Merge remote-tracking branch 'upstream/master' into subsetter-patch

Author: Florian Plaza Oñate

ChangeLog

@@ -1,8 +1,62 @@
+2015-08-31  Dirk Eddelbuettel  <[email protected]>
+
+        * DESCRIPTION (Version, Date): Roll Version and Date
+
+2015-08-30  Dirk Eddelbuettel  <[email protected]>
+
+        * vignettes/Rcpp.bib: Updated RcppGSL entry
+
+2015-08-29  Dirk Eddelbuettel  <[email protected]>
+
+        * vignettes/Rcpp.bib: Add RcppZiggurat entry
+
+        * inst/include/Rcpp/utils/tinyformat.h: Updated to current upstream
+        version keeping our local modifications / adaptations (PR #357)
+
+2015-08-29  Qiang Kou <[email protected]>
+
+        * inst/include/Rcpp/vector/Subsetter.h: Enable logical subsetting on
+        both LHS and RHS, eg 'a[b > 3] = b[b > 3]' (pull request #352 addressing
+        issue #345)
+        * inst/unitTests/cpp/Subset.cpp: Ditto
+        * inst/unitTests/runit.subset.R: Unit tests for above
+
+2015-08-26  Dirk Eddelbuettel  <[email protected]>
+
+        * inst/unitTests/testRcppClass/src/rcpp_module.cpp: Renamed Module
+        'World' to 'RcppClassWorld' to avoid multiple modules with same name
+        (pull request #351, fixed issue #350)
+
+        * inst/unitTests/testRcppClass/man/Rcpp_class_examples.Rd: Ditto
+        * inst/unitTests/testRcppClass/R/load.R: Ditto
+        * inst/unitTests/testRcppClass/NAMESPACE: Ditto
+        * inst/unitTests/runit.Module.client.package.R: Re-enable test
+
+        * inst/unitTests/testRcppModule/src/rcpp_module.cpp: Renamed Module
+        'World' to 'RcppModuleWorld' to avoid multiple modules with same name
+
+        * inst/unitTests/cpp/modref.cpp: Rename 'World' to 'ModRefWorld'
+        * inst/unitTests/runit.modref.R (test.modRef): Ditto
+
+        * inst/unitTests/cpp/Module.cpp: Rename 'World' to 'ModuleWorld'
+        * inst/unitTests/runit.Module.R (test.Module): Ditto
+
+2015-08-25  Kurt Hornik  <[email protected]>
+
+        * R/loadModule.R: For now=TRUE, always set .botched to FALSE which
+        corresponds to the case of the methods package being in the search path
+        * inst/include/Rcpp/Reference.h: Call call with the internal Namespace
+
 2015-08-24  Dirk Eddelbuettel  <[email protected]>
 
         * vignettes/Rcpp.bib: Updated R / R Core references
 
-2015-08-19  Florian Plaza Oñate <[email protected]>
+2015-08-23  Romain Francois <[email protected]>
+
+        * inst/include/Rcpp/Benchmark/Timer.h: Silence 'g++ -pedantic' by
+        replaceing one R_xlen_t by size_t (pull request #348)
+
+2015-08-19  Florian Plaza Onate <[email protected]>
         * inst/include/Rcpp/vector/Vector.h: Add 'at' methods which implement
         accessors with bounds cheking (pull request #342, fixes issue #341)
         * inst/include/Rcpp/vector/Matrix.h: Ditto
@@ -16,12 +70,12 @@
         * inst/unitTests/runit.Module.client.package.R: Disabled for bad
         interaction of Rcpp Modules and R 3.2.2
 
-2015-08-15  Florian Plaza Oñate <[email protected]>
+2015-08-15  Florian Plaza Onate <[email protected]>
 
         * inst/include/Rcpp/vector/converter.h: Correct conversion from const
         char argument (pull request #344, fixes issue #343)
 
-2015-08-14  Florian Plaza Oñate <[email protected]>
+2015-08-14  Florian Plaza Onate <[email protected]>
 
         * inst/include/Rcpp/vector/DimNameProxy.h: Add assignment operator,
         refactor code, update error message formatting (pull request #339)
@@ -33,7 +87,8 @@
 2015-08-02  Dirk Eddelbuettel  <[email protected]>
 
         * R/Attributes.R (sourceCpp): In no-rebuild-needed case, also set a
-        default directory restoration via on.exit()
+        default directory restoration via on.exit() (pull request #335,
+        addressing issue #309)
 
 2015-07-24  Dirk Eddelbuettel  <[email protected]>
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Rcpp
 Title: Seamless R and C++ Integration
-Version: 0.12.0.2
-Date: 2015-08-17
+Version: 0.12.0.5
+Date: 2015-08-31
 Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, 
  Qiang Kou, Douglas Bates and John Chambers
 Maintainer: Dirk Eddelbuettel <[email protected]>

