Docker image

[philastrophist]

The installation process is horrendously complicated and I can't seem to get it right. Can you put a working Dockerfile up there? Thanks!

[AstroVPK]

Can you describe the problems that you're experiencing with the installation process? Let me know what platform you've working on and cut & paste any error messages that you're running across.... Thanks!

[philastrophist]

Yes, I'm attempting to install all of the various dependencies. A few of them fail so I've had to install them using conda or apt-get instead of from source. The main one I'm struggling with at the moment is carmcmc. I get the error message below. If you want to see exactly what I've done. The Dockerfile I'm writing is below as well. Thanks for the help! Your code would be really useful right now!

Dockerfile

FROM ubuntu
SHELL ["/bin/bash", "-c"]
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ENV PATH /opt/conda/bin:$PATH
ENV TINI_VERSION v0.16.1

RUN apt-get update --fix-missing && \
    apt-get install -y wget bzip2 ca-certificates curl git build-essential cmake libgtk2.0-common \
    				   libpango-1.0.0 libasound2-dev xserver-xorg cpio && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh && \
    /opt/conda/bin/conda clean -tipsy && \
    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
    echo "conda activate base" >> ~/.bashrc

ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
RUN chmod +x /usr/bin/tini

COPY parallel_studio_xe_2019_update5_cluster_edition_online.tgz .
COPY mysilent.cfg .
RUN echo "ACTIVATION_SERIAL_NUMBER=$SERIAL_NUMBER"  && echo "ACTIVATION_SERIAL_NUMBER=$SERIAL_NUMBER" >> mysilent.cfg
RUN tar -xvzf parallel_studio_xe_2019_update5_cluster_edition_online.tgz && \
	cd parallel_studio_xe_2019_update5_cluster_edition_online && \
	./install.sh --silent ../mysilent.cfg --cli-mode && \
 	echo "source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64" >> ~/.bashrc 
RUN cd ~

#COPY l_mkl_2019.5.281_online.tgz .
#RUN tar -xvzf l_mkl_2019.5.281_online.tgz -C mkl && cd mkl
RUN conda install mkl
RUN wget https://github.com/stevengj/nlopt/archive/v2.6.1.tar.gz  -O nlopt.tar.gz 
RUN tar -xvzf nlopt.tar.gz && cd nlopt-2.6.1/ && cmake . && make && make install && ldconfig && cd ..

RUN conda update --all && conda install cython future pytest
RUN conda install numpy matplotlib scipy
RUN pip install gatspy multi_key_dict fitsio==0.9.8

# carma_pack
# RUN wget http://sourceforge.net/projects/boost/files/boost/1.54.0/boost_1_54_0.tar.bz2 && tar --bzip2 -xf boost_1_54_0.tar.bz2
# RUN cd boost_1_54_0 && ./bootstrap.sh && sed -i 's/explicit yield_sources ;/explicit allocator_sources ;/g' libs/coroutine/build/Jamfile.v2
# RUN cd boost_1_54_0 && ./b2 install

RUN wget http://sourceforge.net/projects/arma/files/armadillo-9.700.3.tar.xz && \
	tar -xf armadillo-9.700.3.tar.xz && cd armadillo-9.700.3 && \
	cmake -DCMAKE_INSTALL_PREFIX=/opt/armadillo -DBOOST_ROOT=$BOOST_DIR/  .  && \
	make install && cd ~

RUN apt-get update && apt-get install -y libboost-all-dev

RUN echo "export ARMADILLO_DIR=/opt/armadillo" >> ~/.bashrc
ENV ARMADILLO_DIR "/opt/armadillo"

RUN echo "export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}" >> ~/.bashrc
ENV LD_LIBRARY_PATH "/usr/local/lib:${LD_LIBRARY_PATH}"

RUN echo "export LD_LIBRARY_PATH=/opt/armadillo/lib:${LD_LIBRARY_PATH}" >> ~/.bashrc
ENV LD_LIBRARY_PATH "/opt/armadillo/lib:${LD_LIBRARY_PATH}"

RUN echo "export BOOST_DIR=/usr/local" >> ~/.bashrc
ENV BOOST_DIR "/usr/local"

ENV NUMPY_DIR "/opt/conda"

RUN git clone https://github.com/brandonckelly/carma_pack.git
RUN cd carma_pack/src/ && pip install .
RUN pip install acor

RUN git clone https://github.com/AstroVPK/kali.git && cd kali && source ./bin/setup.sh && python setup.py build_ext
RUN echo "source ~/kali/bin/setup.sh" >> ~/.bashrc
RUN pytest tests && cd ~

ENTRYPOINT [ "/usr/bin/tini", "--" ]
CMD [ "/bin/bash" ]

