CMakeLists.txt

@@ -61,7 +61,8 @@ else ()
   # Generate command line args (always add -c to output compressed file to stdout)
   if (${COMPRESS_PROGRAM} STREQUAL "gzip")
     # -n for no timestamp in files (reproducible builds)
-    set (COMPRESS_ARGS -c -n)
+    # -9 for maximum compression (lintian error)
+    set (COMPRESS_ARGS -c -n -9)
   else ()
     set (COMPRESS_ARGS -c)
   endif ()
@@ -74,8 +75,8 @@ if (CMAKE_INSTALL_PREFIX)
 endif (CMAKE_INSTALL_PREFIX)
 
 include (GNUInstallDirs)
-find_package (bpp-phyl 11.0.0 REQUIRED)
-find_package (bpp-popgen 7.0.0 REQUIRED)
+find_package (bpp-phyl 12.0.0 REQUIRED)
+find_package (bpp-popgen 8.0.0 REQUIRED)
 
 # Subdirectories
 add_subdirectory (bppSuite)
@@ -87,10 +88,10 @@ ENDIF(NO_DEP_CHECK)
 # Packager
 SET(CPACK_PACKAGE_NAME "bppsuite")
 SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")
-SET(CPACK_PACKAGE_VERSION "2.3.1")
+SET(CPACK_PACKAGE_VERSION "2.4.0")
 SET(CPACK_PACKAGE_VERSION_MAJOR "2")
-SET(CPACK_PACKAGE_VERSION_MINOR "3")
-SET(CPACK_PACKAGE_VERSION_PATCH "1")
+SET(CPACK_PACKAGE_VERSION_MINOR "4")
+SET(CPACK_PACKAGE_VERSION_PATCH "0")
 SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Program Suite")
 SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")
 SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")

ChangeLog

+19/03/18 -*- Version 2.4.0 -*-
+
+19/02/18 Julien Dutheil
+* Bug fixed in bppPopStats: dN and dS were inverted!
+
+10/12/17 -*- Version 2.3.2 -*-
+
 06/11/17 Julien Dutheil
 * Added estimation of kappa to bppPopStats + bugs fixed
 

Examples/MaximumLikelihood/Codons/BranchModel/ML.bpp

@@ -95,7 +95,7 @@ optimization.final = none
 optimization.verbose = 3
 
 # Parameters to ignore (for instance equilibrium frequencies)
-optimization.ignore_parameter = 
+optimization.ignore_parameters = 
 
 # Maximum number of likelihood evaluations:
 optimization.max_number_f_eval = 10000

Examples/MaximumLikelihood/Codons/CladeModel/ML.bpp

@@ -102,7 +102,7 @@ optimization.final = none
 optimization.verbose = 3
 
 # Parameters to ignore (for instance equilibrium frequencies)
-optimization.ignore_parameter = 
+optimization.ignore_parameters = 
 
 # Maximum number of likelihood evaluations:
 optimization.max_number_f_eval = 10000

Examples/MaximumLikelihood/Codons/M0/ML.bpp

@@ -87,7 +87,7 @@ optimization.final = none
 optimization.verbose = 3
 
 # Parameters to ignore (for instance equilibrium frequencies)
-optimization.ignore_parameter = 
+optimization.ignore_parameters = 
 
 # Maximum number of likelihood evaluations:
 optimization.max_number_f_eval = 10000

Examples/MaximumLikelihood/Codons/M1/ML.bpp

@@ -85,7 +85,7 @@ optimization.final = none
 optimization.verbose = 3
 
 # Parameters to ignore (for instance equilibrium frequencies)
-optimization.ignore_parameter = YNGP_M1.*Full*
+optimization.ignore_parameters = YNGP_M1.*Full*
 
 # Maximum number of likelihood evaluations:
 optimization.max_number_f_eval = 10000

Examples/MaximumLikelihood/Codons/M2/ML.bpp

@@ -85,7 +85,7 @@ optimization.final = none
 optimization.verbose = 3
 
 # Parameters to ignore (for instance equilibrium frequencies)
-optimization.ignore_parameter = YNGP_M1.*Full*
+optimization.ignore_parameters = YNGP_M1.*Full*
 