R/loadModule.R

@@ -1,4 +1,4 @@
-# Copyright (C) 2010 - 2012 John Chambers, Dirk Eddelbuettel and Romain Francois
+# Copyright (C) 2010 - 2015  John Chambers, Dirk Eddelbuettel and Romain Francois
 #
 # This file is part of Rcpp.
 #
@@ -67,7 +67,9 @@ loadModule <- function( module, what = character(), loadNow,
         loadNow <- !is(loadM, "error")
     }
     if(loadNow) {
-        .botched <- isBotchedSession()
+        ## .botched <- isBotchedSession()
+        .botched <- FALSE
+
         if(is.null(loadM))
             loadM <- tryCatch(Module( module, mustStart = TRUE, where = env ),
                               error = function(e)e)

inst/NEWS.Rd

@@ -19,6 +19,12 @@
       \item Correctly reset directory in case of no-rebuilding but Windows code
       (PR #335)
     }
+    \item Changes in Rcpp Modules:
+    \itemize{
+      \item We no longer define multiple Modules objects named \code{World} in
+      the unit tests with was seen to have a bad effect with R 3.2.2 or later.
+      \item Applied patch by Kurt Hornik which improves how Rcpp loads Modules
+    }
   }
 }
 

inst/include/Rcpp/Reference.h

@@ -2,7 +2,7 @@
 //
 // Reference.h: Rcpp R/C++ interface class library -- Reference class objects
 //
-// Copyright (C) 2010 - 2013 Dirk Eddelbuettel and Romain Francois
+// Copyright (C) 2010 - 2015  Dirk Eddelbuettel and Romain Francois
 //
 // This file is part of Rcpp.
 //
@@ -59,15 +59,15 @@ namespace Rcpp{
         Reference_Impl( const std::string& klass ) {
             SEXP newSym = Rf_install("new");
             Shield<SEXP> call( Rf_lang2( newSym, Rf_mkString( klass.c_str() ) ) );
-            Storage::set__( Rcpp_eval( call ) ) ;
+            Storage::set__( Rcpp_eval( call , Rcpp::internal::get_Rcpp_namespace()) );
         }
 
         void update( SEXP x){
-            if( ! ::Rf_isS4(x) ) throw not_reference() ;
+            if( ! ::Rf_isS4(x) ) throw not_reference();
         }
     } ;
 
-    typedef Reference_Impl<PreserveStorage> Reference ;
+    typedef Reference_Impl<PreserveStorage> Reference;
 
 } // namespace Rcpp
 

inst/include/Rcpp/utils/tinyformat.h

@@ -128,6 +128,10 @@ namespace Rcpp {
 }
 #define TINYFORMAT_ERROR(REASON) ::Rcpp::stop(REASON)
 
+// Define for C++11 variadic templates which make the code shorter & more
+// general.  If you don't define this, C++11 support is autodetected below.
+// #define TINYFORMAT_USE_VARIADIC_TEMPLATES
+
 // don't use C++11 features (support older compilers)
 #define TINYFORMAT_NO_VARIADIC_TEMPLATES
 
@@ -148,12 +152,29 @@ namespace Rcpp {
 #   endif
 #endif
 
+#ifdef TINYFORMAT_USE_VARIADIC_TEMPLATES
+#   include <array>
+#   if defined(_MSC_VER) && _MSC_VER <= 1800 // VS2013
+#       define TINYFORMAT_BRACED_INIT_WORKAROUND(x) (x)
+#   else
+#       define TINYFORMAT_BRACED_INIT_WORKAROUND(x) {x}
+#   endif
+#endif
+
 #if defined(__GLIBCXX__) && __GLIBCXX__ < 20080201
 //  std::showpos is broken on old libstdc++ as provided with OSX.  See
 //  http://gcc.gnu.org/ml/libstdc++/2007-11/msg00075.html
 #   define TINYFORMAT_OLD_LIBSTDCPLUSPLUS_WORKAROUND
 #endif
 
+#ifdef __APPLE__
+// Workaround OSX linker warning: xcode uses different default symbol
+// visibilities for static libs vs executables (see issue #25)
+#   define TINYFORMAT_HIDDEN __attribute__((visibility("hidden")))
+#else
+#   define TINYFORMAT_HIDDEN
+#endif
+
 namespace tinyformat {
 
