[med-svn] [libbpp-core] 02/02: Added patch for gcc7.
Julien Dutheil
jdutheil-guest at moszumanska.debian.org
Mon Feb 5 12:11:24 UTC 2018
This is an automated email from the git hooks/post-receive script.
jdutheil-guest pushed a commit to branch master
in repository libbpp-core.
commit 7a94d80ca0f6bd893ae39135be56fe3d9ad31af1
Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
Date: Mon Feb 5 13:11:51 2018 +0100
Added patch for gcc7.
---
debian/patches/gcc-7.patch | 317 +++++++++++++++++++++++++++++++++++++++++++++
1 file changed, 317 insertions(+)
diff --git a/debian/patches/gcc-7.patch b/debian/patches/gcc-7.patch
new file mode 100644
index 0000000..3f41eb0
--- /dev/null
+++ b/debian/patches/gcc-7.patch
@@ -0,0 +1,317 @@
+diff --git a/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h b/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h
+index 64b90e4..c953cdc 100644
+--- a/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h
++++ b/src/Bpp/Numeric/Prob/AbstractDiscreteDistribution.h
+@@ -58,7 +58,7 @@ namespace bpp
+ */
+ class AbstractDiscreteDistribution :
+ public virtual DiscreteDistribution,
+- public virtual AbstractParameterAliasable
++ public AbstractParameterAliasable
+ {
+
+ public:
+diff --git a/src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp b/src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp
+index dc4d0f6..8c62aec 100644
+--- a/src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp
++++ b/src/Bpp/Numeric/Prob/BetaDiscreteDistribution.cpp
+@@ -52,7 +52,6 @@ using namespace std;
+ /** Constructor: **************************************************************/
+
+ BetaDiscreteDistribution::BetaDiscreteDistribution(size_t n, double alpha, double beta) :
+- AbstractParameterAliasable("Beta."),
+ AbstractDiscreteDistribution(n,NumConstants::VERY_TINY(),"Beta."), alpha_(alpha), beta_(beta), diffln_(0)
+ {
+ addParameter_(new Parameter("Beta.alpha", alpha, new IntervalConstraint(1, 0.0001, true), true));
+@@ -67,14 +66,12 @@ BetaDiscreteDistribution::BetaDiscreteDistribution(size_t n, double alpha, doubl
+ }
+
+ BetaDiscreteDistribution::BetaDiscreteDistribution(const BetaDiscreteDistribution& bdd) :
+- AbstractParameterAliasable(bdd),
+ AbstractDiscreteDistribution(bdd), alpha_(bdd.alpha_), beta_(bdd.beta_), diffln_(bdd.diffln_)
+ {
+ }
+
+ BetaDiscreteDistribution& BetaDiscreteDistribution::operator=(const BetaDiscreteDistribution& bdd)
+ {
+- AbstractParameterAliasable::operator=(bdd);
+ AbstractDiscreteDistribution::operator=(bdd);
+
+ alpha_=bdd.alpha_;
+diff --git a/src/Bpp/Numeric/Prob/ConstantDistribution.cpp b/src/Bpp/Numeric/Prob/ConstantDistribution.cpp
+index 600f19b..933e3b3 100644
+--- a/src/Bpp/Numeric/Prob/ConstantDistribution.cpp
++++ b/src/Bpp/Numeric/Prob/ConstantDistribution.cpp
+@@ -48,7 +48,6 @@ using namespace std;
+ /******************************************************************************/
+
+ ConstantDistribution::ConstantDistribution(double value):
+- AbstractParameterAliasable("Constant."),
+ AbstractDiscreteDistribution(1, "Constant."),
+ value_(value)
+ {
+@@ -57,14 +56,12 @@ ConstantDistribution::ConstantDistribution(double value):
+ }
+
+ ConstantDistribution::ConstantDistribution(const ConstantDistribution& cd) :
+- AbstractParameterAliasable(cd),
+ AbstractDiscreteDistribution(cd),
+ value_(cd.value_)
+ {}
+
+ ConstantDistribution& ConstantDistribution::operator=(const ConstantDistribution& cd)
+ {
+- AbstractParameterAliasable::operator=(cd);
+ AbstractDiscreteDistribution::operator=(cd);
+ value_=cd.value_;
+
+diff --git a/src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp b/src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp
+index f4ef78d..f1937f8 100644
+--- a/src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp
++++ b/src/Bpp/Numeric/Prob/GammaDiscreteDistribution.cpp
+@@ -52,7 +52,6 @@ using namespace std;
+ /** Constructor: **************************************************************/
+
+ GammaDiscreteDistribution::GammaDiscreteDistribution(size_t n, double alpha, double beta, double minimumAlpha, double minimumBeta, bool paramOffset, double offset) :
+- AbstractParameterAliasable("Gamma."),
+ AbstractDiscreteDistribution(n, "Gamma."),
+ alpha_(alpha),
+ beta_(beta),
+@@ -76,7 +75,6 @@ GammaDiscreteDistribution::GammaDiscreteDistribution(size_t n, double alpha, dou
+ }
+
+ GammaDiscreteDistribution::GammaDiscreteDistribution(const GammaDiscreteDistribution& gdd) :
+- AbstractParameterAliasable(gdd),
+ AbstractDiscreteDistribution(gdd),
+ alpha_(gdd.alpha_),
+ beta_(gdd.beta_),
+@@ -87,7 +85,6 @@ GammaDiscreteDistribution::GammaDiscreteDistribution(const GammaDiscreteDistribu
+
+ GammaDiscreteDistribution& GammaDiscreteDistribution::operator=(const GammaDiscreteDistribution& gdd)
+ {
+- AbstractParameterAliasable::operator=(gdd);
+ AbstractDiscreteDistribution::operator=(gdd);
+ alpha_=gdd.alpha_;
+ beta_=gdd.beta_;
+diff --git a/src/Bpp/Numeric/Prob/UniformDiscreteDistribution.cpp b/src/Bpp/Numeric/Prob/UniformDiscreteDistribution.cpp
+index 1d2d03a..945f3c9 100644
+--- a/src/Bpp/Numeric/Prob/UniformDiscreteDistribution.cpp
++++ b/src/Bpp/Numeric/Prob/UniformDiscreteDistribution.cpp
+@@ -51,7 +51,6 @@ using namespace std;
+ /** Constructor: **************************************************************/
+
+ UniformDiscreteDistribution::UniformDiscreteDistribution(unsigned int n, double min, double max) :
+- AbstractParameterAliasable("Uniform."),
+ AbstractDiscreteDistribution(n,"Uniform."),
+ min_((min<max)?min:max),
+ max_((min<max)?max:min)
+@@ -63,7 +62,6 @@ UniformDiscreteDistribution::UniformDiscreteDistribution(unsigned int n, double
+ }
+
+ UniformDiscreteDistribution::UniformDiscreteDistribution(const UniformDiscreteDistribution& udd) :
+- AbstractParameterAliasable(udd),
+ AbstractDiscreteDistribution(udd),
+ min_(udd.min_),
+ max_(udd.max_)
+@@ -72,7 +70,6 @@ UniformDiscreteDistribution::UniformDiscreteDistribution(const UniformDiscreteDi
+
+ UniformDiscreteDistribution& UniformDiscreteDistribution::operator=(const UniformDiscreteDistribution& udd)
+ {
+- AbstractParameterAliasable::operator=(udd);
+ AbstractDiscreteDistribution::operator=(udd);
+ min_=udd.min_;
+ max_=udd.max_;
+diff --git a/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.cpp b/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.cpp
+index f63c9fb..8ddec89 100644
+--- a/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.cpp
++++ b/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.cpp
+@@ -51,7 +51,6 @@ using namespace std;
+ /****************************************************************/
+
+ ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(size_t n, double lambda) :
+- AbstractParameterAliasable("Exponential."),
+ AbstractDiscreteDistribution(n, "Exponential."),
+ lambda_(lambda)
+ {
+diff --git a/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.cpp b/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.cpp
+index 68078a9..fecdf7f 100644
+--- a/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.cpp
++++ b/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.cpp
+@@ -48,7 +48,6 @@ using namespace std;
+
+ InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(
+ DiscreteDistribution* dist, double p, double invariant) :
+- AbstractParameterAliasable("Invariant."),
+ AbstractDiscreteDistribution(1, "Invariant."),
+ dist_(dist),
+ invariant_(invariant),
+diff --git a/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.cpp b/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.cpp
