.6
+        * inst/include/Rcpp/config.h: Release 0.10.5
+        * debian/*: Similarly updated for new release to Debian
+
 2013-10-17  JJ Allaire <jj at rstudio.org>
 
         * R/Attributes.R: sourceCpp now correctly binds to Rtools 3.0 and 3.1
@@ -10,12 +17,13 @@
 
 2013-10-16 Romain Francois <romain at r-enthusiasts.com>
 
-        * include/Rcpp/api/meat/is.h : added missing implementation for 
-        is<Language> and is<DottedPair>
+        * include/Rcpp/api/meat/is.h : added missing implementation for
+	is<Language> and is<DottedPair>
 
 2013-10-14 Romain Francois <romain at r-enthusiasts.com>
-	
-	* inst/include/Rcpp/protection/protection.h: added Shield/Shelter/Armor
+
+	* inst/include/Rcpp/protection/protection.h: added
+	Shield/Shelter/Armor
 	* DESCRIPTION: bump to version 0.10.5.3
 
 2013-10-12  Dirk Eddelbuettel  <edd at debian.org>

Modified: pkg/Rcpp/DESCRIPTION
===================================================================
--- pkg/Rcpp/DESCRIPTION	2013-10-27 01:00:06 UTC (rev 4584)
+++ pkg/Rcpp/DESCRIPTION	2013-10-27 22:19:22 UTC (rev 4585)
@@ -1,6 +1,6 @@
 Package: Rcpp
 Title: Seamless R and C++ Integration
-Version: 0.10.5.3
+Version: 0.10.6
 Date: $Date$
 Author: Dirk Eddelbuettel and Romain Francois, with contributions 
  by Douglas Bates, John Chambers and JJ Allaire

Modified: pkg/Rcpp/debian/changelog
===================================================================
--- pkg/Rcpp/debian/changelog	2013-10-27 01:00:06 UTC (rev 4584)
+++ pkg/Rcpp/debian/changelog	2013-10-27 22:19:22 UTC (rev 4585)
@@ -1,3 +1,9 @@
+rcpp (0.10.6-1) unstable; urgency=low
+
+  * New release
+
+ -- Dirk Eddelbuettel <edd at debian.org>  Sun, 27 Oct 2013 16:47:29 -0500
+
 rcpp (0.10.5-1) unstable; urgency=low
 
   * New release

Modified: pkg/Rcpp/debian/copyright
===================================================================
--- pkg/Rcpp/debian/copyright	2013-10-27 01:00:06 UTC (rev 4584)
+++ pkg/Rcpp/debian/copyright	2013-10-27 22:19:22 UTC (rev 4585)
@@ -19,7 +19,7 @@
 
 Copyright (C) 2005 - 2006 Dominick Samperi
 Copyright (C) 2008        Dirk Eddelbuettel
-Copyright (C) 2009 - 2010 Dirk Eddelbuettel and Romain Francois
+Copyright (C) 2009 - 2013 Dirk Eddelbuettel and Romain Francois
 
 Portions Copyright (C) 2008 Simon Urbanek
 Portions Copyright (C) 2010 Doug Bates

Modified: pkg/Rcpp/debian/rules
===================================================================
--- pkg/Rcpp/debian/rules	2013-10-27 01:00:06 UTC (rev 4584)
+++ pkg/Rcpp/debian/rules	2013-10-27 22:19:22 UTC (rev 4585)
@@ -1,6 +1,6 @@
 #!/usr/bin/make -f
 # 							-*- makefile -*-
 # debian/rules file for the Debian/GNU Linux rcpp package
-# Copyright 2003-2008 by Dirk Eddelbuettel <edd at debian.org>
+# Copyright 2003-2013 by Dirk Eddelbuettel <edd at debian.org>
 
 include /usr/share/R/debian/r-cran.mk

Modified: pkg/Rcpp/inst/include/Rcpp/config.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/config.h	2013-10-27 01:00:06 UTC (rev 4584)
+++ pkg/Rcpp/inst/include/Rcpp/config.h	2013-10-27 22:19:22 UTC (rev 4585)
@@ -25,7 +25,7 @@
 #define Rcpp_Version(v,p,s) (((v) * 65536) + ((p) * 256) + (s))
 
 // All three digits have to be integers for g++-4.7 or later
-#define RCPP_VERSION Rcpp_Version(0,10,5)
+#define RCPP_VERSION Rcpp_Version(0,10,6)
 
