@@ -9,8 +9,8 @@ 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), RcppClassic

-LinkingTo: RcppClassic, Rcpp

+Depends: R (>= 2.0.0), Rcpp

+LinkingTo: Rcpp

 Suggests: RUnit

 SystemRequirements: None

 License: GPL-2

@@ -1,3 +1,4 @@

 # 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,subMolecules)

+import(Rcpp)

\ No newline at end of file

@@ -30,13 +30,13 @@

 //

 // R Stuff

 //

-#include <RcppClassic.h>

+#include <Rcpp.h>

 extern "C" {

 #include <Rdefines.h>

 #include <Rinternals.h>

 #include <R_ext/Rdynload.h>

 }

-

+using namespace Rcpp;

 using namespace ims;

 using namespace std;

@@ -169,8 +169,8 @@ RcppExport SEXP decomposeIsotopes(SEXP v_masses, SEXP v_abundances, SEXP s_error

     SEXP  rl=R_NilValue; // Use this when there is nothing to be returned.

     try {

-	RcppVector<double> masses = RcppVector<double>(v_masses);

-	RcppVector<double> abundances = RcppVector<double>(v_abundances);

+	NumericVector masses = NumericVector(v_masses);

+	NumericVector abundances = NumericVector(v_abundances);

 	double error = *REAL(s_error);

 	// converts relative (ppm) in absolute error 

@@ -342,11 +342,13 @@ RcppExport SEXP decomposeIsotopes(SEXP v_masses, SEXP v_abundances, SEXP s_error

 	  rl = rlistScores(scores, Rf_asInteger(z));

 	}

     } catch(std::exception& ex) {

-      exceptionMesg = copyMessageToR(ex.what());

-      error_return(exceptionMesg); 

+      //exceptionMesg = copyMessageToR(ex.what());

+      //error_return(exceptionMesg); 

+      forward_exception_to_r(ex);

     } catch(...) {

-      exceptionMesg = copyMessageToR("unknown reason");

-      error_return(exceptionMesg); 

+      //exceptionMesg = copyMessageToR("unknown reason");

+      //error_return(exceptionMesg); 

+      ::Rf_error("c++ exception (unknown reason)");

     }

     return rl;

@@ -367,8 +369,8 @@ RcppExport SEXP calculateScore(SEXP v_predictMasses, SEXP v_predictAbundances, S

-	RcppVector<double> masses = RcppVector<double>(v_predictMasses);

-	RcppVector<double> abundances = RcppVector<double>(v_predictAbundances);

+	NumericVector masses = NumericVector(v_predictMasses);

+	NumericVector abundances = NumericVector(v_predictAbundances);

 	// fills peaklist masses and abundances, 

 	// since we cannot use masses and abundances - instances of RcppVector object - directly

@@ -384,8 +386,8 @@ RcppExport SEXP calculateScore(SEXP v_predictMasses, SEXP v_predictAbundances, S

 	// initializes distribution probability scorer

 	scorer_type scorer(peaklist_masses, peaklist_abundances);

-	masses = RcppVector<double>(v_measuredMasses);

-	abundances = RcppVector<double>(v_meausuredAbundances);

+	masses = NumericVector(v_measuredMasses);

+	abundances = NumericVector(v_meausuredAbundances);

 	//cout << "Mess:" << masses<<"\n";

 	masses_container mess_masses;

 	abundances_container mess_abundances;

@@ -406,15 +408,8 @@ RcppExport SEXP calculateScore(SEXP v_predictMasses, SEXP v_predictAbundances, S

 	}

 	score_type score=scorer.score(mess_masses, mess_abundances);

-	//SEXP output;

-	//PROTECT(output = NEW_NUMERIC(1));

-	//cout<< score;

-	//REAL(output)[0]=score;

-	//UNPROTECT(1);

- 	//return (output);

-	RcppResultSet rs;

-	rs.add("", score);

-	return(rs.getSEXP());

+	//List output;

+	return(List::create(  _[""]  = score));

 }

 // }}}

@@ -477,11 +472,9 @@ RcppExport SEXP getMolecule(SEXP s_formula, SEXP l_alphabet,

     scores.insert(make_pair(1.0, molecule));

     rl = rlistScores(scores, Rf_asInteger(z));

   } catch(std::exception& ex) {

-    exceptionMesg = copyMessageToR(ex.what());

-    Rf_error(exceptionMesg); 

+    forward_exception_to_r(ex);

   } catch(...) {

-    exceptionMesg = copyMessageToR("unknown reason");

-    error_return(exceptionMesg); 

+    ::Rf_error("c++ exception (unknown reason)");

   }

   return rl;

@@ -625,18 +618,17 @@ SEXP  rlistScores(multimap<score_type, ComposedElement, greater<score_type> > sc

 	// Build result set to be returned as a list to R.

 	vector<string> formula(scores.size());

-	RcppVector<double> score(scores.size());

-	RcppVector<double> exactmass(scores.size());

-	RcppVector<int> charge(scores.size());

+	NumericVector score(scores.size());

+	NumericVector exactmass(scores.size());

+	IntegerVector charge(scores.size());

 	// Chemical rules

 	vector<string> parity(scores.size());

 	vector<string> valid(scores.size());

-	RcppVector<double> DBE(scores.size());

+	NumericVector DBE(scores.size());

 	SEXP isotopes = PROTECT(Rf_allocVector(VECSXP, scores.size()));

- 	RcppResultSet rs;

 	unsigned int i = 0;

 	vector<string> colNames(2);

@@ -676,26 +668,21 @@ SEXP  rlistScores(multimap<score_type, ComposedElement, greater<score_type> > sc

 		i++;

 	}

-	rs.add("formula", formula);

-	rs.add("score", score);

-	rs.add("exactmass", exactmass);

-	rs.add("charge", z);

-

-	rs.add("parity", parity);

-	rs.add("valid", valid);

-	rs.add("DBE", DBE);

-

-	rs.add("isotopes", isotopes, true);

-

-	// Get the list to be returned to R.

-	SEXP rl = rs.getReturnList();

 	UNPROTECT(1); // SEXP isotopes

 	if(exceptionMesg != NULL) {

 	  Rf_error(exceptionMesg);

 	}

-	return rl;

+	

+	return(List::create(  _["formula"]  = formula,

+                       _["score"]  = score,

+                       _["exactmass"]  = exactmass,

+                       _["charge"]  = charge,

+                       _["parity"]  = parity,

+                       _["valid"]  = valid,

+                       _["DBE"]  = DBE,

+                       _["isotopes"]  = isotopes));

 	// }}}

 }