fixed int compare error

inst/include/interface/rcpp/rcpp_objects/rcpp_data.hpp

@@ -94,7 +94,7 @@ class AgeCompDataInterface : public DataInterfaceBase {
     ss << " \"rank\": " << 2 << ",\n";
     ss << " \"dimensions\": [" << this->ymax << "," << this->amax << "],\n";
     ss << " \"values\": [";
-    for (size_t i = 0; i < age_comp_data.size() - 1; i++) {
+    for (R_xlen_t i = 0; i < age_comp_data.size() - 1; i++) {
       ss << age_comp_data[i] << ", ";
     }
     ss << age_comp_data[age_comp_data.size() - 1] << "]\n";
@@ -183,7 +183,7 @@ class LengthCompDataInterface : public DataInterfaceBase {
     ss << " \"rank\": " << 2 << ",\n";
     ss << " \"dimensions\": [" << this->ymax << "," << this->lmax << "],\n";
     ss << " \"values\": [";
-    for (size_t i = 0; i < length_comp_data.size() - 1; i++) {
+    for (R_xlen_t i = 0; i < length_comp_data.size() - 1; i++) {
       ss << length_comp_data[i] << ", ";
     }
     ss << length_comp_data[length_comp_data.size() - 1] << "]\n";
@@ -268,7 +268,7 @@ class IndexDataInterface : public DataInterfaceBase {
     ss << " \"rank\": " << 1 << ",\n";
     ss << " \"dimensions\": [" << this->ymax << "],\n";
     ss << " \"values\": [";
-    for (size_t i = 0; i < index_data.size() - 1; i++) {
+    for (R_xlen_t i = 0; i < index_data.size() - 1; i++) {
       ss << index_data[i] << ", ";
     }
     ss << index_data[index_data.size() - 1] << "]\n";

inst/include/interface/rcpp/rcpp_objects/rcpp_fleet.hpp

@@ -181,15 +181,15 @@ class FleetInterface : public FleetInterfaceBase {
                     std::dynamic_pointer_cast<fims_popdy::Fleet<double> >(it->second);
 
 
-            for (size_t i = 0; i < this->log_Fmort.size(); i++) {
+            for (R_xlen_t i = 0; i < this->log_Fmort.size(); i++) {
                 if (this->log_Fmort[i].estimated_m) {
                     this->log_Fmort[i].final_value_m = fleet->log_Fmort[i];
                 } else {
                     this->log_Fmort[i].final_value_m = this->log_Fmort[i].initial_value_m;
                 }
             }
 
-            for (size_t i = 0; i < this->log_q.size(); i++) {
+            for (R_xlen_t i = 0; i < this->log_q.size(); i++) {
                 if (this->log_q[i].estimated_m) {
                     this->log_q[i].final_value_m = fleet->log_q[i];
                 } else {
@@ -198,32 +198,32 @@ class FleetInterface : public FleetInterfaceBase {
             }
 
             this->derived_cnaa = Rcpp::NumericVector(fleet->catch_numbers_at_age.size());
-            for (size_t i = 0; i < this->derived_cnaa.size(); i++) {
+            for (R_xlen_t i = 0; i < this->derived_cnaa.size(); i++) {
                 this->derived_cnaa[i] = fleet->catch_numbers_at_age[i];
             }
 
             this->derived_cnal = Rcpp::NumericVector(fleet->catch_numbers_at_length.size());
-            for (size_t i = 0; i < this->derived_cnal.size(); i++) {
+            for (R_xlen_t i = 0; i < this->derived_cnal.size(); i++) {
                 this->derived_cnal[i] = fleet->catch_numbers_at_length[i];
             }
 
             this->derived_cwaa = Rcpp::NumericVector(fleet->catch_weight_at_age.size());
-            for (size_t i = 0; i < this->derived_cwaa.size(); i++) {
+            for (R_xlen_t i = 0; i < this->derived_cwaa.size(); i++) {
                 this->derived_cwaa[i] = fleet->catch_weight_at_age[i];
             }
 
