@@ -1,3 +1,7 @@

+2012-02-23  Steffen Neumann  <sneumann@ipb-halle.de>

+	* Moved from the ancient embedded Rcpp to RcppClassic,

+  	  thanks to the work of Dirk Eddelbuettel who did the porting

+	

 2010-11-04  Steffen Neumann  <sneumann@ipb-halle.de>

 	* Corrected bug that leads to wrong monoisotopic masses for molecules 

 	  containing elements where the most abundant isotope is not the first one,

@@ -1,7 +1,7 @@

 Package: Rdisop

 Title: Decomposition of Isotopic Patterns

-Version: 1.15.2

-Date: 2011-10-05

+Version: 1.15.3

+Date: 2012-02-23

 Author: Anton Pervukhin <apervukh@minet.uni-jena.de>, Steffen Neumann <sneumann@ipb-halle.de> 

 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>

 Description: Identification of metabolites using high precision mass

@@ -9,9 +9,11 @@ Description: Identification of metabolites using high precision mass

              of sum formulae, alternatively for a given sum formula

              the theoretical isotope distribution can be calculated 

              to search in MS peak lists.

-Depends: R (>= 2.0.0)

+Depends: R (>= 2.0.0), RcppClassic, Rcpp

+LinkingTo: RcppClassic, Rcpp

 Suggests: RUnit

 SystemRequirements: None

 License: GPL-2

 URL: http://msbi.ipb-halle.de/

 biocViews: MassSpectrometry

+Packaged: 2012-02-16 14:03:45.877398 UTC; edd

@@ -1,3 +1,3 @@

 # echo "useDynLib(Rdisop)" ; echo -n "export(" ; grep --no-filename "<- function" R/*.R | cut -d" " -f 1 | grep -v First.lib | grep -v getElement | sort |  xargs echo -n | tr " " , ; echo ")"

 useDynLib(Rdisop)

-export(addMolecules,decomposeIsotopes,decomposeMass,getMass,getFormula,getIsotope,getValid,getMolecule,getScore,initializeCHNOPS,initializeCHNOPSMgKCaFe,initializeCHNOPSNaK,initializeElements,initializePSE,initializeCharges,isotopeScore,RcppVersion,subMolecules)

+export(addMolecules,decomposeIsotopes,decomposeMass,getMass,getFormula,getIsotope,getValid,getMolecule,getScore,initializeCHNOPS,initializeCHNOPSMgKCaFe,initializeCHNOPSNaK,initializeElements,initializePSE,initializeCharges,isotopeScore,subMolecules)

deleted file mode 100644

@@ -1,4 +0,0 @@

-RcppVersion <- function() {

-  licenseFile <- file(system.file(".","Rcpp-license.txt",package="RcppTemplate"),"r")

-  writeLines(readLines(licenseFile))

-}

deleted file mode 100644

@@ -1,18 +0,0 @@

-Built using Rcpp/RcppTemplate Version 5.0

-

-Rcpp/RcppTemplate Copyright (c) 2005-2006 by Dominick Samperi

-

-This library is free software; you can redistribute it and/or modify it 

-under the terms of the GNU Lesser General Public License as published by 

-the Free Software Foundation; either version 2.1 of the License, or (at 

-your option) any later version.

-

-This library 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 Lesser General Public 

-License for more details.

-

-You should have received a copy of the GNU Lesser General Public License 

-along with this library; if not, write to the Free Software Foundation, 

-Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 

-

deleted file mode 100644

@@ -1,16 +0,0 @@

-include ${R_HOME}/etc${R_ARCH}/Makeconf

-SRC = Rcpp.cpp

-OBJ = Rcpp.o

-LIB = libRcpp.a

-

-.PHONY: all

-

-all: $(LIB)

-

-clean:

-	rm -f $(OBJ) $(LIB)

-

-$(OBJ): $(SRC)

-

-$(LIB): $(OBJ)

-	ar crs $(LIB) $(OBJ)

deleted file mode 100644

@@ -1,23 +0,0 @@

-include $(R_HOME)/etc/$(R_ARCH)/Makeconf

-

-SRC = Rcpp.cpp

-OBJ = Rcpp.o

-LINKOBJ  = Rcpp.o $(RES)

