[med-svn] [libbpp-core] 01/01: Fixed lintian warnings.
Julien Dutheil
jdutheil-guest at moszumanska.debian.org
Mon Feb 5 19:05:03 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 8e18bee5565159e04064ecd7a9a0f2232286c740
Author: Julien Y. Dutheil <dutheil at evolbio.mpg.de>
Date: Mon Feb 5 20:05:32 2018 +0100
Fixed lintian warnings.
---
debian/control | 2 +-
debian/patches/gcc-7.patch | 54 +++++++++--------------------------
debian/patches/unforce-cxxflags.patch | 2 +-
3 files changed, 15 insertions(+), 43 deletions(-)
diff --git a/debian/control b/debian/control
index 175da85..f05f67d 100644
--- a/debian/control
+++ b/debian/control
@@ -7,7 +7,7 @@ Priority: optional
Build-Depends: debhelper (>= 10),
cmake,
d-shlibs
-Standards-Version: 4.0.1
+Standards-Version: 4.1.2
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libbpp-core.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/libbpp-core.git
Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page
diff --git a/debian/patches/gcc-7.patch b/debian/patches/gcc-7.patch
index 3f41eb0..dc3dd4e 100644
--- a/debian/patches/gcc-7.patch
+++ b/debian/patches/gcc-7.patch
@@ -1,5 +1,3 @@
-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
@@ -11,8 +9,6 @@ index 64b90e4..c953cdc 100644
{
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;
@@ -23,7 +19,7 @@ index dc4d0f6..8c62aec 100644
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
+@@ -67,14 +66,12 @@ BetaDiscreteDistribution::BetaDiscreteDi
}
BetaDiscreteDistribution::BetaDiscreteDistribution(const BetaDiscreteDistribution& bdd) :
@@ -38,8 +34,6 @@ index dc4d0f6..8c62aec 100644
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;
@@ -50,7 +44,7 @@ index 600f19b..933e3b3 100644
AbstractDiscreteDistribution(1, "Constant."),
value_(value)
{
-@@ -57,14 +56,12 @@ ConstantDistribution::ConstantDistribution(double value):
+@@ -57,14 +56,12 @@ ConstantDistribution::ConstantDistributi
}
ConstantDistribution::ConstantDistribution(const ConstantDistribution& cd) :
@@ -65,8 +59,6 @@ index 600f19b..933e3b3 100644
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;
@@ -77,7 +69,7 @@ index f4ef78d..f1937f8 100644
AbstractDiscreteDistribution(n, "Gamma."),
alpha_(alpha),
beta_(beta),
-@@ -76,7 +75,6 @@ GammaDiscreteDistribution::GammaDiscreteDistribution(size_t n, double alpha, dou
+@@ -76,7 +75,6 @@ GammaDiscreteDistribution::GammaDiscrete
}
GammaDiscreteDistribution::GammaDiscreteDistribution(const GammaDiscreteDistribution& gdd) :
@@ -85,7 +77,7 @@ index f4ef78d..f1937f8 100644
AbstractDiscreteDistribution(gdd),
alpha_(gdd.alpha_),
beta_(gdd.beta_),
-@@ -87,7 +85,6 @@ GammaDiscreteDistribution::GammaDiscreteDistribution(const GammaDiscreteDistribu
+@@ -87,7 +85,6 @@ GammaDiscreteDistribution::GammaDiscrete
GammaDiscreteDistribution& GammaDiscreteDistribution::operator=(const GammaDiscreteDistribution& gdd)
{
@@ -93,8 +85,6 @@ index f4ef78d..f1937f8 100644
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;
@@ -105,7 +95,7 @@ index 1d2d03a..945f3c9 100644
AbstractDiscreteDistribution(n,"Uniform."),
min_((min<max)?min:max),
max_((min<max)?max:min)
-@@ -63,7 +62,6 @@ UniformDiscreteDistribution::UniformDiscreteDistribution(unsigned int n, double
+@@ -63,7 +62,6 @@ UniformDiscreteDistribution::UniformDisc
}
UniformDiscreteDistribution::UniformDiscreteDistribution(const UniformDiscreteDistribution& udd) :
@@ -113,7 +103,7 @@ index 1d2d03a..945f3c9 100644
AbstractDiscreteDistribution(udd),
min_(udd.min_),
max_(udd.max_)
-@@ -72,7 +70,6 @@ UniformDiscreteDistribution::UniformDiscreteDistribution(const UniformDiscreteDi
+@@ -72,7 +70,6 @@ UniformDiscreteDistribution::UniformDisc
UniformDiscreteDistribution& UniformDiscreteDistribution::operator=(const UniformDiscreteDistribution& udd)
{
@@ -121,8 +111,6 @@ index 1d2d03a..945f3c9 100644
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;