             this->derived_age_composition = Rcpp::NumericVector(fleet->proportion_catch_numbers_at_age.size());
-            for (size_t i = 0; i < this->derived_age_composition.size(); i++) {
+            for (R_xlen_t i = 0; i < this->derived_age_composition.size(); i++) {
                 this->derived_age_composition[i] = fleet->proportion_catch_numbers_at_age[i];
             }
 
             this->derived_length_composition = Rcpp::NumericVector(fleet->proportion_catch_numbers_at_length.size());
-            for (size_t i = 0; i < this->derived_length_composition.size(); i++) {
+            for (R_xlen_t i = 0; i < this->derived_length_composition.size(); i++) {
                 this->derived_length_composition[i] = fleet->proportion_catch_numbers_at_length[i];
             }
 
             this->derived_index = Rcpp::NumericVector(fleet->expected_index.size());
-            for (size_t i = 0; i < this->derived_index.size(); i++) {
+            for (R_xlen_t i = 0; i < this->derived_index.size(); i++) {
                 this->derived_index[i] = fleet->expected_index[i];
             }
 
@@ -263,7 +263,7 @@ class FleetInterface : public FleetInterfaceBase {
         if (this->derived_cnaa.size() == 0) {
             ss << "]\n";
         } else {
-            for (size_t i = 0; i < this->derived_cnaa.size() - 1; i++) {
+            for (R_xlen_t i = 0; i < this->derived_cnaa.size() - 1; i++) {
                 ss << this->derived_cnaa[i] << ", ";
             }
             ss << this->derived_cnaa[this->derived_cnaa.size() - 1] << "]\n";
@@ -276,7 +276,7 @@ class FleetInterface : public FleetInterfaceBase {
         if (this->derived_cnal.size() == 0) {
             ss << "]\n";
         } else {
-            for (size_t i = 0; i < this->derived_cnal.size() - 1; i++) {
+            for (R_xlen_t i = 0; i < this->derived_cnal.size() - 1; i++) {
                 ss << this->derived_cnal[i] << ", ";
             }
             ss << this->derived_cnal[this->derived_cnal.size() - 1] << "]\n";
@@ -289,7 +289,7 @@ class FleetInterface : public FleetInterfaceBase {
         if (this->derived_cwaa.size() == 0) {
             ss << "]\n";
         } else {
-            for (size_t i = 0; i < this->derived_cwaa.size() - 1; i++) {
+            for (R_xlen_t i = 0; i < this->derived_cwaa.size() - 1; i++) {
                 ss << this->derived_cwaa[i] << ", ";
             }
             ss << this->derived_cwaa[this->derived_cwaa.size() - 1] << "]\n";
@@ -303,7 +303,7 @@ class FleetInterface : public FleetInterfaceBase {
         if (this->derived_age_composition.size() == 0) {
             ss << "]\n";
         } else {
-            for (size_t i = 0; i < this->derived_age_composition.size() - 1; i++) {
+            for (R_xlen_t i = 0; i < this->derived_age_composition.size() - 1; i++) {
                 ss << this->derived_age_composition[i] << ", ";
             }
             ss << this->derived_age_composition[this->derived_age_composition.size() - 1] << "]\n";
@@ -316,7 +316,7 @@ class FleetInterface : public FleetInterfaceBase {
         if (this->derived_length_composition.size() == 0) {
             ss << "]\n";
         } else {
-            for (size_t i = 0; i < this->derived_length_composition.size() - 1; i++) {
+            for (R_xlen_t i = 0; i < this->derived_length_composition.size() - 1; i++) {
                 ss << this->derived_length_composition[i] << ", ";
             }
             ss << this->derived_length_composition[this->derived_length_composition.size() - 1] << "]\n";
@@ -329,7 +329,7 @@ class FleetInterface : public FleetInterfaceBase {
         if (this->derived_index.size() == 0) {
             ss << "]\n";
         } else {
-            for (size_t i = 0; i < this->derived_index.size() - 1; i++) {
+            for (R_xlen_t i = 0; i < this->derived_index.size() - 1; i++) {
                 ss << this->derived_index[i] << ", ";
             }
             ss << this->derived_index[this->derived_index.size() - 1] << "]\n";
@@ -366,7 +366,7 @@ class FleetInterface : public FleetInterfaceBase {
     fleet->fleet_selectivity_id_m = interface_selectivity_id_m;
 