-DLLLIBS = -s -L"$(RHOME)/src/gnuwin32" -lR --no-export-all-symbols --add-stdcall-alias

-LIB  = libRcpp.a

-CXXFLAGS = -I"$(RHOME)/include" -I"$(RHOME)/src/include" $(CPPFLAGS) -Wall -O2

-RM = rm -f

-

-.PHONY: all all-before all-after clean clean-custom

-

-all: all-before libRcpp.a all-after

-

-clean: clean-custom

-	$(RM) $(LINKOBJ) $(LIB)

-

-$(OBJ): $(SRC)

-	$(CXX) -c $(SRC) -o $(OBJ) $(CXXFLAGS)

-	

-$(LIB): $(LINKOBJ)

-	$(AR) rs $(LIB) $(OBJ)

-	$(RM) $(OBJ)

deleted file mode 100644

@@ -1,19 +0,0 @@

-

-Package build used Rcpp/RcppTemplate Version 4.2

-

-Copyright (c) 2005-2006 by Dominick Samperi

-

-This library is free software; you can redistribute it and/or modify it 

-under the terms of the GNU Lesser General Public License as published by 

-the Free Software Foundation; either version 2.1 of the License, or (at 

-your option) any later version.

-

-This library 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 Lesser General Public 

-License for more details.

-

-You should have received a copy of the GNU Lesser General Public License 

-along with this library; if not, write to the Free Software Foundation, 

-Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 

-

deleted file mode 100644

@@ -1,892 +0,0 @@

-// Rcpp.cpp: Part of the R/C++ interface class library, Version 5.0

-//

-// Copyright (C) 2005-2006 Dominick Samperi

-//

-// This library is free software; you can redistribute it and/or modify it 

-// under the terms of the GNU Lesser General Public License as published by 

-// the Free Software Foundation; either version 2.1 of the License, or (at 

-// your option) any later version.

-//

-// This library 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 Lesser General Public 

-// License for more details.

-//

-// You should have received a copy of the GNU Lesser General Public License 

-// along with this library; if not, write to the Free Software Foundation, 

-// Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA 

-

-#include "Rcpp.hpp"

-#include <cstring>

-

-RcppParams::RcppParams(SEXP params) {

-    if(!isNewList(params))

-	throw std::range_error("RcppParams: non-list passed to constructor");

-    int len = length(params);

-    SEXP names = getAttrib(params, R_NamesSymbol);

-    if(names == R_NilValue)

-	throw std::range_error("RcppParams: list must have named elements");

-    for(int i = 0; i < len; i++) {

-	string nm = string(CHAR(STRING_ELT(names,i)));

-	if(nm.size() == 0)

-	    throw std::range_error("RcppParams: all list elements must be named");

-	pmap[nm] = i;

-    }

-    _params = params;

-}

-

-void RcppParams::checkNames(char *inputNames[], int len) {

-    for(int i = 0; i < len; i++) {

-	map<string,int>::iterator iter = pmap.find(inputNames[i]);

-	if(iter == pmap.end()) {

-	    string mesg = "checkNames: missing required parameter ";

-	    throw range_error(mesg+inputNames[i]);

-	}

-    }

-}

-

-RcppFrame::RcppFrame(SEXP df) {

-    if(!isNewList(df))

-	throw std::range_error("RcppFrame::RcppFrame: invalid data frame.");

-    int ncol = length(df);

-    SEXP names = getAttrib(df, R_NamesSymbol);

-    colNames.resize(ncol);

-    SEXP colData = VECTOR_ELT(df,0); // First column of data.

-    int nrow = length(colData);

-    if(nrow == 0)

-	throw std::range_error("RcppFrame::RcppFrame: zero lenth column.");

-

-    // Allocate storage for table.

-    table.resize(nrow);

-    for(int r = 0; r < nrow; r++)

-	table[r].resize(ncol);

-    

-    for(int i=0; i < ncol; i++) {

-	colNames[i] = string(CHAR(STRING_ELT(names,i)));

-	SEXP colData = VECTOR_ELT(df,i);

-	if(!isVector(colData) || length(colData) != nrow)

-	    throw std::range_error("RcppFrame::RcppFrame: invalid column.");

-

-	// Check for Date class. Currently R stores the date ordinal in a

-	// real value. We check for Date under both Real and Integer values

-	// as insurance against future changes.