Error message

Processing /carma_pack/src                                                                                                                                                                            
Building wheels for collected packages: carmcmc                                                                                                                                                       
  Building wheel for carmcmc (setup.py): started                                                                                                                                                      
  Building wheel for carmcmc (setup.py): still running...                                                                                                                                             
  Building wheel for carmcmc (setup.py): finished with status 'error'                                                                                                                                 
  ERROR: Command errored out with exit status 1:                                                                                                                                                      
   command: /opt/conda/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-ORR7mJ/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-ORR7mJ/setup.py'"'"';f=getattr
(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-veJ52d --python-
tag cp27                                                                                                                                                                                              
       cwd: /tmp/pip-req-build-ORR7mJ/                                                                                                                                                                
  Complete output (296 lines):                                                                                                                                                                        
  non-existing path in '.': '/usr/lib64'                                                                                                                                                              
  non-existing path in '.': '/usr/lib64'                                                                                                                                                              
  non-existing path in '.': 'examples'                                                                                                                                                                
  running bdist_wheel                                                                                                                                                                                 
  running build                                                                                                                                                                                       
  running config_cc                                                                                                                                                                                   
  unifing config_cc, config, build_clib, build_ext, build commands --compiler options                                                                                                                 
  running config_fc                                                                                                                                                                                   
  unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options                                                                                                                
  running build_src                                                                                                                                                                                   
  build_src                                                                                                                                                                                           
  building library "carmcmc" sources                                                                                                                                                                  
  building extension "carmcmc._carmcmc" sources                                                                                                                                                       
  building data_files sources                                                                                                                                                                         
  build_src: building npy-pkg config files                                                                                                                                                            
  running build_clib                                                                                                                                                                                  
  customize UnixCCompiler                                                                                                                                                                             
  customize UnixCCompiler using build_clib                                                                                                                                                            
  building 'carmcmc' library                                                                                                                                                                          
  compiling C++ sources                                                                                                                                                                               
  C compiler: g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC                                                              
                                                                                                                                                                                                      