 # Maximum number of likelihood evaluations:
 optimization.max_number_f_eval = 10000

Examples/MaximumLikelihood/Nucleotides/Homogeneous/ML.bpp

@@ -86,7 +86,7 @@ optimization.final = none
 optimization.verbose = 3
 
 # Parameters to ignore (for instance equilibrium frequencies)
-optimization.ignore_parameter =
+optimization.ignore_parameters =
 
 # Maximum number of likelihood evaluations:
 optimization.max_number_f_eval = 10000

Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGG/MLNHGG.bpp

@@ -100,7 +100,7 @@ optimization.topology.tolerance.before=100
 optimization.topology.tolerance.during=100
 optimization.scale_first=no
 optimization.verbose=3
-optimization.ignore_parameter=
+optimization.ignore_parameters=
 
 # Should we write the resulting tree? none or file name.
 output.tree.file = $(DATA).ML.dnd

Examples/MaximumLikelihood/Nucleotides/NonHomogeneousGeneral/MLNH.bpp

@@ -102,7 +102,7 @@ likelihood.recursion_simple.compression = recursive
 optimization=FullD(derivatives=Newton)
 optimization.reparametrization=no
 optimization.verbose = 1
-optimization.ignore_parameter =
+optimization.ignore_parameters =
 optimization.max_number_f_eval = 10000
 optimization.tolerance = 0.000001
 optimization.message_handler = $(DATA).messages

Examples/MaximumLikelihood/Proteins/Homogeneous/ML.bpp

@@ -85,7 +85,7 @@ optimization.final = none
 optimization.verbose = 3
 
 # Parameters to ignore (for instance equilibrium frequencies)
-optimization.ignore_parameter =
+optimization.ignore_parameters =
 
 # Maximum number of likelihood evaluations:
 optimization.max_number_f_eval = 10000

README.md

@@ -6,7 +6,7 @@ BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analy
 
 ### Standalone executables 
 
-Standalone executables are available for [linux64](http://biopp.univ-montp2.fr/repos/exe/lin64/).
+Standalone executables are available for [linux64](https://github.com/BioPP/bppsuite/releases/tag/v2.3.2)
 
 [//]: [win32](http://biopp.univ-montp2.fr/repos/exe/win32/), [win64](http://biopp.univ-montp2.fr/repos/exe/win64/) and [Mac](http://biopp.univ-montp2.fr/repos/exe/mac/)
 
@@ -78,5 +78,5 @@ Many examples are available in the subdirectory of <tt>Examples</tt>.
 
 ### Documentation 
 
-Documentation can be found at http://github.com/bppsuite/releases in pdf or html.
+Documentation can be found at https://github.com/BioPP/bppsuite/releases/tag/v2.3.2 in pdf or html.
  
\ No newline at end of file

bppSuite/CMakeLists.txt

@@ -41,6 +41,7 @@ foreach (target ${bppsuite-targets})
     set_target_properties (${target} PROPERTIES LINK_SEARCH_END_STATIC TRUE)
   else (BUILD_STATIC)
     target_link_libraries (${target} ${BPP_LIBS_SHARED})
+    set_target_properties (${target} PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
   endif (BUILD_STATIC)
 endforeach (target)
 

bppSuite/bppDist.cpp

@@ -182,14 +182,14 @@ int main(int args, char ** argv)
   string mhPath = ApplicationTools::getAFilePath("optimization.message_handler", bppdist.getParams(), false, false);
   OutputStream* messenger = 
     (mhPath == "none") ? 0 :
-      (mhPath == "std") ? ApplicationTools::message :
+      (mhPath == "std") ? ApplicationTools::message.get() :
         new StlOutputStream(new ofstream(mhPath.c_str(), ios::out));
   ApplicationTools::displayResult("Message handler", mhPath);
 
   string prPath = ApplicationTools::getAFilePath("optimization.profiler", bppdist.getParams(), false, false);
   OutputStream* profiler = 
     (prPath == "none") ? 0 :
-      (prPath == "std") ? ApplicationTools::message :
+      (prPath == "std") ? ApplicationTools::message.get() :
         new StlOutputStream(new ofstream(prPath.c_str(), ios::out));
   if(profiler) profiler->setPrecision(20);
   ApplicationTools::displayResult("Profiler", prPath);
@@ -232,11 +232,11 @@ int main(int args, char ** argv)
   