 // Rcpp 0.10.3 has initial support for new preserve/release semantics
 // This switch enables a rollback to the standard R preserve/release semantics


From noreply at r-forge.r-project.org  Sun Oct 27 23:54:07 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Sun, 27 Oct 2013 23:54:07 +0100 (CET)
Subject: [Rcpp-commits] r4586 - pkg/Rcpp
Message-ID: <20131027225407.9249B18625D@r-forge.r-project.org>

Author: edd
Date: 2013-10-27 23:54:07 +0100 (Sun, 27 Oct 2013)
New Revision: 4586

Modified:
   pkg/Rcpp/.Rbuildignore
Log:
add doxyfile to .Rbuildignore as R-devel now complains


Modified: pkg/Rcpp/.Rbuildignore
===================================================================
--- pkg/Rcpp/.Rbuildignore	2013-10-27 22:19:22 UTC (rev 4585)
+++ pkg/Rcpp/.Rbuildignore	2013-10-27 22:54:07 UTC (rev 4586)
@@ -10,3 +10,4 @@
 inst/include/Rcpp/preprocessor
 inst/include/Rcpp/sugar/functions/impl
 vignettes/notyet
+doxyfile


From noreply at r-forge.r-project.org  Mon Oct 28 08:03:44 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Mon, 28 Oct 2013 08:03:44 +0100 (CET)
Subject: [Rcpp-commits] r4587 - in pkg/Rcpp: . inst/include/Rcpp/protection
Message-ID: <20131028070344.995E11807F9@r-forge.r-project.org>

Author: romain
Date: 2013-10-28 08:03:44 +0100 (Mon, 28 Oct 2013)
New Revision: 4587

Modified:
   pkg/Rcpp/ChangeLog
   pkg/Rcpp/inst/include/Rcpp/protection/Armor.h
Log:
operator SEXP has to be const for it to work with wrap

Modified: pkg/Rcpp/ChangeLog
===================================================================
--- pkg/Rcpp/ChangeLog	2013-10-27 22:54:07 UTC (rev 4586)
+++ pkg/Rcpp/ChangeLog	2013-10-28 07:03:44 UTC (rev 4587)
@@ -1,3 +1,8 @@
+2013-10-28 Romain Francois <romain at r-enthusiasts.com>
+
+        * include/Rcpp/protection/Armor.h : Armor::operator SEXP has to be const
+        for it to work properly with wrap. 
+
 2013-10-27  Dirk Eddelbuettel  <edd at debian.org>
 
         * DESCRIPTION: Release 0.10.6

Modified: pkg/Rcpp/inst/include/Rcpp/protection/Armor.h
===================================================================
--- pkg/Rcpp/inst/include/Rcpp/protection/Armor.h	2013-10-27 22:54:07 UTC (rev 4586)
+++ pkg/Rcpp/inst/include/Rcpp/protection/Armor.h	2013-10-28 07:03:44 UTC (rev 4587)
@@ -30,7 +30,7 @@
         
         template <typename U> Armor( U x );
         
-        inline operator SEXP(){
+        inline operator SEXP() const {
             return data ;
         }
               


From noreply at r-forge.r-project.org  Tue Oct 29 02:19:52 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 29 Oct 2013 02:19:52 +0100 (CET)
Subject: [Rcpp-commits] r4588 - pkg/Rcpp/vignettes
Message-ID: <20131029011952.BD19A18532D@r-forge.r-project.org>

Author: edd
Date: 2013-10-29 02:19:52 +0100 (Tue, 29 Oct 2013)
New Revision: 4588

Modified:
   pkg/Rcpp/vignettes/Rcpp-FAQ.Rnw
   pkg/Rcpp/vignettes/Rcpp-attributes.Rnw
   pkg/Rcpp/vignettes/Rcpp-extending.Rnw
   pkg/Rcpp/vignettes/Rcpp-introduction.Rnw
   pkg/Rcpp/vignettes/Rcpp-modules.Rnw
   pkg/Rcpp/vignettes/Rcpp-package.Rnw
   pkg/Rcpp/vignettes/Rcpp-quickref.Rnw
   pkg/Rcpp/vignettes/Rcpp-sugar.Rnw
   pkg/Rcpp/vignettes/Rcpp-unitTests.Rnw
Log:
change VignetteKeyword to VignetteKeywords, add VignetteDepends