-	bool isDateClass = false;

-	SEXP classname = getAttrib(colData, R_ClassSymbol);

-	if(classname != R_NilValue)

-	    isDateClass = (strcmp(CHAR(STRING_ELT(classname,0)),"Date") == 0);

-

-	if(isReal(colData)) {

-	    if(isDateClass) {

-		for(int j=0; j < nrow; j++) // Column of Date's

-		    table[j][i].setDateValue(RcppDate((int)REAL(colData)[j]));

-	    }

-	    else // Column of REAL's

-		for(int j=0; j < nrow; j++)

-		    table[j][i].setDoubleValue(REAL(colData)[j]);

-	}

-	else if(isInteger(colData)) {

-	    if(isDateClass) {

-		for(int j=0; j < nrow; j++) // Column of Date's

-		    table[j][i].setDateValue(RcppDate(INTEGER(colData)[j]));

-	    }

-	    else

-		for(int j=0; j < nrow; j++)

-		    table[j][i].setIntValue(INTEGER(colData)[j]);

-	}

-	else if(isString(colData)) { // Non-factor string column

-	    for(int j=0; j < nrow; j++)

-		table[j][i].setStringValue(string(CHAR(STRING_ELT(colData,j))));

-	}

-	else if (isFactor(colData)) { // Factor column.

-	    SEXP names = getAttrib(colData, R_LevelsSymbol);

-	    int numLevels = length(names);

-	    string *levelNames = new string[numLevels];

-	    for(int k=0; k < numLevels; k++)

-		levelNames[k] = string(CHAR(STRING_ELT(names,k)));

-	    for(int j=0; j < nrow; j++)

-		table[j][i].setFactorValue(levelNames, numLevels,

-					   INTEGER(colData)[j]);

-	    delete [] levelNames;

-	}

-	else if(isLogical(colData)) {

-	    for(int j=0; j < nrow; j++) {

-		table[j][i].setLogicalValue(INTEGER(colData)[j]);

-	    }

-	}

-	else

-	    throw std::range_error("RcppFrame::RcppFrame: unsupported data frame column type.");

-    }

-}

-

-double RcppParams::getDoubleValue(string name) {

-    map<string,int>::iterator iter = pmap.find(name);

-    if(iter == pmap.end()) {

-	string mesg = "getDoubleValue: no such name: ";

-	throw std::range_error(mesg+name);

-    }

-    int posn = iter->second;

-    SEXP elt = VECTOR_ELT(_params,posn);

-    if(!isNumeric(elt) || length(elt) != 1) {

-	string mesg = "getDoubleValue: must be scalar ";

-	throw std::range_error(mesg+name);

-    }

-    if(isInteger(elt))

-	return (double)INTEGER(elt)[0];

-    else if(isReal(elt))

-	return REAL(elt)[0];

-    else {

-	string mesg = "getDoubleValue: invalid value for ";

-	throw std::range_error(mesg+name);

-    }

-    return 0; // never get here

-}

-

-int RcppParams::getIntValue(string name) {

-    map<string,int>::iterator iter = pmap.find(name);

-    if(iter == pmap.end()) {

-	string mesg = "getIntValue: no such name: ";

-	throw std::range_error(mesg+name);

-    }

-    int posn = iter->second;

-    SEXP elt = VECTOR_ELT(_params,posn);

-    if(!isNumeric(elt) || length(elt) != 1) {

-	string mesg = "getIntValue: must be scalar: ";

-	throw std::range_error(mesg+name);

-    }

-    if(isInteger(elt))

-	return INTEGER(elt)[0];

-    else if(isReal(elt))

-	return (int)REAL(elt)[0];

-    else {

-	string mesg = "getIntValue: invalid value for: ";

-	throw std::range_error(mesg+name);

-    }

-    return 0; // never get here

-}

-

-bool RcppParams::getBoolValue(string name) {

-    map<string,int>::iterator iter = pmap.find(name);

-    if(iter == pmap.end()) {

-	string mesg = "getBoolValue: no such name: ";

