fixing C++ One Definition Rule [-Wodr] detected by LTO (part1)

mmollina · Mar 5, 2024 · 2ef4121 · 2ef4121
1 parent 8281193
commit 2ef4121
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Showing 5 changed files with 43 additions and 30 deletions.
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -1,6 +1,10 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
+loglike_hmm_cpp <- function(m, geno, ph1, ph2, rf, verbose) {
+    .Call('_mappoly_loglike_hmm_cpp', PACKAGE = 'mappoly', m, geno, ph1, ph2, rf, verbose)
+}
+
 .vcf_get_probabilities <- function(mat, pl_pos) {
     .Call('_mappoly_vcf_get_probabilities', PACKAGE = 'mappoly', mat, pl_pos)
 }

diff --git a/R/loglike_hmm.R b/R/loglike_hmm.R
@@ -43,14 +43,12 @@ loglike_hmm <- function(input.map, input.data = NULL, verbose = FALSE)
     D[j, D[j, ]  ==  input.map$info$ploidy + 1] <- dp[j] + dq[j] + 1 + as.numeric(dp[j] == 0 || dq[j] == 0)
   for(i in 1:length(input.map$maps)){
     rf.temp <- input.map$maps[[i]]$seq.rf
-    res.temp <- .Call("loglike_hmm",
-                    input.map$info$ploidy,
-                    t(D),
-                    lapply(input.map$maps[[i]]$seq.ph$P, function(x) x-1),
-                    lapply(input.map$maps[[i]]$seq.ph$Q, function(x) x-1),
-                    rf.temp,
-                    verbose,
-                    PACKAGE = "mappoly")
+    res.temp <- loglike_hmm_cpp(input.map$info$ploidy,
+                                t(D),
+                                lapply(input.map$maps[[i]]$seq.ph$P, function(x) x-1),
+                                lapply(input.map$maps[[i]]$seq.ph$Q, function(x) x-1),
+                                rf.temp,
+                                verbose)
     input.map$maps[[i]]$loglike <- res.temp[[1]]
   }
   return(input.map)

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -10,6 +10,22 @@ Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
 Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
 #endif
 
+// loglike_hmm_cpp
+List loglike_hmm_cpp(int m, NumericMatrix geno, List ph1, List ph2, NumericVector rf, int verbose);
+RcppExport SEXP _mappoly_loglike_hmm_cpp(SEXP mSEXP, SEXP genoSEXP, SEXP ph1SEXP, SEXP ph2SEXP, SEXP rfSEXP, SEXP verboseSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< int >::type m(mSEXP);
+    Rcpp::traits::input_parameter< NumericMatrix >::type geno(genoSEXP);
+    Rcpp::traits::input_parameter< List >::type ph1(ph1SEXP);
+    Rcpp::traits::input_parameter< List >::type ph2(ph2SEXP);
+    Rcpp::traits::input_parameter< NumericVector >::type rf(rfSEXP);
+    Rcpp::traits::input_parameter< int >::type verbose(verboseSEXP);
+    rcpp_result_gen = Rcpp::wrap(loglike_hmm_cpp(m, geno, ph1, ph2, rf, verbose));
+    return rcpp_result_gen;
+END_RCPP
+}
 // vcf_get_probabilities
 Rcpp::List vcf_get_probabilities(Rcpp::StringMatrix& mat, int pl_pos);
 RcppExport SEXP _mappoly_vcf_get_probabilities(SEXP matSEXP, SEXP pl_posSEXP) {
@@ -70,13 +86,13 @@ RcppExport SEXP est_hmm_map_single_parent(void *, void *, void *, void *, void *
 RcppExport SEXP est_map_hmm(void *, void *, void *, void *, void *, void *, void *, void *);
 RcppExport SEXP est_map_hmm_highprec(void *, void *, void *, void *, void *, void *, void *, void *);
 RcppExport SEXP get_counts_single_parent_cpp(void *, void *, void *, void *, void *, void *);
-RcppExport SEXP loglike_hmm(void *, void *, void *, void *, void *, void *);
 RcppExport SEXP pairwise_rf_estimation_disc(void *, void *, void *, void *, void *, void *, void *);
 RcppExport SEXP pairwise_rf_estimation_disc_rcpp(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
 RcppExport SEXP pairwise_rf_estimation_prob(void *, void *, void *, void *, void *, void *, void *, void *);
 RcppExport SEXP poly_hmm_est_CPP(void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *, void *);
 
