CMakeLists.txt

@@ -9,7 +9,7 @@ cmake_minimum_required (VERSION 2.8.11)
 project (bpp-core CXX)
 
 # Compile options
-#set (CMAKE_CXX_FLAGS "-std=c++11 -g")
+set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
 
 IF(NOT CMAKE_BUILD_TYPE)
   SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
@@ -25,9 +25,9 @@ ENDIF(NOT CMAKE_BUILD_TYPE)
 #           library implements.
 # In other words, the library implements all the interface numbers in the
 # range from number current - age to current.
-SET(${PROJECT_NAME}_VERSION_CURRENT "4")
+SET(${PROJECT_NAME}_VERSION_CURRENT "5")
 SET(${PROJECT_NAME}_VERSION_REVISION "0")
-SET(${PROJECT_NAME}_VERSION_AGE "0")
+SET(${PROJECT_NAME}_VERSION_AGE "1")
 
 # Effective version number computation
 MATH(EXPR ${PROJECT_NAME}_VERSION_MAJOR "${${PROJECT_NAME}_VERSION_CURRENT} - ${${PROJECT_NAME}_VERSION_AGE}")
@@ -77,10 +77,10 @@ ENDIF (DOXYGEN_FOUND)
 # Packager
 SET(CPACK_PACKAGE_NAME "libbpp-core")
 SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.4.0")
+SET(CPACK_PACKAGE_VERSION "2.4.1")
 SET(CPACK_PACKAGE_VERSION_MAJOR "2")
 SET(CPACK_PACKAGE_VERSION_MINOR "4")
-SET(CPACK_PACKAGE_VERSION_PATCH "0")
+SET(CPACK_PACKAGE_VERSION_PATCH "1")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Core library")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")

ChangeLog

+06/06/18 Julien Dutheil
+* Recursive param argument issue solved (closes #17).
+* New version number: current 4 -> 5, age 0 -> 1 because of new symbol in AttributeTools. 
+
 19/02/17 -*- Version 2.4.0 -*-
 
 04/01/18 Laurent Guéguen

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = bpp-core
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = 2.4.0
+PROJECT_NUMBER         = 2.4.1
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a

bpp-core.spec

@@ -3,7 +3,7 @@
 URL: https://github.com/BioPP/bpp-core
 
 Name: bpp-core
-Version: 2.4.0
+Version: 2.4.1
 Release: 1%{?dist}
 License: CECILL-2.0
 Vendor: The Bio++ Project
@@ -71,6 +71,8 @@ rm -rf $RPM_BUILD_ROOT
 %{_prefix}/include/*
 
 %changelog
+* Fri Aug 10 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.1-1
+- Update for gcc8 + bug fixes
 * Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
 - Increased interface number
 - Removed dynamic exceptions specifications.

debian/changelog

+libbpp-core (2.4.1-1) UNRELEASED; urgency=medium
+
+  * Compatibility with gcc 8.0
+    Ref: #897780
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Sat, 18 Aug 2018 13:32:11 +0200
+
 libbpp-core (2.4.0-3) unstable; urgency=medium
 
   * Provide symbols file only for amd64

debian/control

@@ -8,8 +8,8 @@ Build-Depends: debhelper (>= 11~),
                cmake,
                d-shlibs
 Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-core.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-core.git
+Vcs-Browser: https://salsa.debian.org/med-team/libbpp-core
+Vcs-Git: https://salsa.debian.org/med-team/libbpp-core.git
 Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 
 Package: libbpp-core-dev

src/Bpp/App/ApplicationTools.h

@@ -338,11 +338,12 @@ namespace bpp
      *
      * @param parameterName    The name of the corresponding parameter.
      * @param params           The attribute map where options may be found.
-     * @param separator        The character used to delimit values.
+     * @param separator        The character used to delimit values (cannot be a space character).
      * @param defaultValue     The default value to use if the parameter is not found.
      * @param suffix           A suffix to be applied to the parameter name.
      * @param suffixIsOptional Tell if the suffix is absolutely required.
      * @param warn             Tell if a warning must be sent in case the parameter is not found.
+     * @throw Exception If a space character is used as separator.
      * @return The corresponding value.
      */
     template<class T> static std::vector<T> getVectorParameter(
@@ -354,6 +355,7 @@ namespace bpp
       bool suffixIsOptional = true,
       int warn = 0)
     {
+      if (separator == ' ') throw Exception("ApplicationTools::getVectorParameter(). Separator cannot be a space character.");
       std::string s = getStringParameter(parameterName, params, defaultValue, suffix, suffixIsOptional, warn);
       if (TextTools::isEmpty(s)) return std::vector<T>(0);
       if (s[0] == '(' && s[s.size() - 1] == ')') {

