This is an automated email from the git hooks/post-receive script. jdutheil-guest pushed a commit to branch master in repository libbpp-phyl.
commit d6dea21173b20b172065d3357d6bba9d5ae69327 Author: Julien Y. Dutheil <[email protected]> Date: Tue Feb 6 13:42:17 2018 +0100 Version 2.3.2. --- debian/changelog | 7 ++ debian/control | 6 +- ...-unit-tests-compilation-on-some-platforms.patch | 19 --- .../patches/correct_constructors_inheritance.patch | 48 ++++++++ debian/patches/relax_test_timeout.patch | 13 -- debian/patches/remove_deprecated_warnings.patch | 98 --------------- debian/patches/series | 6 +- debian/patches/test_likelihood_clock.patch | 67 ----------- debian/patches/test_mapping.patch | 132 --------------------- debian/patches/unforce-cxxflags.patch | 2 +- 10 files changed, 60 insertions(+), 338 deletions(-) diff --git a/debian/changelog b/debian/changelog index 4ebfdee..f6e47cb 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +libbpp-phyl (2.3.2-1) UNRELEASED; urgency=medium + + [ Julien Dutheil ] + * Standards-Version: 4.1.2 + + -- Julien Dutheil <[email protected]> Mon, 05 Feb 2018 20:59:41 +0200 + libbpp-phyl (2.3.1-10) unstable; urgency=medium [ Julien Dutheil ] diff --git a/debian/control b/debian/control index 39df795..5bea196 100644 --- a/debian/control +++ b/debian/control @@ -7,8 +7,8 @@ Priority: optional Build-Depends: debhelper (>= 10), cmake, d-shlibs (>= 0.80), - libbpp-seq-dev (>= 2.3.1) -Standards-Version: 4.0.1 + libbpp-seq-dev (>= 2.3.2) +Standards-Version: 4.1.2 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-phyl.git Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-phyl.git Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page @@ -18,7 +18,7 @@ Architecture: any Section: libdevel Depends: libbpp-phyl11 (= ${binary:Version}), ${misc:Depends}, - libbpp-seq-dev (>= 2.3.1) + libbpp-seq-dev (>= 2.3.2) Description: Bio++ Phylogenetic library development files Bio++ is a set of C++ libraries for Bioinformatics, including sequence analysis, phylogenetics, molecular evolution and population genetics. diff --git a/debian/patches/0002-Fixed-unit-tests-compilation-on-some-platforms.patch b/debian/patches/0002-Fixed-unit-tests-compilation-on-some-platforms.patch deleted file mode 100644 index e576257..0000000 --- a/debian/patches/0002-Fixed-unit-tests-compilation-on-some-platforms.patch +++ /dev/null @@ -1,19 +0,0 @@ -From 40b4ee6fb20750e6aacbeaf67cba4f87ed88972a Mon Sep 17 00:00:00 2001 -From: "Julien Y. Dutheil" <[email protected]> -Date: Tue, 27 Jun 2017 10:45:09 +0200 -Subject: [PATCH 2/2] Fixed unit tests compilation on some platforms. - ---- - test/CMakeLists.txt | 1 + - 1 file changed, 1 insertion(+) - ---- a/test/CMakeLists.txt -+++ b/test/CMakeLists.txt -@@ -16,6 +16,7 @@ foreach (test_cpp_file ${test_cpp_files} - get_filename_component (test_name ${test_cpp_file} NAME_WE) - add_executable (${test_name} ${test_cpp_file}) - target_link_libraries (${test_name} ${PROJECT_NAME}-shared) -+ set_target_properties (${test_name} PROPERTIES POSITION_INDEPENDENT_CODE TRUE) - add_test ( - NAME ${test_name} - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} diff --git a/debian/patches/correct_constructors_inheritance.patch b/debian/patches/correct_constructors_inheritance.patch new file mode 100644 index 0000000..e5a74a9 --- /dev/null +++ b/debian/patches/correct_constructors_inheritance.patch @@ -0,0 +1,48 @@ +diff --git a/src/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h b/src/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h +index 93e8f47..593441d 100644 +--- a/src/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h ++++ b/src/Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h +@@ -50,7 +50,6 @@ class ConstantRateDistribution: + { + public: + ConstantRateDistribution(): +- AbstractParameterAliasable("Constant."), + ConstantDistribution(1.) + { + resetParameters_(); +diff --git a/src/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h b/src/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h +index e647f63..7373643 100644 +--- a/src/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h ++++ b/src/Bpp/Phyl/Model/RateDistribution/ExponentialDiscreteRateDistribution.h +@@ -50,7 +50,6 @@ class ExponentialDiscreteRateDistribution: + { + public: + ExponentialDiscreteRateDistribution(size_t nbClasses): +- AbstractParameterAliasable("Exponential."), + ExponentialDiscreteDistribution(nbClasses, 1.) + { + deleteParameter_(0); +diff --git a/src/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h b/src/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h +index 5159ec1..7cbb799 100644 +--- a/src/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h ++++ b/src/Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h +@@ -50,7 +50,6 @@ class GammaDiscreteRateDistribution: + { + public: + GammaDiscreteRateDistribution(size_t nbClasses, double alpha = 1.): +- AbstractParameterAliasable("Gamma."), + GammaDiscreteDistribution(nbClasses, alpha, alpha) + { + aliasParameters("alpha", "beta"); +diff --git a/src/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h b/src/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h +index 75eb37e..bde7c9c 100644 +--- a/src/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h ++++ b/src/Bpp/Phyl/Model/RateDistribution/GaussianDiscreteRateDistribution.h +@@ -50,7 +50,6 @@ class GaussianDiscreteRateDistribution: + { + public: + GaussianDiscreteRateDistribution(size_t nbClasses, double sigma): +- AbstractParameterAliasable("Gaussian."), + GaussianDiscreteDistribution(nbClasses, 1., sigma) + { + deleteParameter_(0); diff --git a/debian/patches/relax_test_timeout.patch b/debian/patches/relax_test_timeout.patch deleted file mode 100644 index eadaa9c..0000000 --- a/debian/patches/relax_test_timeout.patch +++ /dev/null @@ -1,13 +0,0 @@ -Author: Julien Y. Dutheil <[email protected]> -Date: Sat Jun 24 23:41:39 2017 +0200 -Description: Added longer timeout for tests. - ---- a/test/CMakeLists.txt -+++ b/test/CMakeLists.txt -@@ -21,4 +21,6 @@ foreach (test_cpp_file ${test_cpp_files} - WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR} - COMMAND ${test_name} - ) -+ set_tests_properties (${test_name} PROPERTIES TIMEOUT 60000) - endforeach (test_cpp_file) -+ diff --git a/debian/patches/remove_deprecated_warnings.patch b/debian/patches/remove_deprecated_warnings.patch deleted file mode 100644 index 9809bb7..0000000 --- a/debian/patches/remove_deprecated_warnings.patch +++ /dev/null @@ -1,98 +0,0 @@ -Author: Julien Y. Dutheil <[email protected]> -Date: Sun Jul 16 10:45:20 2017 +0200 -Description: Remove deprecated warnings - ---- a/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h -+++ b/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h -@@ -74,7 +74,7 @@ class AbstractNonHomogeneousTreeLikeliho - siteModelDescriptions_(), index_(0), nbModels_(modelSet->getNumberOfModels()) - { - for (size_t i = 0; i < nbModels_; ++i) -- siteModelDescriptions_.push_back(ConstNoPartitionSiteModelDescription(modelSet->getModel(i), modelSet->getNodesWithModel(i))); -+ siteModelDescriptions_.push_back(ConstNoPartitionSiteModelDescription(modelSet->getSubstitutionModel(i), modelSet->getNodesWithModel(i))); - } - - public: ---- a/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp -+++ b/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp -@@ -142,7 +142,7 @@ void DRNonHomogeneousTreeLikelihood::set - data_ = PatternTools::getSequenceSubset(sites, *tree_->getRootNode()); - if (verbose_) - ApplicationTools::displayTask("Initializing data structure"); -- likelihoodData_->initLikelihoods(*data_, *modelSet_->getModel(0)); // We assume here that all models have the same number of states, and that they have the same 'init' method, -+ likelihoodData_->initLikelihoods(*data_, *modelSet_->getSubstitutionModel(0)); // We assume here that all models have the same number of states, and that they have the same 'init' method, - // Which is a reasonable assumption as long as they share the same alphabet. - if (verbose_) - ApplicationTools::displayTaskDone(); ---- a/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp -+++ b/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp -@@ -140,7 +140,7 @@ void RNonHomogeneousTreeLikelihood::setD - if (data_) delete data_; - data_ = PatternTools::getSequenceSubset(sites, *tree_->getRootNode()); - if (verbose_) ApplicationTools::displayTask("Initializing data structure"); -- likelihoodData_->initLikelihoods(*data_, *modelSet_->getModel(0)); //We assume here that all models have the same number of states, and that they have the same 'init' method, -+ likelihoodData_->initLikelihoods(*data_, *modelSet_->getSubstitutionModel(0)); //We assume here that all models have the same number of states, and that they have the same 'init' method, - //Which is a reasonable assumption as long as they share the same alphabet. - if (verbose_) ApplicationTools::displayTaskDone(); - ---- a/src/Bpp/Phyl/Model/SubstitutionModelSet.h -+++ b/src/Bpp/Phyl/Model/SubstitutionModelSet.h -@@ -247,7 +247,6 @@ public: - * @param i Index of the model in the set. - * @return A pointer toward the corresponding model. - */ -- - const SubstitutionModel* getModel(size_t i) const throw (IndexOutOfBoundsException) - { - std::cerr << "#warning : SubstitutionModelSet::getModel function is deprecated in Bio++ 2.3.0. Replace it with SubstitutionModelSet::getSubstitutionModel." << std::endl; ---- a/test/test_likelihood_nh.cpp -+++ b/test/test_likelihood_nh.cpp -@@ -129,11 +129,11 @@ int main() { - cout << c1 << ": " << tl.getValue() << "\t" << c2 << ": " << tl2.getValue() << endl; - - for (size_t i = 0; i < nmodels; ++i) { -- cout << modelSet2->getModel(i)->getParameter("theta").getValue() << "\t" << modelSet3->getModel(i)->getParameter("theta").getValue() << endl; -- //if (abs(modelSet2->getModel(i)->getParameter("theta").getValue() - modelSet3->getModel(i)->getParameter("theta").getValue()) > 0.1) -+ cout << modelSet2->getSubstitutionModel(i)->getParameter("theta").getValue() << "\t" << modelSet3->getSubstitutionModel(i)->getParameter("theta").getValue() << endl; -+ //if (abs(modelSet2->getSubstitutionModel(i)->getParameter("theta").getValue() - modelSet3->getSubstitutionModel(i)->getParameter("theta").getValue()) > 0.1) - // return 1; -- thetasEst1[i] += modelSet2->getModel(i)->getParameter("theta").getValue(); -- thetasEst2[i] += modelSet3->getModel(i)->getParameter("theta").getValue(); -+ thetasEst1[i] += modelSet2->getSubstitutionModel(i)->getParameter("theta").getValue(); -+ thetasEst2[i] += modelSet3->getSubstitutionModel(i)->getParameter("theta").getValue(); - } - } - thetasEst1 /= static_cast<double>(nrep); ---- a/test/test_simulations.cpp -+++ b/test/test_simulations.cpp -@@ -104,8 +104,8 @@ int main() { - - //Now compare estimated values to real ones: - for (size_t i = 0; i < thetas.size(); ++i) { -- cout << thetas[i] << "\t" << modelSet2->getModel(i)->getParameter("theta").getValue() << endl; -- double diff = abs(thetas[i] - modelSet2->getModel(i)->getParameter("theta").getValue()); -+ cout << thetas[i] << "\t" << modelSet2->getSubstitutionModel(i)->getParameter("theta").getValue() << endl; -+ double diff = abs(thetas[i] - modelSet2->getSubstitutionModel(i)->getParameter("theta").getValue()); - if (diff > 0.1) - return 1; - } -@@ -119,7 +119,7 @@ int main() { - VectorSiteContainer sites2(seqNames, alphabet); - for (unsigned int i = 0; i < n; ++i) { - RASiteSimulationResult* result = simulator.dSimulateSite(); -- unique_ptr<Site> site(result->getSite(*simulator.getSubstitutionModelSet()->getModel(0))); -+ unique_ptr<Site> site(result->getSite(*simulator.getSubstitutionModelSet()->getSubstitutionModel(0))); - site->setPosition(static_cast<int>(i)); - sites2.addSite(*site, false); - delete result; -@@ -136,8 +136,8 @@ int main() { - - //Now compare estimated values to real ones: - for (size_t i = 0; i < thetas.size(); ++i) { -- cout << thetas[i] << "\t" << modelSet3->getModel(i)->getParameter("theta").getValue() << endl; -- double diff = abs(thetas[i] - modelSet3->getModel(i)->getParameter("theta").getValue()); -+ cout << thetas[i] << "\t" << modelSet3->getSubstitutionModel(i)->getParameter("theta").getValue() << endl; -+ double diff = abs(thetas[i] - modelSet3->getSubstitutionModel(i)->getParameter("theta").getValue()); - if (diff > 0.1) - return 1; - } diff --git a/debian/patches/series b/debian/patches/series index 572f22c..305f256 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,6 +1,2 @@ unforce-cxxflags.patch -relax_test_timeout.patch -0002-Fixed-unit-tests-compilation-on-some-platforms.patch -remove_deprecated_warnings.patch -test_likelihood_clock.patch -test_mapping.patch +correct_constructors_inheritance.patch diff --git a/debian/patches/test_likelihood_clock.patch b/debian/patches/test_likelihood_clock.patch deleted file mode 100644 index 7cdbeda..0000000 --- a/debian/patches/test_likelihood_clock.patch +++ /dev/null @@ -1,67 +0,0 @@ -Author: Julien Y. Dutheil <[email protected]> -Date: Sun Jul 16 10:45:20 2017 +0200 -Description: Relax test constraint - ---- a/test/test_likelihood_clock.cpp -+++ b/test/test_likelihood_clock.cpp -@@ -41,7 +41,7 @@ knowledge of the CeCILL license and that - #include <Bpp/Seq/Alphabet/AlphabetTools.h> - #include <Bpp/Phyl/TreeTemplate.h> - #include <Bpp/Phyl/Model/Nucleotide/T92.h> --#include <Bpp/Phyl/Model/RateDistribution/GammaDiscreteRateDistribution.h> -+#include <Bpp/Phyl/Model/RateDistribution/ConstantRateDistribution.h> - #include <Bpp/Phyl/Simulation/HomogeneousSequenceSimulator.h> - #include <Bpp/Phyl/Likelihood/RHomogeneousTreeLikelihood.h> - #include <Bpp/Phyl/Likelihood/RHomogeneousClockTreeLikelihood.h> -@@ -60,7 +60,7 @@ void fitModelH(SubstitutionModel* model, - ApplicationTools::displayResult("Test model", model->getName()); - cout << setprecision(20) << tl.getValue() << endl; - ApplicationTools::displayResult("* initial likelihood", tl.getValue()); -- if (abs(tl.getValue() - initialValue) > 0.0001) -+ if (abs(tl.getValue() - initialValue) > 0.001) - throw Exception("Incorrect initial value."); - unique_ptr<OutputStream> messenger(new StlOutputStream(new ofstream("messages.txt", ios::out))); - unique_ptr<OutputStream> profiler(new StlOutputStream(new ofstream("profile.txt", ios::out))); -@@ -69,7 +69,7 @@ void fitModelH(SubstitutionModel* model, - cout << setprecision(20) << tl.getValue() << endl; - ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue()); - tl.getParameters().printParameters(cout); -- if (abs(tl.getValue() - finalValue) > 0.0001) -+ if (abs(tl.getValue() - finalValue) > 0.001) - throw Exception("Incorrect final value."); - } - -@@ -92,7 +92,7 @@ void fitModelHClock(SubstitutionModel* m - ApplicationTools::displayResult("* likelihood after full optimization", tl.getValue()); - tl.getParameters().printParameters(cout); - if (abs(tl.getValue() - finalValue) > 0.001) -- throw Exception("Incorrect final value."); -+ throw Exception("Incorrect final value:" + TextTools::toString(tl.getValue()) + "<>" + TextTools::toString(finalValue)); - } - - int main() { -@@ -103,7 +103,7 @@ int main() { - - const NucleicAlphabet* alphabet = &AlphabetTools::DNA_ALPHABET; - SubstitutionModel* model = new T92(alphabet, 3.); -- DiscreteDistribution* rdist = new GammaDiscreteRateDistribution(4, 1.0); -+ DiscreteDistribution* rdist = new ConstantRateDistribution(); - - VectorSiteContainer sites(alphabet); - sites.addSequence(BasicSequence("A", "AAATGGCTGTGCACGTC", alphabet)); -@@ -112,13 +112,13 @@ int main() { - sites.addSequence(BasicSequence("D", "CAACGGGAGTGCGCCTA", alphabet)); - - try { -- fitModelH(model, rdist, *tree, sites, 93.017264552603336369, 71.265543199977557265); -+ fitModelH(model, rdist, *tree, sites, 94.3957, 71.2657); - } catch (Exception& ex) { - cerr << ex.what() << endl; - return 1; - } - try { -- fitModelHClock(model, rdist, *tree, sites, 92.27912072473920090943, 71.26554020984087856050); -+ fitModelHClock(model, rdist, *tree, sites, 92.3295, 71.2657); - } catch (Exception& ex) { - cerr << ex.what() << endl; - return 1; diff --git a/debian/patches/test_mapping.patch b/debian/patches/test_mapping.patch deleted file mode 100644 index bd9f283..0000000 --- a/debian/patches/test_mapping.patch +++ /dev/null @@ -1,132 +0,0 @@ -Author: Julien Y. Dutheil <[email protected]> -Date: Sun Jul 16 10:45:20 2017 +0200 -Description: More sensible tests - ---- a/test/test_mapping.cpp -+++ b/test/test_mapping.cpp -@@ -64,7 +64,8 @@ using namespace bpp; - using namespace std; - - int main() { -- TreeTemplate<Node>* tree = TreeTemplateTools::parenthesisToTree("((A:0.001, B:0.002):0.008,C:0.01,D:0.1);"); -+ try { -+ TreeTemplate<Node>* tree = TreeTemplateTools::parenthesisToTree("((A:0.001, B:0.002):0.008,C:0.01,D:0.02);"); - vector<int> ids = tree->getNodesId(); - ids.pop_back(); //Ignore root - -@@ -79,23 +80,12 @@ int main() { - TotalSubstitutionRegister* totReg = new TotalSubstitutionRegister(model); - ComprehensiveSubstitutionRegister* detReg = new ComprehensiveSubstitutionRegister(model); - -- -- cout << "test mem" << endl; -- ProteicAlphabet* alphabet2 = new ProteicAlphabet(); -- ReversibleSubstitutionModel* model2 = new JTT92(alphabet2); -- AlphabetIndex1* ind = new GranthamAAVolumeIndex(); -- for (size_t i = 0; i < 1000000; i++) { -- cout << i << endl; -- unique_ptr<DecompositionReward> d(new DecompositionReward(model2, ind)); -- } -- cout << "done" << endl; -- -- unsigned int n = 20000; -+ size_t n = 50000; - vector< vector<double> > realMap(n); - vector< vector< vector<double> > > realMapTotal(n); - vector< vector< vector<double> > > realMapDetailed(n); - VectorSiteContainer sites(tree->getLeavesNames(), alphabet); -- for (unsigned int i = 0; i < n; ++i) { -+ for (size_t i = 0; i < n; ++i) { - ApplicationTools::displayGauge(i, n - 1, '='); - unique_ptr<RASiteSimulationResult> result(simulator.dSimulateSite()); - realMap[i].resize(ids.size()); -@@ -108,12 +98,10 @@ int main() { - result->getSubstitutionCount(ids[j], *totReg, realMapTotal[i][j]); - result->getSubstitutionCount(ids[j], *detReg, realMapDetailed[i][j]); - if (realMapTotal[i][j][0] != realMap[i][j]) { -- cerr << "Error, total substitution register provides wrong result." << endl; -- return 1; -+ throw Exception("Error, total substitution register provides wrong result."); - } - if (abs(VectorTools::sum(realMapDetailed[i][j]) - realMap[i][j]) > 0.000001) { -- cerr << "Error, detailed substitution register provides wrong result." << endl; -- return 1; -+ throw Exception("Error, detailed substitution register provides wrong result."); - } - } - unique_ptr<Site> site(result->getSite(*model)); -@@ -130,9 +118,10 @@ int main() { - drhtl.initialize(); - cout << drhtl.getValue() << endl; - -+ //Laplace transforms: - SubstitutionCount* sCountAna = new LaplaceSubstitutionCount(model, 10); - Matrix<double>* m = sCountAna->getAllNumbersOfSubstitutions(0.001, 1); -- cout << "Analytical total count:" << endl; -+ cout << "Analytical (Laplace) total count:" << endl; - MatrixTools::print(*m); - delete m; - ProbabilisticSubstitutionMapping* probMapAna = -@@ -237,7 +226,7 @@ int main() { - //Check per branch: - - //1. Total: -- for (unsigned int j = 0; j < ids.size(); ++j) { -+ for (size_t j = 0; j < ids.size(); ++j) { - double totalReal = 0; - double totalObs1 = 0; - double totalObs2 = 0; -@@ -246,7 +235,7 @@ int main() { - double totalObs5 = 0; - double totalObs6 = 0; - double totalObs7 = 0; -- for (unsigned int i = 0; i < n; ++i) { -+ for (size_t i = 0; i < n; ++i) { - totalReal += realMap[i][j]; - totalObs1 += probMapAna->getNumberOfSubstitutions(ids[j], i, 0); - totalObs2 += probMapTot->getNumberOfSubstitutions(ids[j], i, 0); -@@ -258,16 +247,16 @@ int main() { - } - if (tree->isLeaf(ids[j])) cout << tree->getNodeName(ids[j]) << "\t"; - cout << tree->getDistanceToFather(ids[j]) << "\t" << totalReal << "\t" << totalObs1 << "\t" << totalObs2 << "\t" << totalObs3 << "\t" << totalObs4 << "\t" << totalObs5 << "\t" << totalObs6 << "\t" << totalObs7 << endl; -- if (abs(totalReal - totalObs1) / totalReal > 0.1) return 1; -- if (abs(totalReal - totalObs2) / totalReal > 0.1) return 1; -- if (abs(totalReal - totalObs3) / totalReal > 0.1) return 1; -- if (abs(totalReal - totalObs4) / totalReal > 0.1) return 1; -- if (abs(totalReal - totalObs5) / totalReal > 0.1) return 1; -- if (abs(totalReal - totalObs6) / totalReal > 0.1) return 1; -- if (abs(totalReal - totalObs7) / totalReal > 0.1) return 1; -+ if (abs(totalReal - totalObs1) / totalReal > 0.1) throw Exception("Laplace substitution mapping failed, observed: " + TextTools::toString(totalObs1) + ", expected " + TextTools::toString(totalReal)); -+ //if (abs(totalReal - totalObs2) / totalReal > 0.1) return 1; //We do not expect the naive mapping to actually give an accurate result! -+ //if (abs(totalReal - totalObs3) / totalReal > 0.1) return 1; -+ if (abs(totalReal - totalObs4) / totalReal > 0.1) throw Exception("Uniformization (total) substitution mapping failed, observed: " + TextTools::toString(totalObs4) + ", expected " + TextTools::toString(totalReal)); -+ if (abs(totalReal - totalObs5) / totalReal > 0.1) throw Exception("Uniformization (detailed) substitution mapping failed, observed: " + TextTools::toString(totalObs5) + ", expected " + TextTools::toString(totalReal)); -+ if (abs(totalReal - totalObs6) / totalReal > 0.1) throw Exception("Decomposition (total) substitution mapping failed, observed: " + TextTools::toString(totalObs6) + ", expected " + TextTools::toString(totalReal)); -+ if (abs(totalReal - totalObs7) / totalReal > 0.1) throw Exception("Decomposition (detailed) substitution mapping failed, observed: " + TextTools::toString(totalObs7) + ", expected " + TextTools::toString(totalReal)); - } - //2. Detail: -- for (unsigned int j = 0; j < ids.size(); ++j) { -+ for (size_t j = 0; j < ids.size(); ++j) { - vector<double> real(4, 0); - vector<double> obs1(4, 0); - vector<double> obs2(4, 0); -@@ -283,7 +272,7 @@ int main() { - } - if (tree->isLeaf(ids[j])) cout << tree->getNodeName(ids[j]) << "\t"; - cout << tree->getDistanceToFather(ids[j]) << "\t"; -- for (unsigned int t = 0; t < 4; ++t) { -+ for (size_t t = 0; t < 4; ++t) { - cout << obs1[t] << "/" << real[t] << "\t"; - cout << obs2[t] << "/" << real[t] << "\t"; - cout << obs3[t] << "/" << real[t] << "\t"; -@@ -306,5 +295,10 @@ int main() { - delete probMapUniTot; - delete probMapUniDet; - //return (abs(obs - 0.001) < 0.001 ? 0 : 1); -+ } catch (exception& e) { -+ cout << "Test failed. Reason:" << endl; -+ cout << e.what() << endl; -+ return 1; -+ } - return 0; - } diff --git a/debian/patches/unforce-cxxflags.patch b/debian/patches/unforce-cxxflags.patch index c2e404d..eecdb93 100644 --- a/debian/patches/unforce-cxxflags.patch +++ b/debian/patches/unforce-cxxflags.patch @@ -11,7 +11,7 @@ Comment: Upstream version 2.3.0 now has additional -std=c++11 which might # Compile options -set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion") -+# set (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion") ++set (CMAKE_CXX_FLAGS "-std=c++11 -Wno-deprecated -g") IF(NOT CMAKE_BUILD_TYPE) SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libbpp-phyl.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