-	throw std::range_error(mesg+name);

-    }

-    int posn = iter->second;

-    SEXP elt = VECTOR_ELT(_params,posn);

-    if(isLogical(elt))

-	return INTEGER(elt)[0];

-    else {

-	string mesg = "getBoolValue: invalid value for: ";

-	throw std::range_error(mesg+name);

-    }

-    return false; // never get here

-}

-

-string RcppParams::getStringValue(string name) {

-    map<string,int>::iterator iter = pmap.find(name);

-    if(iter == pmap.end()) {

-	string mesg = "getStringValue: no such name: ";

-	throw std::range_error(mesg+name);

-    }

-    int posn = iter->second;

-    SEXP elt = VECTOR_ELT(_params,posn);

-    if(isString(elt))

-		return string(CHAR(STRING_ELT(elt,0)));

-    else {

-	string mesg = "getStringValue: invalid value for: ";

-	throw std::range_error(mesg+name);

-    }

-    return ""; // never get here

-}

-

-RcppDate RcppParams::getDateValue(string name) {

-    map<string,int>::iterator iter = pmap.find(name);

-    if(iter == pmap.end()) {

-	string mesg = "getDateValue: no such name: ";

-	throw std::range_error(mesg+name);

-    }

-    int posn = iter->second;

-    SEXP elt = VECTOR_ELT(_params,posn);

-    if(!isNumeric(elt) || length(elt) != 1) {

-	string mesg = "getDateValue: invalide date: ";

-	throw std::range_error(mesg+name);

-    }

-

-    int d;

-    if(isReal(elt)) // R stores julian value in a double.

-	d = (int)REAL(elt)[0];

-    else {

-	string mesg = "getDateValue: invalid value for: ";

-	throw std::range_error(mesg+name);

-    }

-    return RcppDate(d);

-}

-

-RcppDateVector::RcppDateVector(SEXP vec) {

-    int i;

-    if(!isNumeric(vec) || isMatrix(vec) || isLogical(vec))

-	throw std::range_error("RcppVector: invalid numeric vector in constructor");

-    int len = length(vec);

-    if(len == 0)

-	throw std::range_error("RcppVector: null vector in constructor");

-    v = new RcppDate[len];

-    for(i = 0; i < len; i++)

-	v[i] = RcppDate((int)REAL(vec)[i]);

-    length = len;

-}

-

-RcppStringVector::RcppStringVector(SEXP vec) {

-    int i;

-    if(isMatrix(vec) || isLogical(vec))

-	throw std::range_error("RcppVector: invalid numeric vector in constructor");

-    if(!isString(vec))

-	throw std::range_error("RcppStringVector: invalid string");

-    int len = length(vec);

-    if(len == 0)

-	throw std::range_error("RcppVector: null vector in constructor");

-    v = new string[len];

-    for(i = 0; i < len; i++)

-	v[i] = string(CHAR(STRING_ELT(vec,i)));

-    length = len;

-}

-

-template <typename T>

-RcppVector<T>::RcppVector(SEXP vec) {

-    int i;

-

-    // The function isVector returns TRUE for vectors AND

-    // matrices, so it does not distinguish. We could

-    // check the dim attribute here to be sure that it

-    // is not present (i.e., dimAttr == R_NilValue, not 0!).

-    // But it is easier to simply check if it is set via

-    // isMatrix (in which case we don't have a vector).

-    if(!isNumeric(vec) || isMatrix(vec) || isLogical(vec))

-	throw std::range_error("RcppVector: invalid numeric vector in constructor");

-    len = length(vec);

-    v = (T *)R_alloc(len, sizeof(T));

-    if(isInteger(vec)) {

-	for(i = 0; i < len; i++)

-	    v[i] = (T)(INTEGER(vec)[i]);

-    }	

-    else if(isReal(vec)) {

-	for(i = 0; i < len; i++)

-	    v[i] = (T)(REAL(vec)[i]);

-    }

-}

-

-template <typename T>

-RcppVector<T>::RcppVector(int _len) {

-    len = _len;

-    v = (T *)R_alloc(len, sizeof(T));

-    for(int i = 0; i < len; i++)

-	v[i] = 0;