   //Here it is:
   ofstream warn("warnings", ios::out);
-  ApplicationTools::warning = new StlOutputStreamWrapper(&warn);
+  shared_ptr<OutputStream> wout = ApplicationTools::warning;
+  ApplicationTools::warning.reset(new StlOutputStreamWrapper(&warn));
   tree = OptimizationTools::buildDistanceTree(distEstimation, *distMethod, parametersToIgnore, !ignoreBrLen, type, tolerance, nbEvalMax, profiler, messenger, optVerbose);
   warn.close();
-  delete ApplicationTools::warning;
-  ApplicationTools::warning = ApplicationTools::message;
+  ApplicationTools::warning = wout;
 
   string matrixPath = ApplicationTools::getAFilePath("output.matrix.file", bppdist.getParams(), false, false, "", false);
   if (matrixPath != "none")

bppSuite/bppPopStats.cpp

@@ -42,6 +42,7 @@
 #include <fstream>
 #include <iomanip>
 #include <memory>
+#include <cmath>
 
 using namespace std;
 
@@ -152,6 +153,7 @@ int main(int args, char** argv)
       if (ApplicationTools::parameterExists("input.sequence.outgroup.name", bpppopstats.getParams())) {
         vector<string> outgroups = ApplicationTools::getVectorParameter<string>("input.sequence.outgroup.name", bpppopstats.getParams(), ',', "");
         for (auto g : outgroups) {
+          ApplicationTools::displayResult("Sequence from outgroup", g);
           psc->setAsOutgroupMember(g);
         }
       }
@@ -270,7 +272,7 @@ int main(int args, char** argv)
       // Create a likelihood object:
       treeLik = new DRHomogeneousTreeLikelihood(*tree, *aln, model.get(), rDist.get());
       treeLik->initialize();
-      if (isinf(treeLik->getValue()))
+      if (std::isinf(treeLik->getValue()))
         throw Exception("Error: null likelihood. Possible cause: stop codon or numerical underflow (too many sequences).");
       // Optimize parameters:
       treeLik = dynamic_cast<DRTreeLikelihood*>(PhylogeneticsApplicationTools::optimizeParameters(treeLik, treeLik->getParameters(), bpppopstats.getParams(), "", true, true, 2));
@@ -431,8 +433,8 @@ int main(int args, char** argv)
         }
         double piS = SequenceStatistics::piSynonymous(*pscIn, *gCode);
         double piN = SequenceStatistics::piNonSynonymous(*pscIn, *gCode);
-        double nbS = SequenceStatistics::meanNumberOfSynonymousSites(*pscIn, *gCode);
-        double nbN = SequenceStatistics::meanNumberOfNonSynonymousSites(*pscIn, *gCode);
+        double nbS = SequenceStatistics::meanNumberOfSynonymousSites(*pscIn, *gCode, kappa);
+        double nbN = SequenceStatistics::meanNumberOfNonSynonymousSites(*pscIn, *gCode, kappa);
         double r = (piN / nbN) / (piS / nbS);
         ApplicationTools::displayResult("PiN:", piN);
         ApplicationTools::displayResult("PiS:", piS);
@@ -597,27 +599,22 @@ int main(int args, char** argv)
             if (codonAlphabet->isUnresolved(outgroupState) || codonAlphabet->isGap(outgroupState)) {
               out << "\tNA\tNA\tNA";
             } else {
-              if (estimateAncestor) {
-                //This is the same value as for polymorphism, we add it for having consistent output format
-                out << "\t" << CodonSiteTools::numberOfSynonymousPositions(ancestralSequence->getValue(i), *gCode, kappa);
-              } else {
-                //Also average over outgroup (Note: minState and maxState are identical in this case)
-                out << "\t" << (CodonSiteTools::numberOfSynonymousPositions(outgroupState, *gCode, kappa) +
-                                       CodonSiteTools::numberOfSynonymousPositions(minState, *gCode, kappa)) / 2.;
-              }
+              //Average over outgroup (Note: minState and maxState are identical in this case)
+              out << "\t" << (CodonSiteTools::numberOfSynonymousPositions(outgroupState, *gCode, kappa) +
+                                     CodonSiteTools::numberOfSynonymousPositions(minState, *gCode, kappa)) / 2.;
               if (nbAlleles == 1) {
                 //Compare with outgroup:
                 if (site[0] == outgroupState) {
-                  out << "\t0\t0" << endl;
+                  out << "\t0\t0";
                 } else {
                   //This is a real substitution:
-                  int nt = (int)CodonSiteTools::numberOfDifferences(outgroupState, minState, *codonAlphabet);
+                  double nt = static_cast<double>(CodonSiteTools::numberOfDifferences(outgroupState, minState, *codonAlphabet));
                   double ns = CodonSiteTools::numberOfSynonymousDifferences(outgroupState, minState, *gCode); 
-                  out << "\t" << ns << "\t" << (nt - ns);
+                  out << "\t" << (nt - ns) << "\t" << ns;
                 }
               } else {
                 //Site is polymorphic, this is not a substitution    
-                out << "\t0\t0" << endl;
+                out << "\t0\t0";
               }
             }
           }