src/Bpp/Graph/GlobalGraph.cpp

@@ -564,7 +564,7 @@ Graph::EdgeId GlobalGraph::getAnyEdge(Graph::NodeId nodeA, Graph::NodeId nodeB)
     // trying in the given order A->B
     return getEdge(nodeA, nodeB);
   }
-  catch (Exception e)
+  catch (Exception& e)
   {
     // didn’t work, hence trying in the opposite order B->A
     return getEdge(nodeB, nodeA);

src/Bpp/Graph/TreeGraphImpl.h

@@ -272,7 +272,7 @@ namespace bpp
   {
     std::vector<Graph::NodeId> incomers = getIncomingNeighbors(node);
     if (incomers.size() > 1)
-      throw Exception("TreeGraphImpl<GraphImpl>::getFather: more than one father for Node " + TextTools::toString(node) + " : " + VectorTools::paste(incomers, ",") + ". Should never happen since validity has been controled. Please report this bug.");
+      throw Exception("TreeGraphImpl<GraphImpl>::getFather: more than one father for Node " + TextTools::toString(node) + " : " + VectorTools::paste(incomers, ",") + ". Should never happen since validity has been controlled. Please report this bug.");
     if (incomers.size() == 0)
       throw Exception("TreeGraphImpl<GraphImpl>::getFather: node " + TextTools::toString(node) + " has no father.");
     return *incomers.begin();

src/Bpp/Numeric/AbstractParameterAliasable.cpp

@@ -178,8 +178,8 @@ void AbstractParameterAliasable::aliasParameters(map<string, string>& unparsedPa
   size_t unp_s = unparsedParams.size();
   while (unp_s != 0)
   {
-    map<string, string>::iterator it;
-    for (it = unparsedParams.begin(); it != unparsedParams.end(); it++)
+    auto it = unparsedParams.begin();
+    while (it != unparsedParams.end())
     {
       Parameter* pp = 0;
       try
@@ -199,7 +199,7 @@ void AbstractParameterAliasable::aliasParameters(map<string, string>& unparsedPa
       aliasParameters(it->second, it->first);
       if (verbose)
         ApplicationTools::displayResult("Parameter alias found", it->first + " -> " + it->second + " = " + TextTools::toString(pp->getValue()));
-      unparsedParams.erase(it);
+      it = unparsedParams.erase(it);
     }
 
     if (unparsedParams.size() == unp_s)

src/Bpp/Numeric/AbstractParametrizable.h

@@ -193,6 +193,8 @@ class AbstractParametrizable:
      */
     Parameter& getParameter_(const std::string& name)
     {
+      if (!hasParameter(name))
+        throw ParameterNotFoundException("AbstractParametrizable::getParameter_().", prefix_ + name);
       return parameters_.getParameter(prefix_ + name);
     }
   

src/Bpp/Numeric/Function/Operators/ComputationTree.cpp

@@ -157,7 +157,7 @@ std::shared_ptr<Operator> ComputationTree::readFormula_(const std::string& formu
       double v = TextTools::toDouble(formula);
       here =  shared_ptr<Operator>(new ConstantOperator(v));
     }
-    catch (Exception e)
+    catch (Exception& e)
     {
       if (formula[0]=='-')
       {

src/Bpp/Numeric/Function/PowellMultiDimensions.cpp

@@ -99,16 +99,16 @@ double PowellMultiDimensions::doStep()
 {
   size_t n = getParameters().size();
   fp_ = fret_;
-  unsigned int ibig = 0;
+  size_t ibig = 0;
   double del = 0.0; // Will be the biggest function decrease
   Vdouble xit(n);
   
   // In each iteration, loop over all directions in the set.
   double fptt;
-  for(unsigned int i = 0; i < n; i++)
+  for (size_t i = 0; i < n; i++)
   {
     // Copy the direction:
-    for(unsigned int j = 0; j < n; j++)
+    for (size_t j = 0; j < n; j++)
     {
       xit[j] = xi_[j][i];
     }
@@ -127,7 +127,7 @@ double PowellMultiDimensions::doStep()
   }
 