  creating build                                                                                                                                                                                      
  creating build/temp.linux-x86_64-2.7                                                                                                                                                                
  compile options: '-I/opt/conda/include -I/usr/local/include -I/opt/armadillo/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/python
2.7/site-packages/numpy/core/include -c'                                                                                                                                                              
  extra options: '-O3 -std=c++0x'                                                                                                                                                                     
  g++: ./kfilter.cpp                                                                                                                                                                                  
  g++: ./proposals.cpp                                                                                                                                                                                
  ./kfilter.cpp: In member function ‘virtual std::pair<double, double> KalmanFilter1::Predict(double)’:                                                                                               
  ./kfilter.cpp:88:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                           
       for (int i=1; i<ipredict; i++) {                                                                                                                                                               
                     ~^~~~~~~~~                                                                                                                                                                       
  ./kfilter.cpp:124:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
       for (int i=ipredict+1; i<time_.n_elem; i++) {                                                                                                                                                  
                              ~^~~~~~~~~~~~~                                                                                                                                                          
  ./kfilter.cpp: In member function ‘virtual void KalmanFilterp::Reset()’:                                                                                                                            
  ./kfilter.cpp:147:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
    for (int i=2; i<p_; i++) {                                                                                                                                                                        
                  ~^~~                                                                                                                                                                                
  ./kfilter.cpp:165:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
    for (int i=0; i<p_; i++) {                                                                                                                                                                        
                  ~^~~                                                                                                                                                                                
  ./kfilter.cpp:166:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
     for (int j=i; j<p_; j++) {                                                                                                                                                                       
                   ~^~~                                                                                                                                                                               
  ./kfilter.cpp: In member function ‘virtual std::pair<double, double> KalmanFilterp::Predict(double)’:                                                                                               
  ./kfilter.cpp:232:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
       for (int i=1; i<ipredict; i++) {                                                                                                                                                               
                     ~^~~~~~~~~                                                                                                                                                                       
  ./kfilter.cpp:275:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
       for (int i=ipredict+1; i<time_.n_elem; i++) {                                                                                                                                                  
                              ~^~~~~~~~~~~~~                                                                                                                                                          
  In file included from ./kfilter.cpp:10:0:                                                                                                                                                           
  ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                             
  ./include/kfilter.hpp:256:56:   required from here                                                                                                                                                  
  ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time.n_elem; i++) {                                                                                                                                                        
                         ~^~~~~~~~~~~~                                                                                                                                                                
  ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:   
  ./include/kfilter.hpp:369:62:   required from here                                                                                                                                                  
  ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
  g++: ./random.cpp                                                                                                                                                                                   
  ./random.cpp: In member function ‘arma::vec RandomGenerator::normal(arma::mat)’:                                                                                                                    
  ./random.cpp:99:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                            
    for (int i=0; i<z.n_elem; i++) {                                                                                                                                                                  
                  ~^~~~~~~~~                                                                                                                                                                          
  g++: ./carpack.cpp                                                                                                                                                                                  
  g++: ./carmcmc.cpp                                                                                                                                                                                  
  ./carpack.cpp: In member function ‘virtual arma::vec CARp::SetStartingValue(arma::vec)’:                                                                                                            
  ./carpack.cpp:236:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
      if (init.n_elem != (p_+3)) {                                                                                                                                                                    
          ~~~~~~~~~~~~^~~~~~~~~                                                                                                                                                                       
  ./carpack.cpp: In member function ‘arma::vec CARp::StartingAR()’:                                                                                                                                   
  ./carpack.cpp:279:46: warning: ‘typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), const arma::Op<T1, arma::op_sort_vec> >::result arma::sort(const T1&
, arma::uword) [with T1 = arma::Col<double>; typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), const arma::Op<T1, arma::op_sort_vec> >::result = const a
rma::Op<arma::Col<double>, arma::op_sort_vec>; arma::uword = long long unsigned int]’ is deprecated [-Wdeprecated-declarations]                                                                       
       lorentz_cent = arma::sort(lorentz_cent, 1);                                                                                                                                                    
                                                ^                                                                                                                                                     
  In file included from /opt/armadillo/include/armadillo:462:0,                                                                                                                                       
                   from ./carpack.cpp:17:                                                                                                                                                             
  /opt/armadillo/include/armadillo_bits/fn_sort.hpp:74:1: note: declared here                                                                                                                         
   sort                                                                                                                                                                                               
   ^~~~                                                                                                                                                                                               
  ./carpack.cpp: In member function ‘virtual bool CARp::CheckPriorBounds(arma::vec)’:                                                                                                                 
  ./carpack.cpp:355:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
           for (int i=1; i<lorentz_cent.n_elem; i++) {                                                                                                                                                
                         ~^~~~~~~~~~~~~~~~~~~~                                                                                                                                                        
  ./carpack.cpp: In member function ‘double CARp::Variance(arma::cx_vec, arma::vec, double, double)’:                                                                                                 
  ./carpack.cpp:384:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
    for (int k=0; k<alpha_roots.n_elem; k++) {                                                                                                                                                        
                  ~^~~~~~~~~~~~~~~~~~~                                                                                                                                                                
  ./carpack.cpp:387:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
     for (int l=0; l<alpha_roots.n_elem; l++) {                                                                                                                                                       
                   ~^~~~~~~~~~~~~~~~~~~                                                                                                                                                               
  ./carpack.cpp: In member function ‘virtual arma::vec CARMA::SetStartingValue(arma::vec)’:                                                                                                           
  ./carpack.cpp:481:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
      if (init.n_elem != (p_+q_+3)) {                                                                                                                                                                 
          ~~~~~~~~~~~~^~~~~~~~~~~~                                                                                                                                                                    
  ./carpack.cpp: In member function ‘virtual arma::vec ZCARMA::SetStartingValue(arma::vec)’:                                                                                                          
  ./carpack.cpp:648:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
      if (init.n_elem != (p_+4)) {                                                                                                                                                                    
          ~~~~~~~~~~~~^~~~~~~~~                                                                                                                                                                       
  ./carpack.cpp: In function ‘arma::vec polycoefs(arma::cx_vec)’:                                                                                                                                     
  ./carpack.cpp:749:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
       for (int i=0; i<roots.n_elem; i++) {                                                                                                                                                           
                     ~^~~~~~~~~~~~~                                                                                                                                                                   