bppSuite/bppSeqGen.cpp

@@ -79,7 +79,7 @@ using namespace bpp;
 /**
  * @brief Read trees from an input file, with segment annotations. Hudson's MS format.
  */
-void readTreesMs(ifstream& file, vector<Tree*>& trees, vector<double>& pos, unsigned int totPos) throw (Exception)
+void readTreesMs(ifstream& file, vector<Tree*>& trees, vector<double>& pos, unsigned int totPos)
 {
   string line = "";
   unsigned int segsize;
@@ -131,7 +131,7 @@ void readTreesMs(ifstream& file, vector<Tree*>& trees, vector<double>& pos, unsi
 /**
  * @brief Read trees from an input file, with segment annotations. Mailund's CoaSim format.
  */
-void readTreesCoaSim(ifstream& file, vector<Tree*>& trees, vector<double>& pos) throw (Exception)
+void readTreesCoaSim(ifstream& file, vector<Tree*>& trees, vector<double>& pos) 
 {
   string line = "";
   double begin, end;

bppSuite/bppSeqMan.cpp

@@ -298,6 +298,8 @@ int main(int args, char** argv)
     // +--------------+
     else if (cmdName == "RemoveStops")
     {
+      if (!codonAlphabet)
+        throw Exception("RemoveStops: requires a codon alphabet.");
       if (!gCode.get()) {
         string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppseqman.getParams(), "Standard", "", true, 1);
         ApplicationTools::displayResult("Genetic Code", codeDesc);
@@ -338,6 +340,8 @@ int main(int args, char** argv)
       {
         throw Exception("'RemoveColumnsWithStops' can only be used on alignment. You may consider using the 'CoerceToAlignment' command.");
       }
+      if (!codonAlphabet)
+        throw Exception("RemoveColumnsWithStops: requires a codon alphabet.");
       if (!gCode.get()) {
         string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppseqman.getParams(), "Standard", "", true, 1);
         ApplicationTools::displayResult("Genetic Code", codeDesc);
@@ -356,6 +360,8 @@ int main(int args, char** argv)
     // +---------+
     else if (cmdName == "GetCDS")
     {
+      if (!codonAlphabet)
+        throw Exception("GetCDS: requires a codon alphabet.");
       if (!gCode.get()) {
         string codeDesc = ApplicationTools::getStringParameter("genetic_code", bppseqman.getParams(), "Standard", "", true, 1);
         ApplicationTools::displayResult("Genetic Code", codeDesc);

bppsuite.spec

-%define _basename bppsuite
-%define _version 2.3.2
-%define _release 1
 %define _prefix /usr
 
 URL: https://github.com/BioPP
 
-Name: %{_basename}
-Version: %{_version}
-Release: %{_release}
+Name: bppsuite
+Version: 2.4.0
+Release: 1%{?dist}
 License: CECILL-2.0
 Vendor: The Bio++ Project
-Source: %{_basename}-%{_version}.tar.gz
+Source: %{name}-%{version}.tar.gz
 Summary: The Bio++ Program Suite
 Group: Productivity/Scientific/Other
 