+index 628db47..00c9d3f 100644
+--- a/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.cpp
++++ b/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.cpp
+@@ -51,7 +51,6 @@ using namespace std;
+ /** Constructor: **************************************************************/
+
+ TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution(size_t n, double lambda, double truncationPoint) :
+- AbstractParameterAliasable("TruncExponential."),
+ AbstractDiscreteDistribution(n, "TruncExponential."),
+ lambda_(lambda),
+ tp_(truncationPoint),
+diff --git a/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.h b/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.h
+index 26c18ac..3d8c1f2 100644
+--- a/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.h
++++ b/src/Bpp/Numeric/Prob/ExponentialDiscreteDistribution.h
+@@ -70,14 +70,12 @@ public:
+ ExponentialDiscreteDistribution(size_t n, double lambda = 1.);
+
+ ExponentialDiscreteDistribution(const ExponentialDiscreteDistribution& dist) :
+- AbstractParameterAliasable(dist),
+ AbstractDiscreteDistribution(dist),
+ lambda_(dist.lambda_)
+ {}
+
+ ExponentialDiscreteDistribution& operator=(const ExponentialDiscreteDistribution& dist)
+ {
+- AbstractParameterAliasable::operator=(dist);
+ AbstractDiscreteDistribution::operator=(dist);
+ lambda_ = dist.lambda_;
+ return *this;
+diff --git a/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h b/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h
+index 7742ac1..1930211 100644
+--- a/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h
++++ b/src/Bpp/Numeric/Prob/InvariantMixedDiscreteDistribution.h
+@@ -76,7 +76,6 @@ public:
+ }
+
+ InvariantMixedDiscreteDistribution(const InvariantMixedDiscreteDistribution& imdd) :
+- AbstractParameterAliasable(imdd),
+ AbstractDiscreteDistribution(imdd),
+ dist_(dynamic_cast<DiscreteDistribution*>(imdd.dist_->clone())),
+ invariant_(imdd.invariant_),
+@@ -86,7 +85,6 @@ public:
+
+ InvariantMixedDiscreteDistribution& operator=(const InvariantMixedDiscreteDistribution& imdd)
+ {
+- AbstractParameterAliasable::operator=(imdd);
+ AbstractDiscreteDistribution::operator=(imdd);
+ dist_ = dynamic_cast<DiscreteDistribution*>(imdd.dist_->clone());
+ invariant_ = imdd.invariant_;
+diff --git a/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.h b/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.h
+index 8ed06af..dad8c39 100644
+--- a/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.h
++++ b/src/Bpp/Numeric/Prob/TruncatedExponentialDiscreteDistribution.h
+@@ -85,7 +85,6 @@ public:
+ TruncatedExponentialDiscreteDistribution(size_t n, double lambda = 1., double truncationPoint = 10);
+
+ TruncatedExponentialDiscreteDistribution(const TruncatedExponentialDiscreteDistribution& dist) :
+- AbstractParameterAliasable(dist),
+ AbstractDiscreteDistribution(dist),
+ lambda_(dist.lambda_),
+ tp_(dist.tp_),
+@@ -94,7 +93,6 @@ public:
+
+ TruncatedExponentialDiscreteDistribution& operator=(const TruncatedExponentialDiscreteDistribution& dist)
+ {
+- AbstractParameterAliasable::operator=(dist);
+ AbstractDiscreteDistribution::operator=(dist);
+ lambda_= dist.lambda_;
+ tp_ = dist.tp_;
+diff --git a/src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.cpp b/src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.cpp
+index 833aa55..2e40a23 100644
+--- a/src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.cpp
++++ b/src/Bpp/Numeric/Prob/GaussianDiscreteDistribution.cpp
+@@ -52,7 +52,6 @@ using namespace std;
+ /** Constructor: **************************************************************/
+
+ GaussianDiscreteDistribution::GaussianDiscreteDistribution(size_t n, double mu, double sigma) :
+- AbstractParameterAliasable("Gaussian."),
