C++ registration

.Rbuildignore

@@ -1 +1,3 @@
 .travis.yml
+^.*\.Rproj$
+^\.Rproj\.user$

.gitignore

@@ -0,0 +1,7 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+src/*.o
+src/*.so
+src/*.dll

NAMESPACE

@@ -33,4 +33,4 @@ importFrom(graphics,title)
 importFrom(stats,embed)
 importFrom(stats,optimize)
 importFrom(utils,data)
-useDynLib(Peptides)
+useDynLib(Peptides, .registration = TRUE)

Peptides.Rproj

@@ -0,0 +1,18 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageCheckArgs: --as-cran

R/RcppExports.R

@@ -9,3 +9,7 @@ absoluteCharge <- function(seq, pH = 7, pKscale = "Lehninger") {
     .Call('Peptides_absoluteCharge', PACKAGE = 'Peptides', seq, pH, pKscale)
 }
 
+# Register entry points for exported C++ functions
+methods::setLoadAction(function(ns) {
+    .Call('Peptides_RcppExport_registerCCallable', PACKAGE = 'Peptides')
+})

R/cppFunctions.R

@@ -1,3 +1,3 @@
-#' @useDynLib Peptides
+#' @useDynLib Peptides, .registration = TRUE
 #' @importFrom Rcpp sourceCpp
 NULL

inst/include/Peptides.h

@@ -0,0 +1,9 @@
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#ifndef RCPP_Peptides_H_GEN_
+#define RCPP_Peptides_H_GEN_
+
+#include "Peptides_RcppExports.h"
+
+#endif // RCPP_Peptides_H_GEN_

inst/include/Peptides_RcppExports.h

@@ -0,0 +1,67 @@
+// Generated by using Rcpp::compileAttributes() -> do not edit by hand
+// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+#ifndef RCPP_Peptides_RCPPEXPORTS_H_GEN_
+#define RCPP_Peptides_RCPPEXPORTS_H_GEN_
+
+#include <Rcpp.h>
+
+namespace Peptides {
+
+    using namespace Rcpp;
+
+    namespace {
+        void validateSignature(const char* sig) {
+            Rcpp::Function require = Rcpp::Environment::base_env()["require"];
+            require("Peptides", Rcpp::Named("quietly") = true);
+            typedef int(*Ptr_validate)(const char*);
+            static Ptr_validate p_validate = (Ptr_validate)
+                R_GetCCallable("Peptides", "Peptides_RcppExport_validate");
+            if (!p_validate(sig)) {
+                throw Rcpp::function_not_exported(
+                    "C++ function with signature '" + std::string(sig) + "' not found in Peptides");
+            }
+        }
+    }
+
+    inline Rcpp::List chargeList(std::vector< std::string > seq, NumericVector pH, std::string pKscale = "Lehninger") {
+        typedef SEXP(*Ptr_chargeList)(SEXP,SEXP,SEXP);
+        static Ptr_chargeList p_chargeList = NULL;
+        if (p_chargeList == NULL) {
+            validateSignature("Rcpp::List(*chargeList)(std::vector< std::string >,NumericVector,std::string)");
+            p_chargeList = (Ptr_chargeList)R_GetCCallable("Peptides", "Peptides_chargeList");
+        }
+        RObject rcpp_result_gen;
+        {
+            RNGScope RCPP_rngScope_gen;
+            rcpp_result_gen = p_chargeList(Rcpp::wrap(seq), Rcpp::wrap(pH), Rcpp::wrap(pKscale));
+        }
+        if (rcpp_result_gen.inherits("interrupted-error"))
+            throw Rcpp::internal::InterruptedException();
+        if (rcpp_result_gen.inherits("try-error"))
+            throw Rcpp::exception(as<std::string>(rcpp_result_gen).c_str());
+        return Rcpp::as<Rcpp::List >(rcpp_result_gen);
+    }
+
+    inline double absoluteCharge(std::string seq, double pH = 7, std::string pKscale = "Lehninger") {
+        typedef SEXP(*Ptr_absoluteCharge)(SEXP,SEXP,SEXP);
+        static Ptr_absoluteCharge p_absoluteCharge = NULL;
+        if (p_absoluteCharge == NULL) {
+            validateSignature("double(*absoluteCharge)(std::string,double,std::string)");
+            p_absoluteCharge = (Ptr_absoluteCharge)R_GetCCallable("Peptides", "Peptides_absoluteCharge");
+        }
+        RObject rcpp_result_gen;
+        {
+            RNGScope RCPP_rngScope_gen;
+            rcpp_result_gen = p_absoluteCharge(Rcpp::wrap(seq), Rcpp::wrap(pH), Rcpp::wrap(pKscale));
+        }
+        if (rcpp_result_gen.inherits("interrupted-error"))
+            throw Rcpp::internal::InterruptedException();
+        if (rcpp_result_gen.inherits("try-error"))
+            throw Rcpp::exception(as<std::string>(rcpp_result_gen).c_str());
+        return Rcpp::as<double >(rcpp_result_gen);
+    }
+
+}
+
+#endif // RCPP_Peptides_RCPPEXPORTS_H_GEN_

