compilation problem on a Mac OSX 10.8.5

[Bastien Boussau]

Hi, 

I downloaded the libraries from the git yesterday, and tried to compile them. Bpp-core and bpp-seq went fine, but bpp-phyl did not compile:

In file included from /Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40:

In file included from /Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:

In file included from /Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/SubstitutionModel.h:51:

In file included from /usr/local/include/Bpp/Numeric/VectorTools.h:44:

/usr/local/include/Bpp/Numeric/NumTools.h:116:50: error: call to function 'operator*' that is neither visible in the template definition nor found by argument-dependent lookup

  template<class T> static T sqr(T a) { return a * a; }

                                                 ^

/Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:281:45: note: in instantiation of function template specialization

      'bpp::NumTools::sqr<std::vector<double, std::allocator<double> > >' requested here

      MatrixTools::mult(rightEigenVectors_, NumTools::sqr(rate_ * eigenValues_) * VectorTools::exp(eigenValues_ * (rate_ * t)), leftEigenVectors_, d2pijt_);

                                            ^

/usr/local/include/Bpp/Numeric/VectorTools.h:128:16: note: 'operator*' should be declared prior to the call site

std::vector<T> operator*(const std::vector<T>& v1, const std::vector<T>& v2) throw (DimensionException)

               ^

2 warnings and 1 error generated.

make[2]: *** [src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o] Error 1

make[1]: *** [src/CMakeFiles/bppphyl-shared.dir/all] Error 2

make: *** [all] Error 2

 

I suspect the latest version of mac OS X is picky about the order of declarations, or just includes files in a different order compared to other systems. Do you know how I could solve that?

Thanks!

Bastien.

[Bastien Boussau]

An update: the same problem occurs if I use the stable versions: 

[ 21%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o

/Users/boussau/Programs/Biopp/Stable/bpp-phyl-2.1.0/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:393:11: warning: implicit conversion changes signedness: 'int' to 'size_type'

      (aka 'unsigned long') [-Wsign-conversion]

    freq_[i] = freqs[i];

    ~~~~~ ^

In file included from /Users/boussau/Programs/Biopp/Stable/bpp-phyl-2.1.0/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:40:

In file included from /Users/boussau/Programs/Biopp/Stable/bpp-phyl-2.1.0/src/Bpp/Phyl/Model/AbstractSubstitutionModel.h:43:

In file included from /Users/boussau/Programs/Biopp/Stable/bpp-phyl-2.1.0/src/Bpp/Phyl/Model/SubstitutionModel.h:51:

In file included from /usr/local/include/Bpp/Numeric/VectorTools.h:44:

/usr/local/include/Bpp/Numeric/NumTools.h:116:50: error: call to function 'operator*' that is neither visible in the template definition nor found by argument-dependent lookup

  template<class T> static T sqr(T a) { return a * a; }

                                                 ^

/Users/boussau/Programs/Biopp/Stable/bpp-phyl-2.1.0/src/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp:281:45: note: in instantiation of function template specialization

      'bpp::NumTools::sqr<std::vector<double, std::allocator<double> > >' requested here

      MatrixTools::mult(rightEigenVectors_, NumTools::sqr(rate_ * eigenValues_) * VectorTools::exp(eigenValues_ * (rate_ * t)), leftEigenVectors_, d2pijt_);

                                            ^

/usr/local/include/Bpp/Numeric/VectorTools.h:128:16: note: 'operator*' should be declared prior to the call site

std::vector<T> operator*(const std::vector<T>& v1, const std::vector<T>& v2) throw (DimensionException)

               ^

1 warning and 1 error generated.

make[2]: *** [src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/AbstractSubstitutionModel.cpp.o] Error 1

make[1]: *** [src/CMakeFiles/bppphyl-shared.dir/all] Error 2

make: *** [all] Error 2

[Julien Yann Dutheil]

Hi Bastien,

I have to admit that your compiler is definitely in its own rights: as eigenValues_ is a vector, it should nit be NumTools::sqr but VectorTools::sqr which should have been used here. Just amazed this error did not pop up earlier! I have fixed it on the master branch on git. Also fixed the warning. Tell me if that solves the issue...

Cheers,

J.

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Julien Y. Dutheil, Ph-D
0 (+49) 6421 178 986

§ Max Planck Institute for Terrestrial Microbiology
Department of Organismic Interactions
Marburg -- GERMANY

§ Intitute of Evolutionary Sciences - Montpellier
University of Montpellier 2 -- FRANCE

[Bastien Boussau]

Hi Julien, 

There was a similar problem in MarkovModulatedSubstitutionModel.cpp: 

[ 22%] Building CXX object src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o

In file included from /Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:40:

In file included from /Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h:43:

In file included from /Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/SubstitutionModel.h:57:

/Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:164:7: warning: variable 'x' is uninitialized when used here [-Wuninitialized]

      x+=freq_[i];

      ^

/Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/FrequenciesSet.h:162:13: note: initialize the variable 'x' to silence this warning

    double x;

            ^

             = 0.0

In file included from /Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:40:

In file included from /Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.h:43:

In file included from /Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/SubstitutionModel.h:51:

In file included from /usr/local/include/Bpp/Numeric/VectorTools.h:44:

/usr/local/include/Bpp/Numeric/NumTools.h:116:50: error: call to function 'operator*' that is neither visible in the template definition nor found by argument-dependent lookup

  template<class T> static T sqr(T a) { return a * a; }

                                                 ^

/Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp:198:41: note: in instantiation of function template specialization

      'bpp::NumTools::sqr<std::vector<double, std::allocator<double> > >' requested here

  MatrixTools::mult(rightEigenVectors_, NumTools::sqr(eigenValues_) * VectorTools::exp(eigenValues_ * t), leftEigenVectors_, d2pijt_);

                                        ^

/usr/local/include/Bpp/Numeric/VectorTools.h:128:16: note: 'operator*' should be declared prior to the call site

std::vector<T> operator*(const std::vector<T>& v1, const std::vector<T>& v2) throw (DimensionException)

               ^

1 warning and 1 error generated.

make[2]: *** [src/CMakeFiles/bppphyl-shared.dir/Bpp/Phyl/Model/MarkovModulatedSubstitutionModel.cpp.o] Error 1

make[1]: *** [src/CMakeFiles/bppphyl-shared.dir/all] Error 2

make: *** [all] Error 2

I changed the NumTools::sqr into VectorTools::sqr, and it compiled this file.

I'm about to commit that change.

However, there is another problem later:

/Users/boussau/Programs/Biopp/bpp-phyl/src/Bpp/Phyl/Model/FrequenciesSet/WordFrequenciesSet.cpp:161:19: error: variable length array of non-POD element type 'vector<double>'

  vector<double> f[l];

 Not sure what that is...

Bastien.

[Julien Yann Dutheil]

Hi Bastien,

Thanks a lot for the commit ! As for the other error, this is amazing that linux compilers have never complained about that! VLA are not standard C++, so I replaced it with a VVdouble. This should solve the issue!

Cheers,

J.

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[Bastien Boussau]

It worked, thanks!
Bastien.