+ AbstractDiscreteDistribution(n,"Gaussian."), mu_(mu), sigma_(sigma)
+ {
+ addParameter_(new Parameter("Gaussian.mu", mu));
+@@ -61,7 +60,6 @@ GaussianDiscreteDistribution::GaussianDiscreteDistribution(size_t n, double mu,
+ }
+
+ GaussianDiscreteDistribution::GaussianDiscreteDistribution(const GaussianDiscreteDistribution& gdd) :
+- AbstractParameterAliasable(gdd),
+ AbstractDiscreteDistribution(gdd),
+ mu_(gdd.mu_),
+ sigma_(gdd.sigma_)
+@@ -70,7 +68,6 @@ GaussianDiscreteDistribution::GaussianDiscreteDistribution(const GaussianDiscret
+
+ GaussianDiscreteDistribution& GaussianDiscreteDistribution::operator=(const GaussianDiscreteDistribution& gdd)
+ {
+- AbstractParameterAliasable::operator=(gdd);
+ AbstractDiscreteDistribution::operator=(gdd);
+ mu_=gdd.mu_;
+ sigma_=gdd.sigma_;
+diff --git a/src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.cpp b/src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.cpp
+index e5872d2..ec26c4f 100644
+--- a/src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.cpp
++++ b/src/Bpp/Numeric/Prob/MixtureOfDiscreteDistributions.cpp
+@@ -47,7 +47,6 @@ using namespace std;
+
+ MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(const vector<DiscreteDistribution*>& distributions,
+ const vector<double>& probas ) :
+- AbstractParameterAliasable("Mixture."),
+ AbstractDiscreteDistribution(1, "Mixture."),
+ vdd_(),
+ probas_(),
+@@ -108,7 +107,6 @@ MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(const vector<Disc
+ }
+
+ MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(const MixtureOfDiscreteDistributions& mdd) :
+- AbstractParameterAliasable(mdd),
+ AbstractDiscreteDistribution(mdd),
+ vdd_(),
+ probas_(),
+@@ -124,7 +122,6 @@ MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(const MixtureOfDi
+
+ MixtureOfDiscreteDistributions& MixtureOfDiscreteDistributions::operator=(const MixtureOfDiscreteDistributions& mdd)
+ {
+- AbstractParameterAliasable::operator=(mdd);
+ AbstractDiscreteDistribution::operator=(mdd);
+ vdd_.clear();
+ probas_.clear();
+diff --git a/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp b/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp
+index 8fc0145..33abea0 100644
+--- a/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp
++++ b/src/Bpp/Numeric/Prob/SimpleDiscreteDistribution.cpp
+@@ -49,7 +49,6 @@ using namespace std;
+ SimpleDiscreteDistribution::SimpleDiscreteDistribution(const map<double, double>& distribution,
+ double prec,
+ bool fixed) :
+- AbstractParameterAliasable("Simple."),
+ AbstractDiscreteDistribution(distribution.size(), prec, "Simple."),
+ givenRanges_()
+ {
+@@ -87,7 +86,6 @@ SimpleDiscreteDistribution::SimpleDiscreteDistribution(const vector<double>& val
+ double prec,
+ bool fixed
+ ) :
+- AbstractParameterAliasable("Simple."),
+ AbstractDiscreteDistribution(values.size(), prec, "Simple."),
+ givenRanges_()
+ {
+@@ -129,7 +127,6 @@ SimpleDiscreteDistribution::SimpleDiscreteDistribution(const std::vector<double>
+ const std::vector<double>& probas,
+ double prec,
+ bool fixed) :
+- AbstractParameterAliasable("Simple."),
+ AbstractDiscreteDistribution(values.size(), prec, "Simple."),
+ givenRanges_()
+ {
+@@ -193,14 +190,12 @@ SimpleDiscreteDistribution::SimpleDiscreteDistribution(const std::vector<double>
+
+
+ SimpleDiscreteDistribution::SimpleDiscreteDistribution(const SimpleDiscreteDistribution& sdd) :
+- AbstractParameterAliasable(sdd),
+ AbstractDiscreteDistribution(sdd),
+ givenRanges_(sdd.givenRanges_)
+ {}
+
+ SimpleDiscreteDistribution& SimpleDiscreteDistribution::operator=(const SimpleDiscreteDistribution& sdd)
+ {
+- AbstractParameterAliasable::operator=(sdd);
+ AbstractDiscreteDistribution::operator=(sdd);
+ givenRanges_ = sdd.givenRanges_;
+
--
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