Modified: pkg/Rcpp/vignettes/Rcpp-FAQ.Rnw
===================================================================
--- pkg/Rcpp/vignettes/Rcpp-FAQ.Rnw	2013-10-28 07:03:44 UTC (rev 4587)
+++ pkg/Rcpp/vignettes/Rcpp-FAQ.Rnw	2013-10-29 01:19:52 UTC (rev 4588)
@@ -1,6 +1,8 @@
 \documentclass[10pt]{article}
 %\VignetteIndexEntry{Rcpp-FAQ}
 %\VignetteEngine{highlight::highlight}
+%\VignetteKeywords{Rcpp, FAQ}
+%\VignetteDepends{Rcpp}
 \usepackage[USletter]{vmargin}
 \setmargrb{0.75in}{0.75in}{0.75in}{0.75in}
 

Modified: pkg/Rcpp/vignettes/Rcpp-attributes.Rnw
===================================================================
--- pkg/Rcpp/vignettes/Rcpp-attributes.Rnw	2013-10-28 07:03:44 UTC (rev 4587)
+++ pkg/Rcpp/vignettes/Rcpp-attributes.Rnw	2013-10-29 01:19:52 UTC (rev 4588)
@@ -1,6 +1,8 @@
 \documentclass[11pt]{article}
 %\VignetteIndexEntry{Rcpp-attributes}
 %\VignetteEngine{highlight::highlight}
+%\VignetteKeywords{Rcpp, attributes}
+%\VignetteDepends{Rcpp}
 \usepackage[USletter]{vmargin}
 \setmargrb{1.25in}{1.25in}{1.25in}{1.25in}
 

Modified: pkg/Rcpp/vignettes/Rcpp-extending.Rnw
===================================================================
--- pkg/Rcpp/vignettes/Rcpp-extending.Rnw	2013-10-28 07:03:44 UTC (rev 4587)
+++ pkg/Rcpp/vignettes/Rcpp-extending.Rnw	2013-10-29 01:19:52 UTC (rev 4588)
@@ -1,6 +1,8 @@
 \documentclass[10pt]{article}
 %\VignetteIndexEntry{Rcpp-extending}
 %\VignetteEngine{highlight::highlight}
+%\VignetteKeywords{Rcpp, package}
+%\VignetteDepends{Rcpp}
 \usepackage[USletter]{vmargin}
 \setmargrb{0.75in}{0.75in}{0.75in}{0.75in}
 

Modified: pkg/Rcpp/vignettes/Rcpp-introduction.Rnw
===================================================================
--- pkg/Rcpp/vignettes/Rcpp-introduction.Rnw	2013-10-28 07:03:44 UTC (rev 4587)
+++ pkg/Rcpp/vignettes/Rcpp-introduction.Rnw	2013-10-29 01:19:52 UTC (rev 4588)
@@ -2,8 +2,8 @@
 \documentclass[shortnames,nojss,article]{jss}
 \usepackage{booktabs,flafter,thumbpdf}
 %\VignetteIndexEntry{Rcpp-introduction}
-%\VignetteKeywords{foreign function interface, .Call, C++, R}
-%\VignettePackage{Rcpp}
+%\VignetteKeywords{Rcpp, foreign function interface, .Call, C++, R}
+%\VignetteDepends{Rcpp}
 
 \author{Dirk Eddelbuettel\\Debian Project \And Romain Fran\c{c}ois\\\proglang{R} Enthusiasts}
 \Plainauthor{Dirk Eddelbuettel, Romain Fran\c{c}ois}

Modified: pkg/Rcpp/vignettes/Rcpp-modules.Rnw
===================================================================
--- pkg/Rcpp/vignettes/Rcpp-modules.Rnw	2013-10-28 07:03:44 UTC (rev 4587)
+++ pkg/Rcpp/vignettes/Rcpp-modules.Rnw	2013-10-29 01:19:52 UTC (rev 4588)
@@ -1,6 +1,9 @@
 \documentclass[10pt]{article}
 %\VignetteIndexEntry{Rcpp-modules}
 %\VignetteEngine{highlight::highlight}
+%\VignetteKeywords{Rcpp, module}
+%\VignetteDepends{Rcpp}
+
 \usepackage[USletter]{vmargin}
 \setmargrb{0.75in}{0.75in}{0.75in}{0.75in}
 