src/.gitignore

@@ -0,0 +1,3 @@
+*.o
+*.so
+*.dll

src/RcppExports.cpp

@@ -1,33 +1,92 @@
 // Generated by using Rcpp::compileAttributes() -> do not edit by hand
 // Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+#include "../inst/include/Peptides.h"
 #include <Rcpp.h>
+#include <string>
+#include <set>
 
 using namespace Rcpp;
 
 // chargeList
 Rcpp::List chargeList(std::vector< std::string > seq, NumericVector pH, std::string pKscale);
-RcppExport SEXP Peptides_chargeList(SEXP seqSEXP, SEXP pHSEXP, SEXP pKscaleSEXP) {
+static SEXP Peptides_chargeList_try(SEXP seqSEXP, SEXP pHSEXP, SEXP pKscaleSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< std::vector< std::string > >::type seq(seqSEXP);
     Rcpp::traits::input_parameter< NumericVector >::type pH(pHSEXP);
     Rcpp::traits::input_parameter< std::string >::type pKscale(pKscaleSEXP);
     rcpp_result_gen = Rcpp::wrap(chargeList(seq, pH, pKscale));
     return rcpp_result_gen;
-END_RCPP
+END_RCPP_RETURN_ERROR
+}
+RcppExport SEXP Peptides_chargeList(SEXP seqSEXP, SEXP pHSEXP, SEXP pKscaleSEXP) {
+    SEXP rcpp_result_gen;
+    {
+        Rcpp::RNGScope rcpp_rngScope_gen;
+        rcpp_result_gen = PROTECT(Peptides_chargeList_try(seqSEXP, pHSEXP, pKscaleSEXP));
+    }
+    Rboolean rcpp_isInterrupt_gen = Rf_inherits(rcpp_result_gen, "interrupted-error");
+    if (rcpp_isInterrupt_gen) {
+        UNPROTECT(1);
+        Rf_onintr();
+    }
+    Rboolean rcpp_isError_gen = Rf_inherits(rcpp_result_gen, "try-error");
+    if (rcpp_isError_gen) {
+        SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
+        UNPROTECT(1);
+        Rf_error(CHAR(rcpp_msgSEXP_gen));
+    }
+    UNPROTECT(1);
+    return rcpp_result_gen;
 }
 // absoluteCharge
 double absoluteCharge(std::string seq, double pH, std::string pKscale);
-RcppExport SEXP Peptides_absoluteCharge(SEXP seqSEXP, SEXP pHSEXP, SEXP pKscaleSEXP) {
+static SEXP Peptides_absoluteCharge_try(SEXP seqSEXP, SEXP pHSEXP, SEXP pKscaleSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
-    Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< std::string >::type seq(seqSEXP);
     Rcpp::traits::input_parameter< double >::type pH(pHSEXP);
     Rcpp::traits::input_parameter< std::string >::type pKscale(pKscaleSEXP);
     rcpp_result_gen = Rcpp::wrap(absoluteCharge(seq, pH, pKscale));
     return rcpp_result_gen;
-END_RCPP
+END_RCPP_RETURN_ERROR
+}
+RcppExport SEXP Peptides_absoluteCharge(SEXP seqSEXP, SEXP pHSEXP, SEXP pKscaleSEXP) {
+    SEXP rcpp_result_gen;
+    {
+        Rcpp::RNGScope rcpp_rngScope_gen;
+        rcpp_result_gen = PROTECT(Peptides_absoluteCharge_try(seqSEXP, pHSEXP, pKscaleSEXP));
+    }
+    Rboolean rcpp_isInterrupt_gen = Rf_inherits(rcpp_result_gen, "interrupted-error");
+    if (rcpp_isInterrupt_gen) {
+        UNPROTECT(1);
+        Rf_onintr();
+    }
+    Rboolean rcpp_isError_gen = Rf_inherits(rcpp_result_gen, "try-error");
+    if (rcpp_isError_gen) {
+        SEXP rcpp_msgSEXP_gen = Rf_asChar(rcpp_result_gen);
+        UNPROTECT(1);
+        Rf_error(CHAR(rcpp_msgSEXP_gen));
+    }
+    UNPROTECT(1);
+    return rcpp_result_gen;
+}
+
+// validate (ensure exported C++ functions exist before calling them)
+static int Peptides_RcppExport_validate(const char* sig) { 
+    static std::set<std::string> signatures;
+    if (signatures.empty()) {
+        signatures.insert("Rcpp::List(*chargeList)(std::vector< std::string >,NumericVector,std::string)");
+        signatures.insert("double(*absoluteCharge)(std::string,double,std::string)");
+    }
+    return signatures.find(sig) != signatures.end();
+}
+
+// registerCCallable (register entry points for exported C++ functions)
+RcppExport SEXP Peptides_RcppExport_registerCCallable() { 
+    R_RegisterCCallable("Peptides", "Peptides_chargeList", (DL_FUNC)Peptides_chargeList_try);
+    R_RegisterCCallable("Peptides", "Peptides_absoluteCharge", (DL_FUNC)Peptides_absoluteCharge_try);
+    R_RegisterCCallable("Peptides", "Peptides_RcppExport_validate", (DL_FUNC)Peptides_RcppExport_validate);
+    return R_NilValue;
 }