-}

-

-template <typename T>

-T *RcppVector<T>::cVector() {

-    T* tmp = (T *)R_alloc(len, sizeof(T));

-    for(int i = 0; i < len; i++)

-	tmp[i] = v[i];

-    return tmp;

-}

-

-template <typename T>

-vector<T> RcppVector<T>::stlVector() {

-    vector<T> tmp(len);

-    for(int i = 0; i < len; i++)

-	tmp[i] = v[i];

-    return tmp;

-}

-

-template <typename T>

-RcppMatrix<T>::RcppMatrix(SEXP mat) {

-

-    if(!isNumeric(mat) || !isMatrix(mat))

-	throw std::range_error("RcppMatrix: invalid numeric matrix in constructor");

-

-    // Get matrix dimensions

-    SEXP dimAttr = getAttrib(mat, R_DimSymbol);

-    dim1 = INTEGER(dimAttr)[0];

-    dim2 = INTEGER(dimAttr)[1];

-

-    // We guard against  the possibility that R might pass an integer matrix.

-    // Can be prevented using R code: temp <- as.double(a), dim(temp) <- dim(a)

-    int i,j;

-    int isInt = isInteger(mat);

-    T *m = (T *)R_alloc(dim1*dim2, sizeof(T));

-    a = (T **)R_alloc(dim1, sizeof(T *));

-    for(i = 0; i < dim1; i++)

-	a[i] = m + i*dim2;

-    if(isInt) {

-	for(i=0; i < dim1; i++)

-	    for(j=0; j < dim2; j++)

-		a[i][j] = (T)(INTEGER(mat)[i+dim1*j]);

-    }	

-    else {

-	for(i=0; i < dim1; i++)

-	    for(j=0; j < dim2; j++)

-		a[i][j] = (T)(REAL(mat)[i+dim1*j]);

-    }	

-}

-

-template <typename T>

-RcppMatrix<T>::RcppMatrix(int _dim1, int _dim2) {

-    dim1 = _dim1;

-    dim2 = _dim2;

-    int i,j;

-    T *m = (T *)R_alloc(dim1*dim2, sizeof(T));

-    a = (T **)R_alloc(dim1, sizeof(T *));

-    for(i = 0; i < dim1; i++)

-	a[i] = m + i*dim2;

-    for(i=0; i < dim1; i++)

-	for(j=0; j < dim2; j++)

-	    a[i][j] = 0;

-}

-

-template <typename T>

-vector<vector<T> > RcppMatrix<T>::stlMatrix() {

-    int i,j;

-    vector<vector<T> > temp;

-    for(i = 0; i < dim1; i++) {

-	temp.push_back(vector<T>(dim2));

-    }

-    for(i = 0; i < dim1; i++)

-	for(j = 0; j < dim2; j++)

-	    temp[i][j] = a[i][j];

-    return temp;

-}

-

-template <typename T>

-T **RcppMatrix<T>::cMatrix() {

-    int i,j;

-    T *m = (T *)R_alloc(dim1*dim2, sizeof(T));

-    T **tmp = (T **)R_alloc(dim1, sizeof(T *));

-    for(i = 0; i < dim1; i++)

-	tmp[i] = m + i*dim2;

-    for(i=0; i < dim1; i++)

-	for(j=0; j < dim2; j++)

-	    tmp[i][j] = a[i][j];

-    return tmp;

-}

-

-// Explicit instantiation (required for external linkage)

-template class RcppVector<int>;

-template class RcppVector<double>;

-template class RcppMatrix<int>;

-template class RcppMatrix<double>;

-

-void RcppResultSet::add(string name, RcppDate& date) {

-    SEXP value = PROTECT(allocVector(REALSXP, 1));

-    numProtected++;

-    REAL(value)[0] = date.getJDN() - RcppDate::Jan1970Offset;

-    SEXP dateclass = PROTECT(allocVector(STRSXP,1));

-    numProtected++;

-    SET_STRING_ELT(dateclass, 0, mkChar("Date"));

-    setAttrib(value, R_ClassSymbol, dateclass); 

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, double x) {

-    SEXP value = PROTECT(allocVector(REALSXP, 1));

-    numProtected++;

-    REAL(value)[0] = x;