   ParameterList ptt = getParameters();
-  for (unsigned int j = 0; j < n; j++)
+  for (size_t j = 0; j < n; j++)
   {
     ptt[j].setValue(2.0 * getParameters()[j].getValue() - pt_[j].getValue());
     xit[j] = getParameters()[j].getValue() - pt_[j].getValue();
@@ -144,8 +144,9 @@ double PowellMultiDimensions::doStep()
           getParameters_(), xit, getStopCondition()->getTolerance(),
           0, getMessageHandler(), getVerbose() > 0 ? getVerbose() - 1 : 0);
       fret_ = getFunction()->f(getParameters());
-      if (fret_ > fp_) throw Exception("DEBUG: PowellMultiDimensions::doStep(). Line minimization failed!");
-      for (unsigned int j = 0; j < n; j++)
+      if (fret_ > fp_)
+        throw Exception("DEBUG: PowellMultiDimensions::doStep(). Line minimization failed!");
+      for (size_t j = 0; j < n; j++)
       {
         xi_[j][ibig]  = xi_[j][n - 1];
         xi_[j][n - 1] = xit[j];

src/Bpp/Numeric/Matrix/MatrixTools.h

@@ -450,7 +450,7 @@ namespace bpp
       size_t nrA = A.getNumberOfRows();
       size_t nrB = B.getNumberOfRows();
       size_t ncB = B.getNumberOfColumns();
-      if (ncA > ncB) throw DimensionException("MatrixTools::operator+=(). A and B must have the same number of colums.", ncB, ncA);
+      if (ncA > ncB) throw DimensionException("MatrixTools::operator+=(). A and B must have the same number of columns.", ncB, ncA);
       if (nrA > nrB) throw DimensionException("MatrixTools::operator+=(). A and B must have the same number of rows.", nrB, nrA);
       
       
@@ -478,7 +478,7 @@ namespace bpp
       size_t nrA = A.getNumberOfRows();
       size_t nrB = B.getNumberOfRows();
       size_t ncB = B.getNumberOfColumns();
-      if (ncA != ncB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of colums.", ncB, ncA);
+      if (ncA != ncB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of columns.", ncB, ncA);
       if (nrA != nrB) throw DimensionException("MatrixTools::operator+(). A and B must have the same number of rows.", nrB, nrA);
       
       for (size_t i = 0; i < nrA; i++)

src/Bpp/Numeric/ParameterList.cpp

@@ -496,13 +496,11 @@ void ParameterList::matchParameters(const ParameterList& params)
 /******************************************************************************/
 void ParameterList::deleteParameter(const std::string& name)
 {
-  for (unsigned int i = 0; i < size(); i++)
+  for (auto it = parameters_.begin(); it != parameters_.end(); ++it)
   {
-    Parameter* p = parameters_[i].get();
-    
-    if (p->getName() == name)
+    if ((*it)->getName() == name)
     {
-      parameters_.erase(parameters_.begin() + i);
+      it = parameters_.erase(it);
       return;
     }
   }
@@ -512,11 +510,11 @@ void ParameterList::deleteParameter(const std::string& name)
 /******************************************************************************/
 void ParameterList::deleteParameters(const std::vector<std::string>& names, bool mustExist)
 {
-  for (unsigned int i = 0; i < names.size(); i++)
+  for (auto it = names.begin(); it != names.end(); ++it)
   {
     try
     {
-      deleteParameter(names[i]);
+      deleteParameter(*it);
     }
     catch (ParameterNotFoundException& e)
     {
@@ -532,8 +530,6 @@ void ParameterList::deleteParameters(const std::vector<std::string>& names, bool
 void ParameterList::deleteParameter(size_t index)
 {
   if (index >= size()) throw IndexOutOfBoundsException("ParameterList::deleteParameter.", index, 0, size());
-  // Parameter* p = parameters_[index].get();
-  // delete p;
   parameters_.erase(parameters_.begin() + static_cast<ptrdiff_t>(index));
 }
 

src/Bpp/Numeric/Random/RandomTools.cpp

@@ -517,10 +517,10 @@ double RandomTools::qBeta(double prob, double alpha, double beta)
   volatile double xinbta;
 
   if (alpha <= 0. || beta < 0.)
-    throw ("RandomTools::qBeta wih non positive parameters");
+    throw ("RandomTools::qBeta with non positive parameters");
 
   if (prob < 0. || prob > 1.)
-    throw ("RandomTools::qBeta wih bad probability");
+    throw ("RandomTools::qBeta with bad probability");
 
   /* initialize */
   logbeta = lnBeta(alpha, beta);

src/Bpp/Utils/AttributesTools.cpp

@@ -44,6 +44,7 @@
 #include <fstream>
 #include <algorithm>
 
+
 using namespace std;
 
 #include "AttributesTools.h"
@@ -53,6 +54,8 @@ using namespace std;
 
 using namespace bpp;
 
