update fix #72

DEploid-dev · Oct 14, 2024 · d5b2425 · d5b2425
1 parent d2649ef
commit d5b2425
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Showing 4 changed files with 10 additions and 8 deletions.
diff --git a/src/DEploid/dEploidIO.cpp b/src/DEploid/dEploidIO.cpp
@@ -190,7 +190,7 @@ void DEploidIO::reInit() {
 
 
 void DEploidIO::finalize() {
-    if ( this->doIbdPainting() | this->doComputeLLK() | this->doIbdViterbiPainting() ) {
+    if ( this->doIbdPainting() || this->doComputeLLK() || this->doIbdViterbiPainting() ) {
         if (!initialPropWasGiven()) {
             throw InitialPropUngiven("");
         }
@@ -541,7 +541,7 @@ void DEploidIO::checkInput() {
             // set k strain by proportion length
         }
     }
-    if (this->useBestPractice() & (!this->usePanel())){
+    if (this->useBestPractice() && (!this->usePanel())){
         throw FlagsConflict("-best" , string("-noPanel. Reference panel is") +
             string("required for using best-practices."));
     }
@@ -764,7 +764,7 @@ void DEploidIO::readPanel() {
     if ( this->usePanel() == false ) {
         return;
     }
-    if ( this->doIbdPainting() | this->doComputeLLK() ) {
+    if ( this->doIbdPainting() || this->doComputeLLK() ) {
         return;
     }
 

diff --git a/src/DEploid/exceptions.hpp b/src/DEploid/exceptions.hpp
@@ -39,7 +39,8 @@ struct ShouldNotBeCalled : std::exception{
   ShouldNotBeCalled() { }
   virtual ~ShouldNotBeCalled() throw() {}
   virtual const char* what() const noexcept {
-      return string("Should not reach here").c_str();
+      static const std::string msg = "Should not reach here";
+      return msg.c_str();
   }
 };
 
@@ -75,7 +76,8 @@ struct OutOfVectorSize : std::exception{
   OutOfVectorSize() { }
   virtual ~OutOfVectorSize() throw() {}
   virtual const char* what() const noexcept {
-      return string("Out of vector size!").c_str();
+      static const std::string msg = "Out of vector size!";
+      return msg.c_str();
   }
 };
 

diff --git a/src/DEploid/mcmc.cpp b/src/DEploid/mcmc.cpp
@@ -314,7 +314,7 @@ void McmcMachinery::runMcmcChain( bool showProgress, bool useIBD, bool notInR )
         this->mcmcSample_->siteOfOneMissCopyOne[atSiteI] /= (double)this->maxIteration_;
     }
 
-    if ( notInR & ((jobbrief == "lassoK") | (jobbrief == "ibd") | (jobbrief == "classic")) ) { // notInPython
+    if ( notInR & ((jobbrief == "lassoK") || (jobbrief == "ibd") || (jobbrief == "classic")) ) { // notInPython
         this->dEploidIO_->writeMcmcRelated(this->mcmcSample_, jobbrief, useIBD);
     }
 

diff --git a/src/init.c b/src/init.c
@@ -10,9 +10,9 @@
 /* .Call calls */
 extern SEXP _DEploid_dEploid(SEXP);
 extern SEXP _DEploid_extractVcf(SEXP);
-extern SEXP _DEploid_test_RRG_sample();
+extern SEXP _DEploid_test_RRG_sample(void);
 extern SEXP _DEploid_test_RRG_sampleExpoExpoLimit(SEXP, SEXP, SEXP);
-extern SEXP _DEploid_test_RRG_sampleUnitExpo();
+extern SEXP _DEploid_test_RRG_sampleUnitExpo(void);
 
 static const R_CallMethodDef CallEntries[] = {
     {"_DEploid_dEploid",                      (DL_FUNC) &_DEploid_dEploid,                      1},