 static const R_CallMethodDef CallEntries[] = {
+    {"_mappoly_loglike_hmm_cpp", (DL_FUNC) &_mappoly_loglike_hmm_cpp, 6},
     {"_mappoly_vcf_get_probabilities", (DL_FUNC) &_mappoly_vcf_get_probabilities, 2},
     {"_mappoly_vcf_transform_dosage", (DL_FUNC) &_mappoly_vcf_transform_dosage, 2},
     {"_mappoly_vcf_get_ploidy", (DL_FUNC) &_mappoly_vcf_get_ploidy, 2},
@@ -92,7 +108,6 @@ static const R_CallMethodDef CallEntries[] = {
     {"est_map_hmm",                      (DL_FUNC) &est_map_hmm,                       8},
     {"est_map_hmm_highprec",             (DL_FUNC) &est_map_hmm_highprec,              8},
     {"get_counts_single_parent_cpp",     (DL_FUNC) &get_counts_single_parent_cpp,      6},
-    {"loglike_hmm",                      (DL_FUNC) &loglike_hmm,                       6},
     {"pairwise_rf_estimation_disc",      (DL_FUNC) &pairwise_rf_estimation_disc,       7},
     {"pairwise_rf_estimation_disc_rcpp", (DL_FUNC) &pairwise_rf_estimation_disc_rcpp, 12},
     {"pairwise_rf_estimation_prob",      (DL_FUNC) &pairwise_rf_estimation_prob,       8},

diff --git a/src/calc_loglike_given_map.cpp b/src/calc_loglike_given_map.cpp
@@ -49,21 +49,14 @@
 using namespace std;
 using namespace Rcpp;
 
-RcppExport SEXP loglike_hmm(SEXP ploidyR,
-                            SEXP genoR,
-                            SEXP phPR,
-                            SEXP phQR,
-                            SEXP rfR,
-                            SEXP verboseR)
+// [[Rcpp::export]]
+List loglike_hmm_cpp(int m,
+                     NumericMatrix geno,
+                     List ph1,
+                     List ph2,
+                     NumericVector rf,
+                     int verbose)
 {
-  //*convert input to C++ types
-  int m = Rcpp::as<int>(ploidyR);
-  Rcpp::NumericMatrix geno(genoR); //(n.ind x n.col)
-  Rcpp::List ph1(phPR);
-  Rcpp::List ph2(phQR);
-  Rcpp::NumericVector rf(rfR);
-  int verbose = Rcpp::as<int>(verboseR);
-
   //*Initializing some variables
   int g = nChoosek(m, m/2);
   int n_mar = geno.ncol(); // markers are disposed in columns

diff --git a/src/calc_loglike_given_map.h b/src/calc_loglike_given_map.h
@@ -28,9 +28,12 @@
 #include <R_ext/PrtUtil.h>
 #include "combinatorial.h"
 
-RcppExport SEXP loglike_hmm(SEXP ploidyR,
-                            SEXP genoR,
-                            SEXP phPR,
-                            SEXP phQR,
-                            SEXP rfR,
-                            SEXP verboseR);
+using namespace std;
+using namespace Rcpp;
+
+List loglike_hmm_cpp(int m,
+                     NumericMatrix geno,
+                     List ph1,
+                     List ph2,
+                     NumericVector rf,
+                     int verbose);