     fleet->log_q.resize(this->log_q.size());
-    for (size_t i = 0; i < this->log_q.size(); i++) {
+    for (R_xlen_t i = 0; i < this->log_q.size(); i++) {
         fleet->log_q[i] = this->log_q[i].initial_value_m;
 
       if (this->log_q[i].estimated_m) {
@@ -381,7 +381,7 @@ class FleetInterface : public FleetInterfaceBase {
 
 
     fleet->log_Fmort.resize(this->log_Fmort.size());
-    for (size_t i = 0; i < log_Fmort.size(); i++) {
+    for (R_xlen_t i = 0; i < log_Fmort.size(); i++) {
       fleet->log_Fmort[i] = this->log_Fmort[i].initial_value_m;
 
       if (this->log_Fmort[i].estimated_m) {
@@ -404,7 +404,7 @@ class FleetInterface : public FleetInterfaceBase {
     if(this->nlengths > 0){
       fleet->proportion_catch_numbers_at_length.resize(nyears * nlengths);
       fleet->age_length_conversion_matrix.resize(nages * nlengths);
-      for (size_t i = 0; i < fleet->age_length_conversion_matrix.size(); i++){
+      for (R_xlen_t i = 0; i < fleet->age_length_conversion_matrix.size(); i++){
         fleet->age_length_conversion_matrix[i] = this->age_length_conversion_matrix[i].initial_value_m;
 
         if (this->age_length_conversion_matrix[i].estimated_m) {

inst/include/interface/rcpp/rcpp_objects/rcpp_interface_base.hpp

@@ -193,7 +193,8 @@ class ParameterVector{
      *  @param pos return a Parameter at position "pos".
      */
     SEXP at(R_xlen_t pos){
-        if (pos == 0 || pos > this->storage_m->size()) {
+        if (static_cast<size_t>(pos) == 0 ||
+                static_cast<size_t>(pos)  > this->storage_m->size()) {
             Rcpp::Rcout << "ParameterVector: Index out of range.\n";
             FIMS_ERROR_LOG(fims::to_string(pos) + "!<" + fims::to_string(this->size()));
             return NULL;

inst/include/interface/rcpp/rcpp_objects/rcpp_population.hpp

@@ -135,17 +135,17 @@ class PopulationInterface : public PopulationInterfaceBase {
 
 
         this->estimated_log_M = Rcpp::NumericVector(this->log_M.size());
-        for (size_t i = 0; i < this->log_M.size(); i++) {
+        for (R_xlen_t i = 0; i < this->log_M.size(); i++) {
             this->estimated_log_M[i] = this->log_M[i].initial_value_m;
         }
 
         this->estimated_log_init_naa = Rcpp::NumericVector(this->log_init_naa.size());
-        for (size_t i = 0; i < this->log_init_naa.size(); i++) {
+        for (R_xlen_t i = 0; i < this->log_init_naa.size(); i++) {
             this->estimated_log_init_naa[i] = this->log_init_naa[i].initial_value_m;
         }
 
         this->estimated_proportion_female = Rcpp::NumericVector(this->proportion_female.size());
-        for (size_t i = 0; i < this->proportion_female.size(); i++) {
+        for (R_xlen_t i = 0; i < this->proportion_female.size(); i++) {
             this->estimated_proportion_female[i] = this->proportion_female[i];
         }
 
@@ -163,19 +163,19 @@ class PopulationInterface : public PopulationInterfaceBase {
         } else {
 
             if (this->estimated_log_M) {
-                for (size_t i = 0; i < this->log_M.size(); i++) {
+                for (R_xlen_t i = 0; i < this->log_M.size(); i++) {
                     this->estimated_log_M[i] = pop->log_M[i];
                 }
             }
 
             if (this->estimated_log_init_naa) {
-                for (size_t i = 0; i < this->log_init_naa.size(); i++) {
+                for (R_xlen_t i = 0; i < this->log_init_naa.size(); i++) {
                     this->estimated_log_init_naa[i] = pop->log_init_naa[i];
                 }
             }
 
             if (this->estimate_prop_female) {
-                for (size_t i = 0; i < this->proportion_female.size(); i++) {
+                for (R_xlen_t i = 0; i < this->proportion_female.size(); i++) {
                     this->estimated_proportion_female[i] = pop->proportion_female[i];
                 }
             }
@@ -186,22 +186,22 @@ class PopulationInterface : public PopulationInterfaceBase {
             this->derived_recruitment = Rcpp::NumericVector(pop->expected_recruitment.size());
 