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, int i) {

-    SEXP value = PROTECT(allocVector(INTSXP, 1));

-    numProtected++;

-    INTEGER(value)[0] = i;

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, string strvalue) {

-    SEXP value = PROTECT(allocVector(STRSXP, 1));

-    numProtected++;

-    SET_STRING_ELT(value, 0, mkChar(strvalue.c_str()));

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, double *vec, int len) {

-    if(vec == 0)

-	throw std::range_error("RcppResultSet::add: NULL double vector");

-    SEXP value = PROTECT(allocVector(REALSXP, len));

-    numProtected++;

-    for(int i = 0; i < len; i++)

-	REAL(value)[i] = vec[i];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, RcppDateVector& datevec) {

-    SEXP value = PROTECT(allocVector(REALSXP, datevec.size()));

-    numProtected++;

-    for(int i = 0; i < datevec.size(); i++) {

-	REAL(value)[i] = datevec(i).getJDN() - RcppDate::Jan1970Offset;

-    }

-    SEXP dateclass = PROTECT(allocVector(STRSXP,1));

-    numProtected++;

-    SET_STRING_ELT(dateclass, 0, mkChar("Date"));

-    setAttrib(value, R_ClassSymbol, dateclass); 

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, RcppStringVector& stringvec) {

-    int len = (int)stringvec.size();

-    SEXP value = PROTECT(allocVector(STRSXP, len));

-    numProtected++;

-    for(int i = 0; i < len; i++)

-        SET_STRING_ELT(value, i, mkChar(stringvec(i).c_str()));

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, int *vec, int len) {

-    if(vec == 0)

-	throw std::range_error("RcppResultSet::add: NULL int vector");

-    SEXP value = PROTECT(allocVector(INTSXP, len));

-    numProtected++;

-    for(int i = 0; i < len; i++)

-	INTEGER(value)[i] = vec[i];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, double **mat, int nx, int ny) {

-    if(mat == 0)

-	throw std::range_error("RcppResultSet::add: NULL double matrix");

-    SEXP value = PROTECT(allocMatrix(REALSXP, nx, ny));

-    numProtected++;

-    for(int i = 0; i < nx; i++)

-	for(int j = 0; j < ny; j++)

-	    REAL(value)[i + nx*j] = mat[i][j];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, int **mat, int nx, int ny) {

-    if(mat == 0)

-	throw std::range_error("RcppResultSet::add: NULL int matrix");

-    SEXP value = PROTECT(allocMatrix(INTSXP, nx, ny));

-    numProtected++;

-    for(int i = 0; i < nx; i++)

-	for(int j = 0; j < ny; j++)

-	    INTEGER(value)[i + nx*j] = mat[i][j];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, vector<string>& vec) {

-    if(vec.size() == 0)

-	throw std::range_error("RcppResultSet::add; zero length vector<string>");

-    int len = (int)vec.size();

-    SEXP value = PROTECT(allocVector(STRSXP, len));

-    numProtected++;

-    for(int i = 0; i < len; i++)

-        SET_STRING_ELT(value, i, mkChar(vec[i].c_str()));

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, vector<int>& vec) {

-    if(vec.size() == 0)

-	throw std::range_error("RcppResultSet::add; zero length vector<int>");

-    int len = (int)vec.size();

-    SEXP value = PROTECT(allocVector(INTSXP, len));

-    numProtected++;

-    for(int i = 0; i < len; i++)

-	INTEGER(value)[i] = vec[i];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, vector<double>& vec) {

-    if(vec.size() == 0)

-	throw std::range_error("RcppResultSet::add; zero length vector<double>");

-    int len = (int)vec.size();

-    SEXP value = PROTECT(allocVector(REALSXP, len));

-    numProtected++;

-    for(int i = 0; i < len; i++)

-	REAL(value)[i] = vec[i];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, vector<vector<int> >& mat) {

-    if(mat.size() == 0)

-	throw std::range_error("RcppResultSet::add: zero length vector<vector<int> >");

-    else if(mat[0].size() == 0)

-	throw std::range_error("RcppResultSet::add: no columns in vector<vector<int> >");

-    int nx = (int)mat.size();

-    int ny = (int)mat[0].size();

