@@ -1,8 +1,8 @@

 Package: OncoSimulR

 Type: Package

 Title: Forward Genetic Simulation of Cancer Progression with Epistasis 

-Version: 2.9.2

-Date: 2017-11-24

+Version: 2.9.3

+Date: 2017-11-27

 Authors@R: c(person("Ramon", "Diaz-Uriarte", role = c("aut", "cre"),

 		     email = "rdiaz02@gmail.com"),

 	      person("Mark", "Taylor", role = "ctb", email = "ningkiling@gmail.com"))

@@ -1,3 +1,6 @@

+Changes in version 2.9.3 (2017-11-27):

+	- Make clang happy (do not use flandscape as DataFrame)

+	

 Changes in version 2.9.2 (2017-11-24):

 	- LOD: using only the strict Szendro et al. meaning.

 	- POM: computed in C++.

@@ -407,8 +407,11 @@ std::vector<int> GeneToModule(const std::vector<int>& Drv,

 }

+// fitnessLandscape_struct convertFitnessLandscape(Rcpp::List flg,

+// 						Rcpp::DataFrame fl_df) {

 fitnessLandscape_struct convertFitnessLandscape(Rcpp::List flg,

-						Rcpp::DataFrame fl_df) {

+						Rcpp::List fl_df) {

+

   fitnessLandscape_struct flS;

   flS.names = Rcpp::as<std::vector<std::string> >(flg["Gene"]);

   flS.NumID = Rcpp::as<std::vector<int> >(flg["GeneNumID"]);

@@ -419,7 +422,8 @@ fitnessLandscape_struct convertFitnessLandscape(Rcpp::List flg,

   Rcpp::NumericVector fitness = fl_df["Fitness"];

   // Fill up the map genotypes(as string) to fitness

-  for(size_t i = 0; i != fl_df.nrows(); ++i) {

+  //for(size_t i = 0; i != fl_df.nrows(); ++i) {

+  for(size_t i = 0; i != genotNames.size(); ++i) {

     flS.flmap.insert({genotNames[i], fitness[i]});

   }

@@ -505,7 +509,10 @@ fitnessEffectsAll convertFitnessEffects(Rcpp::List rFE) {

   Rcpp::IntegerVector drv = rFE["drv"];

   Rcpp::List flg = rFE["fitnessLandscape_gene_id"];

-  Rcpp::DataFrame fl_df = rFE["fitnessLandscape_df"];

+  // clang does not like this

+  // Rcpp::DataFrame fl_df = rFE["fitnessLandscape_df"];

+  Rcpp::List fl_df = rFE["fitnessLandscape_df"];

+  

@@ -514,7 +521,8 @@ fitnessEffectsAll convertFitnessEffects(Rcpp::List rFE) {

   // of noInt. So we can use noInt with shift being those in fitnessLandscape.

   // BEWARE: will need to modify also createNewGenotype.

-  if(fl_df.nrows()) {

+  // if(fl_df.nrows()) {

+  if(fl_df.size()) {

     fe.fitnessLandscape = convertFitnessLandscape(flg, fl_df);

   }

@@ -534,13 +542,16 @@ fitnessEffectsAll convertFitnessEffects(Rcpp::List rFE) {

   }

   // If this is null, use the nullFitnessEffects function; never

   // end up here.

-  if( (rrt.size() + re.size() + ro.size() + rgi.size() + fl_df.nrows()) == 0) {

+  

+  //   if( (rrt.size() + re.size() + ro.size() + rgi.size() + fl_df.nrows()) == 0) {

+  if( (rrt.size() + re.size() + ro.size() + rgi.size() + fl_df.size()) == 0) {

       throw std::logic_error("\n Nothing inside this fitnessEffects; why are you here?"

 			     "  Bug in R code.");

   }

   // At least for now, if fitness landscape nothing else allowed

-  if(fl_df.nrows() && ((rrt.size() + re.size() + ro.size() + rgi.size()) > 0)) {

+  // if(fl_df.nrows() && ((rrt.size() + re.size() + ro.size() + rgi.size()) > 0)) {

+  if(fl_df.size() && ((rrt.size() + re.size() + ro.size() + rgi.size()) > 0)) {

     throw std::logic_error("\n Fitness landscape specification."

 			   " There should be no other terms. "

 			   " Bug in R code");