-Requires: libbpp-phyl11 = %{_version}
-Requires: libbpp-seq11 = %{_version}
-Requires: libbpp-core3 = %{_version}
+Requires: libbpp-popgen8 = %{version}
+Requires: libbpp-phyl12 = %{version}
+Requires: libbpp-seq12 = %{version}
+Requires: libbpp-core4 = %{version}
 
-BuildRoot: %{_builddir}/%{_basename}-root
+BuildRoot: %{_builddir}/%{name}-root
 BuildRequires: cmake >= 2.8.11
 BuildRequires: gcc-c++ >= 4.7.0
 BuildRequires: groff
 BuildRequires: texinfo >= 4.0.0
-BuildRequires: libbpp-core3 = %{_version}
-BuildRequires: libbpp-core-devel = %{_version}
-BuildRequires: libbpp-seq11 = %{_version}
-BuildRequires: libbpp-seq-devel = %{_version}
-BuildRequires: libbpp-phyl11 = %{_version}
-BuildRequires: libbpp-phyl-devel = %{_version}
-BuildRequires: libbpp-popgen7 = %{_version}
-BuildRequires: libbpp-popgen-devel = %{_version}
+BuildRequires: libbpp-core4 = %{version}
+BuildRequires: libbpp-core-devel = %{version}
+BuildRequires: libbpp-seq12 = %{version}
+BuildRequires: libbpp-seq-devel = %{version}
+BuildRequires: libbpp-phyl12 = %{version}
+BuildRequires: libbpp-phyl-devel = %{version}
+BuildRequires: libbpp-popgen8 = %{version}
+BuildRequires: libbpp-popgen-devel = %{version}
 
 
 AutoReq: yes
@@ -90,12 +88,13 @@ rm -rf $RPM_BUILD_ROOT
 %{_prefix}/share/man/man1/*.1*
 
 %changelog
+* Mon Mar 12 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1
 * Tue Jun 06 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.1-1
 * Wed May 10 2017 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.3.0-1
 - New BppPopStats program
 - BppPhySamp is now distributed separately
 - Several bugs fixed and improvements
-* Mon Sep 28 2014 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.2.0-1
+* Mon Sep 29 2014 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.2.0-1
 - Compatibility update. Bio++ Program Suite version number is now indexed
   on Bio++'s version.
 - Programs support the --seed argument for setting the random seed.
@@ -112,5 +111,5 @@ rm -rf $RPM_BUILD_ROOT
 * Thu Mar 25 2010 Julien Dutheil <julien.dutheil@univ-montp2.fr> 0.5.0-1
 * Wed Jun 10 2009 Julien Dutheil <jdutheil@birc.au.dk> 0.4.0-1
 * Thu Dec 11 2008 Julien Dutheil <jdutheil@birc.au.dk> 0.3.1-1
-* Thu Sep 23 2008 Julien Dutheil <jdutheil@birc.au.dk> 0.3.0-1
+* Tue Sep 23 2008 Julien Dutheil <jdutheil@birc.au.dk> 0.3.0-1
 - Initial spec file.

debian/changelog

+bppsuite (2.4.0-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * Added full text of CeCILL license.
+  * Compiles with -DCMAKE_BUILD_TYPE=RelWithDebInfo to generate debug info
+    (lintian warning)
+  * Removed Vcs-Git and Vcs-Browser entries
+    (vcs-deprecated-in-debian-infrastructure)
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Sun, 08 Apr 2018 08:46:29 +0200
+
 bppsuite (2.3.2-1) unstable; urgency=medium
 
   [ Julien Dutheil ]

debian/control

@@ -7,11 +7,9 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
                texinfo,
-               libbpp-phyl-dev (>= 2.3.2),
-               libbpp-popgen-dev (>= 2.3.2)
+               libbpp-phyl-dev (>= 2.4.0),
+               libbpp-popgen-dev (>= 2.4.0)
 Standards-Version: 4.1.3
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bppsuite.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/bppsuite.git
 Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
 
 Package: bppsuite