-    SEXP value = PROTECT(allocMatrix(INTSXP, nx, ny));

-    numProtected++;

-    for(int i = 0; i < nx; i++)

-	for(int j = 0; j < ny; j++)

-	    INTEGER(value)[i + nx*j] = mat[i][j];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, vector<vector<double> >& mat) {

-    if(mat.size() == 0)

-	throw std::range_error("RcppResultSet::add: zero length vector<vector<double> >");

-    else if(mat[0].size() == 0)

-	throw std::range_error("RcppResultSet::add: no columns in vector<vector<double> >");

-    int nx = (int)mat.size();

-    int ny = (int)mat[0].size();

-    SEXP value = PROTECT(allocMatrix(REALSXP, nx, ny));

-    numProtected++;

-    for(int i = 0; i < nx; i++)

-	for(int j = 0; j < ny; j++)

-	    REAL(value)[i + nx*j] = mat[i][j];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, RcppVector<int>& vec) {

-    int len = vec.size();

-    int *a = vec.cVector();

-    SEXP value = PROTECT(allocVector(INTSXP, len));

-    numProtected++;

-    for(int i = 0; i < len; i++)

-	INTEGER(value)[i] = a[i];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, RcppVector<double>& vec) {

-    int len = vec.size();

-    double *a = vec.cVector();

-    SEXP value = PROTECT(allocVector(REALSXP, len));

-    numProtected++;

-    for(int i = 0; i < len; i++)

-	REAL(value)[i] = a[i];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, RcppMatrix<int>& mat) {

-    int nx = mat.getDim1();

-    int ny = mat.getDim2();

-    int **a = mat.cMatrix();

-    SEXP value = PROTECT(allocMatrix(INTSXP, nx, ny));

-    numProtected++;

-    for(int i = 0; i < nx; i++)

-	for(int j = 0; j < ny; j++)

-	    INTEGER(value)[i + nx*j] = a[i][j];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, RcppMatrix<double>& mat) {

-    int nx = mat.getDim1();

-    int ny = mat.getDim2();

-    double **a = mat.cMatrix();

-    SEXP value = PROTECT(allocMatrix(REALSXP, nx, ny));

-    numProtected++;

-    for(int i = 0; i < nx; i++)

-	for(int j = 0; j < ny; j++)

-	    REAL(value)[i + nx*j] = a[i][j];

-    values.push_back(make_pair(name, value));

-}

-

-void RcppResultSet::add(string name, RcppFrame& frame) {

-    vector<string> colNames = frame.getColNames();

-    vector<vector<ColDatum> > table = frame.getTableData();

-    int ncol = colNames.size();

-    int nrow = table.size();

-    SEXP rl = PROTECT(allocVector(VECSXP,ncol));

-    SEXP nm = PROTECT(allocVector(STRSXP,ncol));

-    numProtected += 2;

-    for(int i=0; i < ncol; i++) {

-	SEXP value, names;

-	if(table[0][i].getType() == COLTYPE_DOUBLE) {

-	    value = PROTECT(allocVector(REALSXP,nrow));

-	    numProtected++;

-	    for(int j=0; j < nrow; j++)

-		REAL(value)[j] = table[j][i].getDoubleValue();

-	}

-	else if(table[0][i].getType() == COLTYPE_INT) {

-	    value = PROTECT(allocVector(INTSXP,nrow));

-	    numProtected++;

-	    for(int j=0; j < nrow; j++)

-		INTEGER(value)[j] = table[j][i].getIntValue();

-	}

-	else if(table[0][i].getType() == COLTYPE_FACTOR) {

-	    value = PROTECT(allocVector(INTSXP,nrow));

-	    numProtected++;

-	    int levels = table[0][i].getFactorNumLevels();

-	    names = PROTECT(allocVector(STRSXP,levels));

-	    numProtected++;

-	    string *levelNames = table[0][i].getFactorLevelNames();

-	    for(int k=0; k < levels; k++)

-		SET_STRING_ELT(names, k, mkChar(levelNames[k].c_str()));

-	    for(int j=0; j < nrow; j++) {

-		int level = table[j][i].getFactorLevel();

-		INTEGER(value)[j] = level;

-	    }

-	    setAttrib(value, R_LevelsSymbol, names);