 //------------------------------------------------------------------------------
@@ -203,7 +224,7 @@ template<int n> struct is_wchar<wchar_t[n]> {};
 template<typename T, typename fmtT, bool convertible = is_convertible<T, fmtT>::value>
 struct formatValueAsType
 {
-    static void invoke(std::ostream& /*out*/, const T& /*value*/) {}
+    static void invoke(std::ostream& /*out*/, const T& /*value*/) { /*assert(0);*/ }
 };
 // Specialized version for types that can actually be converted to fmtT, as
 // indicated by the "convertible" template parameter.
@@ -311,8 +332,8 @@ inline void formatValue(std::ostream& out, const char* /*fmtBegin*/,
     // void* respectively and format that instead of the value itself.  For the
     // %p conversion it's important to avoid dereferencing the pointer, which
     // could otherwise lead to a crash when printing a dangling (const char*).
-    const bool canConvertToChar = detail::is_convertible<T,char>::value;
-    const bool canConvertToVoidPtr = detail::is_convertible<T, const void*>::value;
+    bool canConvertToChar = detail::is_convertible<T,char>::value;
+    bool canConvertToVoidPtr = detail::is_convertible<T, const void*>::value;
     if(canConvertToChar && *(fmtEnd-1) == 'c')
         detail::formatValueAsType<T, char>::invoke(out, value);
     else if(canConvertToVoidPtr && *(fmtEnd-1) == 'p')
@@ -502,14 +523,14 @@ class FormatArg
 
     private:
         template<typename T>
-        static void formatImpl(std::ostream& out, const char* fmtBegin,
+        TINYFORMAT_HIDDEN static void formatImpl(std::ostream& out, const char* fmtBegin,
                         const char* fmtEnd, int ntrunc, const void* value)
         {
             formatValue(out, fmtBegin, fmtEnd, ntrunc, *static_cast<const T*>(value));
         }
 
         template<typename T>
-        static int toIntImpl(const void* value)
+        TINYFORMAT_HIDDEN static int toIntImpl(const void* value)
         {
             return convertToInt<T>::invoke(*static_cast<const T*>(value));
         }
@@ -540,7 +561,7 @@ inline int parseIntAndAdvance(const char*& c)
 inline const char* printFormatStringLiteral(std::ostream& out, const char* fmt)
 {
     const char* c = fmt;
-    for(; true; ++c)
+    for(;; ++c)
     {
         switch(*c)
         {
@@ -848,7 +869,7 @@ class FormatListN : public FormatList
         template<typename... Args>
         FormatListN(const Args&... args)
             : FormatList(&m_formatterStore[0], N),
-            m_formatterStore{FormatArg(args)...}
+            m_formatterStore TINYFORMAT_BRACED_INIT_WORKAROUND({ FormatArg(args)... })
         { static_assert(sizeof...(args) == N, "Number of args must be N"); }
 #else // C++98 version
         void init(int) {}
@@ -857,7 +878,7 @@ class FormatListN : public FormatList
         template<TINYFORMAT_ARGTYPES(n)>                       \
         FormatListN(TINYFORMAT_VARARGS(n))                     \
             : FormatList(&m_formatterStore[0], n)              \
-        { init(0, TINYFORMAT_PASSARGS(n)); }                   \
+        {/*assert*n == N);*/init(0, TINYFORMAT_PASSARGS(n)); } \
                                                                \
         template<TINYFORMAT_ARGTYPES(n)>                       \
         void init(int i, TINYFORMAT_VARARGS(n))                \
@@ -871,7 +892,11 @@ class FormatListN : public FormatList
 #endif
 
     private:
+#ifdef TINYFORMAT_USE_VARIADIC_TEMPLATES
+        std::array<FormatArg, N> m_formatterStore;
+#else // C++98 version
         FormatArg m_formatterStore[N];
+#endif
 };
 
 // Special 0-arg version - MSVC says zero-sized C array in struct is nonstandard

inst/include/Rcpp/vector/Subsetter.h

@@ -97,6 +97,30 @@ class SubsetProxy {
         return *this;
     }
 
+    template <int RTYPE_OTHER, template <class> class StoragePolicyOther,int RHS_RTYPE_OTHER, bool RHS_NA_OTHER, typename RHS_T_OTHER>
+    SubsetProxy& operator=(const SubsetProxy<RTYPE_OTHER, StoragePolicyOther, RHS_RTYPE_OTHER, RHS_NA_OTHER, RHS_T_OTHER>& other) {
+
+        Vector<RTYPE_OTHER, StoragePolicyOther> other_vec = other;
+        *this = other_vec;
+        return *this;
+    }
+
+    SubsetProxy& operator=(const SubsetProxy& other) {
+        if (other.indices_n == 1) {
+            for (int i=0; i < indices_n; ++i) {
+                lhs[ indices[i] ] = other.lhs[other.indices[0]];
+            }
+        }
+        else if (indices_n == other.indices_n) {
+            for (int i=0; i < indices_n; ++i)
+                lhs[ indices[i] ] = other.lhs[other.indices[i]];
+            }
+        else {
+            stop("index error");
+        }
+        return *this;
+    }
+
     operator Vector<RTYPE, StoragePolicy>() const {
         return get_vec();
     }