+std::vector<std::string> AttributesTools::vParam_;
+
 /******************************************************************************/
 
 std::vector<std::string> AttributesTools::getVector(int argc, char* argv[])
@@ -119,13 +122,16 @@ void AttributesTools::getAttributesMap(
     {
       string name  = string(arg.begin(), arg.begin() + static_cast<ptrdiff_t>(limit));
       string value = string(arg.begin() + static_cast<ptrdiff_t>(limit + delimiter.size()), arg.end());
-      // if ((name == "param") || (name == "params"))
-      // {
-      //   //Recursive inclusion:
-      //   getAttributesMapFromFile(value, am, delimiter);
-      // }
-      // else
-      am[name] = value;
+      if ((name == "param") || (name == "params"))
+      {
+        if (std::find(vParam_.begin(),vParam_.end(),value)!=vParam_.end())
+          throw Exception("Param name " + value + " already seen.");
+        
+        //Recursive inclusion:
+        getAttributesMapFromFile(value, am, delimiter);
+        vParam_.push_back(value);
+      }
+      else am[name] = value;
     }
   }
 }
@@ -162,7 +168,6 @@ void AttributesTools::actualizeAttributesMap(
 {
   for (map<string, string>::const_iterator i = atts.begin(); i != atts.end(); i++)
   {
-    if ((i->first != "param") && (i->first != "params"))
     attMap[i->first] = i->second;
   }
 }
@@ -248,14 +253,18 @@ std::map<std::string, std::string> AttributesTools::parseOptions(int args, char*
 
   // Look for a specified file with parameters:
   map<string, string> params;
-  std::map<std::string, std::string>::iterator it;
-
+  if (cmdParams.find("param") != cmdParams.end() || cmdParams.find("params") != cmdParams.end())
+  {
+    string file;
     if (cmdParams.find("param") != cmdParams.end())
     {
-    string file = cmdParams["param"];
+      file=cmdParams["param"];
+      if (std::find(vParam_.begin(),vParam_.end(),file)!=vParam_.end())
+        throw Exception("Param name " + file + " already seen.");
+
       if (!FileTools::fileExists(file))
       {
-      throw Exception("AttributesTools::parseOptions(). Parameter file not found.");
+        throw Exception("AttributesTools::parseOptions(). Parameter file not found.: " + file);
       }
       else
       {
@@ -263,53 +272,34 @@ std::map<std::string, std::string> AttributesTools::parseOptions(int args, char*
         // Actualize attributes with ones passed to command line:
         actualizeAttributesMap(params, cmdParams);
       }
+      vParam_.push_back(file);
+      
     }
-  else
+    if (cmdParams.find("params") != cmdParams.end())
     {
-    params = cmdParams;
-  }
-  // Resolve variables:
-  resolveVariables(params);
-
-  std::vector<string> mapfile;
-  std::vector<string>::iterator imapfile;
-  string file;
+      file=cmdParams["params"];
+      if (std::find(vParam_.begin(),vParam_.end(),file)!=vParam_.end())
+        throw Exception("Param name " + file + " already seen.");
 
-  while (true)
-  {
-    it = params.find("param");
-    if (it != params.end())
-    {
-      file = it->second;
-      if (std::find(mapfile.begin(), mapfile.end(), file) == mapfile.end())
+      if (!FileTools::fileExists(file))
       {
-        params.erase(it);
-        mapfile.push_back(file);
-        getAttributesMapFromFile(file, params, "=");
-        resolveVariables(params);
-        continue;
+        throw Exception("AttributesTools::parseOptions(). Parameter file not found.: " + file);
       }
       else
-        throw Exception("parsing error : Already used file " + file);
-    }
-    it = params.find("params");
-    if (it != params.end())
-    {
-      file = it->second;
-      if (find(mapfile.begin(), mapfile.end(), file) == mapfile.end())
       {
-        params.erase(it);
-        mapfile.push_back(file);
-        getAttributesMapFromFile(file, params, "=");
-        resolveVariables(params);
-        continue;
+        params = getAttributesMapFromFile(file, "=");
+        // Actualize attributes with ones passed to command line:
+        actualizeAttributesMap(params, cmdParams);
       }
-      else
-        throw Exception("parsing error : Already used file " + file);
+      vParam_.push_back(file);
     }
-    break;
   }
-
+  else
+  {
+    params = cmdParams;
+  }
+  // Resolve variables:
+  resolveVariables(params);
   return params;
 }
 

src/Bpp/Utils/AttributesTools.h

@@ -126,6 +126,14 @@ namespace bpp
  */
 class AttributesTools
 {
+private:
+  /*
+   * vector of param names already seen, to avoid infinite recursion
+   *
+   */
+  
+  static std::vector<std::string> vParam_;
+  
 public:
   AttributesTools() {}
   virtual ~AttributesTools() {}