             //set naa from Information/
-            for (size_t i = 0; i < this->derived_naa.size(); i++) {
+            for (R_xlen_t i = 0; i < this->derived_naa.size(); i++) {
                 this->derived_naa[i] = pop->numbers_at_age[i];
             }
 
             //set ssb from Information/
-            for (size_t i = 0; i < this->derived_ssb.size(); i++) {
+            for (R_xlen_t i = 0; i < this->derived_ssb.size(); i++) {
                 this->derived_ssb[i] = pop->spawning_biomass[i];
             }
 
             //set biomass from Information
-            for (size_t i = 0; i < this->derived_biomass.size(); i++) {
+            for (R_xlen_t i = 0; i < this->derived_biomass.size(); i++) {
                 this->derived_biomass[i] = pop->biomass[i];
             }
 
             //set recruitment from Information/
-            for (size_t i = 0; i < this->derived_recruitment.size(); i++) {
+            for (R_xlen_t i = 0; i < this->derived_recruitment.size(); i++) {
                 this->derived_recruitment[i] = pop->expected_recruitment[i];
             }
 
@@ -250,7 +250,7 @@ class PopulationInterface : public PopulationInterfaceBase {
         if (this->derived_ssb.size() == 0) {
             ss << "]\n";
         } else {
-            for (size_t i = 0; i < this->derived_ssb.size() - 1; i++) {
+            for (R_xlen_t i = 0; i < this->derived_ssb.size() - 1; i++) {
                 ss << this->derived_ssb[i] << ", ";
             }
             ss << this->derived_ssb[this->derived_ssb.size() - 1] << "]\n";
@@ -263,7 +263,7 @@ class PopulationInterface : public PopulationInterfaceBase {
         if (this->derived_naa.size() == 0) {
             ss << "]\n";
         } else {
-            for (size_t i = 0; i < this->derived_naa.size() - 1; i++) {
+            for (R_xlen_t i = 0; i < this->derived_naa.size() - 1; i++) {
                 ss << this->derived_naa[i] << ", ";
             }
             ss << this->derived_naa[this->derived_naa.size() - 1] << "]\n";
@@ -276,7 +276,7 @@ class PopulationInterface : public PopulationInterfaceBase {
         if (this->derived_biomass.size() == 0) {
             ss << "]\n";
         } else {
-            for (size_t i = 0; i < this->derived_biomass.size() - 1; i++) {
+            for (R_xlen_t i = 0; i < this->derived_biomass.size() - 1; i++) {
                 ss << this->derived_biomass[i] << ", ";
             }
             ss << this->derived_biomass[this->derived_biomass.size() - 1] << "]\n";
@@ -289,7 +289,7 @@ class PopulationInterface : public PopulationInterfaceBase {
         if (this->derived_recruitment.size() == 0) {
             ss << "]\n";
         } else {
-            for (size_t i = 0; i < this->derived_recruitment.size() - 1; i++) {
+            for (R_xlen_t i = 0; i < this->derived_recruitment.size() - 1; i++) {
                 ss << this->derived_recruitment[i] << ", ";
             }
             ss << this->derived_recruitment[this->derived_recruitment.size() - 1] << "]\n";
@@ -329,7 +329,7 @@ class PopulationInterface : public PopulationInterfaceBase {
     population->maturity_id = this->maturity_id;
     population->log_M.resize(this->log_M.size());
     population->log_init_naa.resize(this->log_init_naa.size());
-    for (size_t i = 0; i < log_M.size(); i++) {
+    for (R_xlen_t i = 0; i < log_M.size(); i++) {
       population->log_M[i] = this->log_M[i].initial_value_m;
       if (this->log_M[i].estimated_m) {
           info->RegisterParameterName("log_M");
@@ -338,18 +338,18 @@ class PopulationInterface : public PopulationInterfaceBase {
     }
     info->variable_map[this->log_M.id_m] = &(population)->log_M;
 