Modified: pkg/Rcpp/vignettes/Rcpp-package.Rnw
===================================================================
--- pkg/Rcpp/vignettes/Rcpp-package.Rnw	2013-10-28 07:03:44 UTC (rev 4587)
+++ pkg/Rcpp/vignettes/Rcpp-package.Rnw	2013-10-29 01:19:52 UTC (rev 4588)
@@ -1,6 +1,9 @@
 \documentclass[10pt]{article}
 %\VignetteIndexEntry{Rcpp-package}
 %\VignetteEngine{highlight::highlight}
+%\VignetteKeywords{Rcpp, package}
+%\VignetteDepends{Rcpp}
+
 \usepackage[USletter]{vmargin}
 \setmargrb{0.75in}{0.75in}{0.75in}{0.75in}
 \usepackage{color,alltt}

Modified: pkg/Rcpp/vignettes/Rcpp-quickref.Rnw
===================================================================
--- pkg/Rcpp/vignettes/Rcpp-quickref.Rnw	2013-10-28 07:03:44 UTC (rev 4587)
+++ pkg/Rcpp/vignettes/Rcpp-quickref.Rnw	2013-10-29 01:19:52 UTC (rev 4588)
@@ -1,6 +1,8 @@
 \documentclass[8pt,twocolumn,a4paper]{article}
 %\VignetteIndexEntry{Rcpp-quickref}
 %\VignetteEngine{highlight::highlight}
+%\VignetteKeywords{Rcpp, reference}
+%\VignetteDepends{Rcpp}
 
 \setlength{\hoffset}{-0.8in}
 \setlength{\voffset}{-0.8in}

Modified: pkg/Rcpp/vignettes/Rcpp-sugar.Rnw
===================================================================
--- pkg/Rcpp/vignettes/Rcpp-sugar.Rnw	2013-10-28 07:03:44 UTC (rev 4587)
+++ pkg/Rcpp/vignettes/Rcpp-sugar.Rnw	2013-10-29 01:19:52 UTC (rev 4588)
@@ -1,6 +1,9 @@
 \documentclass[10pt]{article}
 %\VignetteIndexEntry{Rcpp-sugar}
 %\VignetteEngine{highlight::highlight}
+%\VignetteKeywords{Rcpp, syntactic sugar}
+%\VignetteDepends{Rcpp}
+
 \usepackage[USletter]{vmargin}
 \setmargrb{0.75in}{0.75in}{0.75in}{0.75in}
 

Modified: pkg/Rcpp/vignettes/Rcpp-unitTests.Rnw
===================================================================
--- pkg/Rcpp/vignettes/Rcpp-unitTests.Rnw	2013-10-28 07:03:44 UTC (rev 4587)
+++ pkg/Rcpp/vignettes/Rcpp-unitTests.Rnw	2013-10-29 01:19:52 UTC (rev 4588)
@@ -1,7 +1,7 @@
 \documentclass[10pt]{article}
 %\VignetteIndexEntry{Rcpp-unitTests}
 %\VignetteKeywords{R,Rcpp,unit tests}
-%\VignettePackage{Rcpp}
+%\VignetteDepends{Rcpp}
 
 \usepackage{vmargin}
 \setmargrb{0.75in}{0.75in}{0.75in}{0.75in}


From noreply at r-forge.r-project.org  Tue Oct 29 02:20:25 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 29 Oct 2013 02:20:25 +0100 (CET)
Subject: [Rcpp-commits] r4589 - pkg/Rcpp
Message-ID: <20131029012025.8239B18532D@r-forge.r-project.org>

Author: edd
Date: 2013-10-29 02:20:25 +0100 (Tue, 29 Oct 2013)
New Revision: 4589

Modified:
   pkg/Rcpp/.Rbuildignore
Log:
no exclude the build/ directory as we want build/vignette.rds


Modified: pkg/Rcpp/.Rbuildignore
===================================================================
--- pkg/Rcpp/.Rbuildignore	2013-10-29 01:19:52 UTC (rev 4588)
+++ pkg/Rcpp/.Rbuildignore	2013-10-29 01:20:25 UTC (rev 4589)
@@ -2,7 +2,6 @@
 inst/doc/html
 inst/doc/latex
 inst/doc/man
-build
 inst/doc/jss.bst
 vignettes/jss.bst
 ^.*\.Rproj$


From noreply at r-forge.r-project.org  Tue Oct 29 15:33:42 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 29 Oct 2013 15:33:42 +0100 (CET)
Subject: [Rcpp-commits] r4590 - pkg/RcppClassic
Message-ID: <20131029143342.DB88318619D@r-forge.r-project.org>

Author: edd
Date: 2013-10-29 15:33:40 +0100 (Tue, 29 Oct 2013)
New Revision: 4590

