[med-svn] [libbpp-phyl] 01/01: Added patch to remove deprecation warnings.
Julien Dutheil
jdutheil-guest at moszumanska.debian.org
Fri Jul 14 12:08:34 UTC 2017
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jdutheil-guest pushed a commit to branch master
in repository libbpp-phyl.
commit dc0e95c149ecda048f87cd1facb48522800fb8c9
Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
Date: Fri Jul 14 14:07:02 2017 +0200
Added patch to remove deprecation warnings.
These warnings, generated in loops, might explain why some unit tests
were failing because of timeout.
---
debian/patches/remove_deprecated_warnings.patch | 106 ++++++++++++++++++++++++
debian/patches/series | 1 +
2 files changed, 107 insertions(+)
diff --git a/debian/patches/remove_deprecated_warnings.patch b/debian/patches/remove_deprecated_warnings.patch
new file mode 100644
index 0000000..d8f89f3
--- /dev/null
+++ b/debian/patches/remove_deprecated_warnings.patch
@@ -0,0 +1,106 @@
+diff --git a/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h b/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
+index cc1b85a..1bf7a5b 100644
+--- a/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
++++ b/src/Bpp/Phyl/Likelihood/AbstractNonHomogeneousTreeLikelihood.h
+@@ -74,7 +74,7 @@ class AbstractNonHomogeneousTreeLikelihood:
+ 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:
+diff --git a/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp b/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
+index dafd301..ccf34e8 100644
+--- a/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
++++ b/src/Bpp/Phyl/Likelihood/DRNonHomogeneousTreeLikelihood.cpp
+@@ -142,7 +142,7 @@ void DRNonHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (
+ 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();
+diff --git a/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp b/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
+index f736bf4..05a4c8c 100644
+--- a/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
++++ b/src/Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.cpp
+@@ -140,7 +140,7 @@ void RNonHomogeneousTreeLikelihood::setData(const SiteContainer& sites) throw (E
+ 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();
+
+diff --git a/src/Bpp/Phyl/Model/SubstitutionModelSet.h b/src/Bpp/Phyl/Model/SubstitutionModelSet.h
+index fbb6b3c..97a027b 100644
+--- 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;
+diff --git a/test/test_likelihood_nh.cpp b/test/test_likelihood_nh.cpp
+index b4cd485..1486b80 100644
+--- 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);
+diff --git a/test/test_simulations.cpp b/test/test_simulations.cpp
+index fa97a9c..f4fea6c 100644
+--- 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 0bc967d..771eb4d 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
relax_test_timeout.patch
0001-Decreased-threshold-for-application-to-a-broader-ran.patch
0002-Fixed-unit-tests-compilation-on-some-platforms.patch
+remove_deprecated_warnings.patch
--
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