@@ -133,8 +121,6 @@ index f63c9fb..8ddec89 100644
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;
@@ -145,8 +131,6 @@ index 68078a9..fecdf7f 100644
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;
@@ -157,8 +141,6 @@ index 628db47..00c9d3f 100644
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:
@@ -176,8 +158,6 @@ index 26c18ac..3d8c1f2 100644
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:
@@ -196,8 +176,6 @@ index 7742ac1..1930211 100644
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:
@@ -216,8 +194,6 @@ index 8ed06af..dad8c39 100644
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;
@@ -228,7 +204,7 @@ index 833aa55..2e40a23 100644
AbstractDiscreteDistribution(n,"Gaussian."), mu_(mu), sigma_(sigma)
{
addParameter_(new Parameter("Gaussian.mu", mu));
-@@ -61,7 +60,6 @@ GaussianDiscreteDistribution::GaussianDiscreteDistribution(size_t n, double mu,
+@@ -61,7 +60,6 @@ GaussianDiscreteDistribution::GaussianDi
}
GaussianDiscreteDistribution::GaussianDiscreteDistribution(const GaussianDiscreteDistribution& gdd) :
@@ -236,7 +212,7 @@ index 833aa55..2e40a23 100644
AbstractDiscreteDistribution(gdd),
mu_(gdd.mu_),
sigma_(gdd.sigma_)
-@@ -70,7 +68,6 @@ GaussianDiscreteDistribution::GaussianDiscreteDistribution(const GaussianDiscret
+@@ -70,7 +68,6 @@ GaussianDiscreteDistribution::GaussianDi
GaussianDiscreteDistribution& GaussianDiscreteDistribution::operator=(const GaussianDiscreteDistribution& gdd)
{
@@ -244,8 +220,6 @@ index 833aa55..2e40a23 100644
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;
@@ -256,7 +230,7 @@ index e5872d2..ec26c4f 100644
AbstractDiscreteDistribution(1, "Mixture."),
vdd_(),
probas_(),
-@@ -108,7 +107,6 @@ MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(const vector<Disc
+@@ -108,7 +107,6 @@ MixtureOfDiscreteDistributions::MixtureO
}
MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(const MixtureOfDiscreteDistributions& mdd) :
@@ -264,7 +238,7 @@ index e5872d2..ec26c4f 100644
AbstractDiscreteDistribution(mdd),
vdd_(),
probas_(),
-@@ -124,7 +122,6 @@ MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(const MixtureOfDi
+@@ -124,7 +122,6 @@ MixtureOfDiscreteDistributions::MixtureO
MixtureOfDiscreteDistributions& MixtureOfDiscreteDistributions::operator=(const MixtureOfDiscreteDistributions& mdd)
{
@@ -272,8 +246,6 @@ index e5872d2..ec26c4f 100644
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;
@@ -284,7 +256,7 @@ index 8fc0145..33abea0 100644
AbstractDiscreteDistribution(distribution.size(), prec, "Simple."),
givenRanges_()
{
-@@ -87,7 +86,6 @@ SimpleDiscreteDistribution::SimpleDiscreteDistribution(const vector<double>& val
+@@ -87,7 +86,6 @@ SimpleDiscreteDistribution::SimpleDiscre
double prec,
bool fixed
) :
@@ -292,7 +264,7 @@ index 8fc0145..33abea0 100644
AbstractDiscreteDistribution(values.size(), prec, "Simple."),
givenRanges_()
{
-@@ -129,7 +127,6 @@ SimpleDiscreteDistribution::SimpleDiscreteDistribution(const std::vector<double>
+@@ -129,7 +127,6 @@ SimpleDiscreteDistribution::SimpleDiscre
const std::vector<double>& probas,
double prec,
bool fixed) :
@@ -300,7 +272,7 @@ index 8fc0145..33abea0 100644
AbstractDiscreteDistribution(values.size(), prec, "Simple."),
givenRanges_()
{
-@@ -193,14 +190,12 @@ SimpleDiscreteDistribution::SimpleDiscreteDistribution(const std::vector<double>
+@@ -193,14 +190,12 @@ SimpleDiscreteDistribution::SimpleDiscre
SimpleDiscreteDistribution::SimpleDiscreteDistribution(const SimpleDiscreteDistribution& sdd) :
diff --git a/debian/patches/unforce-cxxflags.patch b/debian/patches/unforce-cxxflags.patch
index e91745e..6adeb77 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 -Wno-deprecated")
++set (CMAKE_CXX_FLAGS "-std=c++11 -Wno-deprecated -g")
IF(NOT CMAKE_BUILD_TYPE)
SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
--
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