Removed:
   pkg/RcppClassic/.Rbuildignore
Log:
remove .Rbuildignore which was a leftover from the actual Rcpp

Deleted: pkg/RcppClassic/.Rbuildignore
===================================================================
--- pkg/RcppClassic/.Rbuildignore	2013-10-29 01:20:25 UTC (rev 4589)
+++ pkg/RcppClassic/.Rbuildignore	2013-10-29 14:33:40 UTC (rev 4590)
@@ -1,5 +0,0 @@
-debian
-inst/doc/html
-inst/doc/latex
-inst/doc/man
-build


From noreply at r-forge.r-project.org  Tue Oct 29 15:42:58 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 29 Oct 2013 15:42:58 +0100 (CET)
Subject: [Rcpp-commits] r4591 - pkg/Rcpp/debian
Message-ID: <20131029144258.C459918618B@r-forge.r-project.org>

Author: edd
Date: 2013-10-29 15:42:58 +0100 (Tue, 29 Oct 2013)
New Revision: 4591

Modified:
   pkg/Rcpp/debian/changelog
   pkg/Rcpp/debian/control
Log:
minor cosmetics for the Debian build


Modified: pkg/Rcpp/debian/changelog
===================================================================
--- pkg/Rcpp/debian/changelog	2013-10-29 14:33:40 UTC (rev 4590)
+++ pkg/Rcpp/debian/changelog	2013-10-29 14:42:58 UTC (rev 4591)
@@ -1,9 +1,13 @@
 rcpp (0.10.6-1) unstable; urgency=low
 
   * New release
+  * debian/control: Set Build-Depends: to current R version 
+  * debian/control: Set Standards-Version: to current version 
+  * debian/control: Add 'r-cran-codetools' to Build-Depends (as it is 
+    used at preparation for LazuyLoading stage) 
+  
+ -- Dirk Eddelbuettel <edd at debian.org>  Tue, 29 Oct 2013 09:42:30 -0500
 
- -- Dirk Eddelbuettel <edd at debian.org>  Sun, 27 Oct 2013 16:47:29 -0500
-
 rcpp (0.10.5-1) unstable; urgency=low
 
   * New release

Modified: pkg/Rcpp/debian/control
===================================================================
--- pkg/Rcpp/debian/control	2013-10-29 14:33:40 UTC (rev 4590)
+++ pkg/Rcpp/debian/control	2013-10-29 14:42:58 UTC (rev 4591)
@@ -2,8 +2,8 @@
 Section: gnu-r
 Priority: optional
 Maintainer: Dirk Eddelbuettel <edd at debian.org>
-Build-Depends: debhelper (>= 7.0.0), r-base-dev (>= 3.0.2), cdbs
-Standards-Version: 3.9.4
+Build-Depends: debhelper (>= 7.0.0), r-base-dev (>= 3.0.2), cdbs, r-cran-codetools
+Standards-Version: 3.9.5
 Homepage: http://dirk.eddelbuettel.com/code/rcpp.html
 
 Package: r-cran-rcpp


From noreply at r-forge.r-project.org  Tue Oct 29 16:29:40 2013
From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org)
Date: Tue, 29 Oct 2013 16:29:40 +0100 (CET)
Subject: [Rcpp-commits] r4592 - pkg/Rcpp/inst
Message-ID: <20131029152940.25B6F186168@r-forge.r-project.org>

Author: edd
Date: 2013-10-29 16:29:39 +0100 (Tue, 29 Oct 2013)
New Revision: 4592

Modified:
   pkg/Rcpp/inst/NEWS.Rd
Log:
belatedly fix NEWS header for 0.10.6 release


Modified: pkg/Rcpp/inst/NEWS.Rd
===================================================================
--- pkg/Rcpp/inst/NEWS.Rd	2013-10-29 14:42:58 UTC (rev 4591)
+++ pkg/Rcpp/inst/NEWS.Rd	2013-10-29 15:29:39 UTC (rev 4592)
@@ -2,7 +2,7 @@
 \title{News for Package 'Rcpp'}
 \newcommand{\cpkg}{\href{http://CRAN.R-project.org/package=#1}{\pkg{#1}}}
 
-\section{Changes in Rcpp version 0.10.5.2 (2013-10-08)}{
+\section{Changes in Rcpp version 0.10.6 (2013-10-27)}{
   \itemize{
     \item Changes in Rcpp API:
     \itemize{