-    for (size_t i = 0; i < log_init_naa.size(); i++) {
+    for (R_xlen_t i = 0; i < log_init_naa.size(); i++) {
       population->log_init_naa[i] = this->log_init_naa[i].initial_value_m;
       if (this->log_init_naa[i].estimated_m) {
         info->RegisterParameterName("log_init_naa");
         info->RegisterParameter(population->log_init_naa[i]);
       }
     }
     info->variable_map[this->log_init_naa.id_m] = &(population)->log_init_naa;
-    for (int i = 0; i < ages.size(); i++) {
+    for (R_xlen_t i = 0; i < ages.size(); i++) {
       population->ages[i] = this->ages[i];
     }
-    for (int i = 0; i < proportion_female.size(); i++) {
+    for (R_xlen_t i = 0; i < proportion_female.size(); i++) {
       population->proportion_female[i] = this->proportion_female[i];
       if (estimate_prop_female) {
         info->RegisterParameter(population->proportion_female[i]);

inst/include/interface/rcpp/rcpp_objects/rcpp_recruitment.hpp

@@ -123,23 +123,23 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
             std::shared_ptr<fims_popdy::SRBevertonHolt<double> > recr =
                     std::dynamic_pointer_cast<fims_popdy::SRBevertonHolt<double> >(it->second);
 
-            for (size_t i = 0; i < this->logit_steep.size(); i++) {
+            for (R_xlen_t i = 0; i < this->logit_steep.size(); i++) {
                 if (this->logit_steep[i].estimated_m) {
                     this->logit_steep[i].final_value_m = recr->logit_steep[i];
                 } else {
                     this->logit_steep[i].final_value_m = this->logit_steep[i].initial_value_m;
                 }
             }
 
-            for (size_t i = 0; i < log_rzero.size(); i++) {
+            for (R_xlen_t i = 0; i < log_rzero.size(); i++) {
                 if (log_rzero[i].estimated_m) {
                     this->log_rzero[i].final_value_m = recr->log_rzero[i];
                 } else {
                     this->log_rzero[i].final_value_m = this->log_rzero[i].initial_value_m;
                 }
             }
 
-            for (size_t i = 0; i < this->estimated_log_devs.size(); i++) {
+            for (R_xlen_t i = 0; i < this->estimated_log_devs.size(); i++) {
                 if (this->log_devs[i].estimated_m) {
                     this->log_devs[i].final_value_m = recr->log_recruit_devs[i];
                 } else {
@@ -198,7 +198,7 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
     recruitment->id = this->id;
     //set logit_steep
         recruitment->logit_steep.resize(this->logit_steep.size());
-        for (size_t i = 0; i < this->logit_steep.size(); i++) {
+        for (R_xlen_t i = 0; i < this->logit_steep.size(); i++) {
 
             recruitment->logit_steep[i] = this->logit_steep[i].initial_value_m;
 
@@ -218,7 +218,7 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
 
         //set log_rzero
         recruitment->log_rzero.resize(this->log_rzero.size());
-        for (size_t i = 0; i < this->log_rzero.size(); i++) {
+        for (R_xlen_t i = 0; i < this->log_rzero.size(); i++) {
 
             recruitment->log_rzero[i] = this->log_rzero[i].initial_value_m;
 
@@ -236,7 +236,7 @@ class BevertonHoltRecruitmentInterface : public RecruitmentInterfaceBase {
 
         //set log_recruit_devs
         recruitment->log_recruit_devs.resize(this->log_devs.size());
-        for (size_t i = 0; i < this->log_devs.size(); i++) {
+        for (R_xlen_t i = 0; i < this->log_devs.size(); i++) {
             recruitment->log_recruit_devs[i] = this->log_devs[i].initial_value_m;
             if (this->log_devs[i].estimated_m) {
                 info->RegisterParameter(recruitment->log_recruit_devs[i]);