src/charge_pI.cpp

@@ -278,6 +278,7 @@ NumericVector pHsequence(std::string seq, NumericVector pH, std::string pKscale
   return charges;
 }
 
+// [[Rcpp::interfaces(r, cpp)]]
 // [[Rcpp::export]]
 Rcpp::List chargeList(std::vector< std::string > seq, NumericVector pH, std::string pKscale = "Lehninger"){
   int size = seq.size();
@@ -288,6 +289,7 @@ Rcpp::List chargeList(std::vector< std::string > seq, NumericVector pH, std::str
   return sequences;
 }
 
+// [[Rcpp::interfaces(r, cpp)]]
 // [[Rcpp::export]]
 double absoluteCharge(std::string seq, double pH = 7, std::string pKscale = "Lehninger"){
   double charge = 0;

src/init.c

@@ -0,0 +1,26 @@
+#include <R.h>
+#include <Rinternals.h>
+#include <stdlib.h> // for NULL
+#include <R_ext/Rdynload.h>
+
+/* FIXME: 
+ Check these declarations against the C/Fortran source code.
+ */
+
+/* .Call calls */
+extern SEXP Peptides_absoluteCharge(SEXP, SEXP, SEXP);
+extern SEXP Peptides_chargeList(SEXP, SEXP, SEXP);
+extern SEXP Peptides_RcppExport_registerCCallable();
+
+static const R_CallMethodDef CallEntries[] = {
+  {"Peptides_absoluteCharge",               (DL_FUNC) &Peptides_absoluteCharge,               3},
+  {"Peptides_chargeList",                   (DL_FUNC) &Peptides_chargeList,                   3},
+  {"Peptides_RcppExport_registerCCallable", (DL_FUNC) &Peptides_RcppExport_registerCCallable, 0},
+  {NULL, NULL, 0}
+};
+
+void R_init_Peptides(DllInfo *dll)
+{
+  R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);
+  R_useDynamicSymbols(dll, FALSE);
+}