-	    SEXP factorclass = PROTECT(allocVector(STRSXP,1));

-	    numProtected++;

-	    SET_STRING_ELT(factorclass, 0, mkChar("factor"));

-	    setAttrib(value, R_ClassSymbol, factorclass); 

-	}

-	else if(table[0][i].getType() == COLTYPE_STRING) {

-	    value = PROTECT(allocVector(STRSXP,nrow));

-	    numProtected++;

-	    for(int j=0; j < nrow; j++) {

-		SET_STRING_ELT(value, j, mkChar(table[j][i].getStringValue().c_str()));

-	    }

-		

-	}

-	else if(table[0][i].getType() == COLTYPE_LOGICAL) {

-	    value = PROTECT(allocVector(LGLSXP,nrow));

-	    numProtected++;

-	    for(int j=0; j < nrow; j++) {

-		LOGICAL(value)[j] = table[j][i].getLogicalValue();

-	    }

-	}

-	else if(table[0][i].getType() == COLTYPE_DATE) {

-	    value = PROTECT(allocVector(REALSXP,nrow));

-	    numProtected++;

-	    for(int j=0; j < nrow; j++)

-		REAL(value)[j] = table[j][i].getDateRCode();

-	    SEXP dateclass = PROTECT(allocVector(STRSXP,1));

-	    numProtected++;

-	    SET_STRING_ELT(dateclass, 0, mkChar("Date"));

-	    setAttrib(value, R_ClassSymbol, dateclass); 

-	}

-	else {

-	    throw std::range_error("RcppResultSet::add invalid column type");

-	}

-	SET_VECTOR_ELT(rl, i, value);

-	SET_STRING_ELT(nm, i, mkChar(colNames[i].c_str()));

-    }

-    setAttrib(rl, R_NamesSymbol, nm);

-    values.push_back(make_pair(name, rl));

-}

-

-void RcppResultSet::add(string name, SEXP sexp, bool isProtected) {

-    values.push_back(make_pair(name, sexp));

-    if(isProtected)

-	numProtected++;

-}

-

-SEXP RcppResultSet::getReturnList() {

-    int nret = (int)values.size();

-    SEXP rl = PROTECT(allocVector(VECSXP,nret));

-    SEXP nm = PROTECT(allocVector(STRSXP,nret));

-    list<pair<string,SEXP> >::iterator iter = values.begin();

-    for(int i = 0; iter != values.end(); iter++, i++) {

-	SET_VECTOR_ELT(rl, i, iter->second);

-	SET_STRING_ELT(nm, i, mkChar(iter->first.c_str()));

-    }

-    setAttrib(rl, R_NamesSymbol, nm);

-    UNPROTECT(numProtected+2);

-    return rl;

-}

-

-#ifdef USING_QUANTLIB

-

-// Conversion from QuantLib Date to RcppDate.

-RcppDate::RcppDate(Date dateQL) {

-    day = (int)dateQL.dayOfMonth();

-    month = (int)dateQL.month();

-    year  = (int)dateQL.year();

-    mdy2jdn();

-}

-

-// Conversion from RcppDate to QuantLib Date.

-RcppDate::operator Date() const {

-    Date d(day, (Month)month, year);

-    return d;

-}

-

-// Print a QuantLib Date.

-ostringstream& operator<<(ostringstream& os, const Date& d) {

-    os << d.month() << " " << d.weekday() << ", " << d.year();

-    return os;

-}

-

-#endif

-

-// Print an RcppDate.

-ostream& operator<<(ostream& os, const RcppDate& date) {

-    os << date.getYear() << "-" << date.getMonth() << "-" << date.getDay();

-    return os;

-}

-

-#ifdef RCPP_DATE_OPS

-

-// A few basic date operations.

-RcppDate operator+(const RcppDate& date, int offset) {

-    RcppDate temp(date.month, date.day, date.year);

-    temp.jdn += offset;

-    temp.jdn2mdy();

-    return temp;

-}

-

-int operator-(const RcppDate& date2, const RcppDate& date1) {

-    return date2.jdn - date1.jdn;

-}

-

-bool  operator<(const RcppDate &date1, const RcppDate& date2) {