  In file included from ./include/carpack.hpp:24:0,                                                                                                                                                   
                   from ./carpack.cpp:23:                                                                                                                                                             
  ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                             
  ./include/kfilter.hpp:256:56:   required from here                                                                                                                                                  
  ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time.n_elem; i++) {                                                                                                                                                        
                         ~^~~~~~~~~~~~                                                                                                                                                                
  ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:   
  ./include/kfilter.hpp:369:62:   required from here                                                                                                                                                  
  ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
  ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:                                                                                      
  ./carpack.cpp:78:23:   required from here                                                                                                                                                           
  ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=1; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  In file included from ./carpack.cpp:23:0:                                                                                                                                                           
  ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                                          
  ./carpack.cpp:90:36:   required from here                                                                                                                                                           
  ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  In file included from ./include/carpack.hpp:24:0,                                                                                                                                                   
                   from ./carpack.cpp:23:                                                                                                                                                             
  ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:                                                            
  ./carpack.cpp:218:27:   required from here                                                                                                                                                          
  ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=1; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  In file included from ./carpack.cpp:23:0:                                                                                                                                                           
  ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:                
  ./carpack.cpp:220:42:   required from here                                                                                                                                                          
  ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::basic
_string<char>]’:                                                                                                                                                                                      
  ./carpack.cpp:756:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                   
           for (int i=0; i<value_.n_elem; i++) {                                                                                                                                                      
                         ~^~~~~~~~~~~~~~                                                                                                                                                              
  ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:          
  ./carpack.cpp:756:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                   
  ./carmcmc.cpp: In function ‘std::shared_ptr<CAR1> RunCar1Sampler(int, int, std::vector<double>, std::vector<double>, std::vector<double>, int, const std::vector<double>&)’:                        
  ./carmcmc.cpp:43:9: warning: unused variable ‘report_iter’ [-Wunused-variable]                                                                                                                      
       int report_iter = burnin + thin * sample_size;                                                                                                                                                 
           ^~~~~~~~~~~                                                                                                                                                                                
  In file included from ./include/carpack.hpp:24:0,                                                                                                                                                   
                   from ./carmcmc.cpp:27:                                                                                                                                                             
  ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                             
  ./include/kfilter.hpp:256:56:   required from here                                                                                                                                                  
  ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time.n_elem; i++) {                                                                                                                                                        
                         ~^~~~~~~~~~~~                                                                                                                                                                
  ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:   
  ./include/kfilter.hpp:369:62:   required from here                                                                                                                                                  
  ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
  In file included from ./carmcmc.cpp:27:0:                                                                                                                                                           
  ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::basic
_string<char>]’:                                                                                                                                                                                      
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                   
           for (int i=0; i<value_.n_elem; i++) {                                                                                                                                                      
                         ~^~~~~~~~~~~~~~                                                                                                                                                              
  ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:                
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:          
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                   
           for (int i=0; i<value_.n_elem; i++) {                                                                                                                                                      
                         ~^~~~~~~~~~~~~~                                                                                                                                                              
  ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                                          
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  ./include/carpack.hpp: In instantiation of ‘void CARMA_Base<OmegaType>::Save(arma::vec&) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:                       
  ./include/steps.hpp:344:13:   required from ‘void ExchangeStep<ParValueType, ParameterType>::DoStep() [with ParValueType = arma::Col<double>; ParameterType = CARp]’                                
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  In file included from ./include/carpack.hpp:24:0,                                                                                                                                                   
                   from ./carmcmc.cpp:27:                                                                                                                                                             
  ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:                                                            
  ./include/carpack.hpp:155:13:   required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’              
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=1; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:                                                                                      
  ./include/carpack.hpp:155:13:   required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’                                        
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
  g++: ./steps.cpp                                                                                                                                                                                    
  g++: ./samplers.cpp                                                                                                                                                                                 
  ./steps.cpp: In member function ‘virtual void AdaptiveMetro::DoStep()’:                                                                                                                             
  ./steps.cpp:66:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                             
    for (int i=0; i<old_value.n_rows; i++) {                                                                                                                                                          
                  ~^~~~~~~~~~~~~~~~~                                                                                                                                                                  
  ./steps.cpp: In function ‘void CholUpdateR1(arma::mat&, arma::vec&, bool)’:                                                                                                                         
  ./steps.cpp:118:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                            
    for (int k=0; k<L.n_rows; k++) {                                                                                                                                                                  
                  ~^~~~~~~~~                                                                                                                                                                          
  ./steps.cpp:123:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                             
     if (k < L.n_rows-1) {                                                                                                                                                                            
         ~~^~~~~~~~~~~~                                                                                                                                                                               
  ./samplers.cpp: In member function ‘void Sampler::Iterate(int, bool)’:                                                                                                                              
  ./samplers.cpp:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
      for(int i = 0; i < steps_.size(); ++i) {                                                                                                                                                        
                     ~~^~~~~~~~~~~~~~~                                                                                                                                                                
  ./samplers.cpp:49:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
      for(int i = 0; i < steps_.size(); ++i) {                                                                                                                                                        
                     ~~^~~~~~~~~~~~~~~                                                                                                                                                                
  ./samplers.cpp: In member function ‘void Sampler::Run(arma::vec)’:                                                                                                                                  
  ./samplers.cpp:76:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
    bool useInit = (init.n_elem == npar);                                                                                                                                                             
                    ~~~~~~~~~~~~^~~~~~~                                                                                                                                                               
  ar: adding 7 object files to build/temp.linux-x86_64-2.7/libcarmcmc.a                                                                                                                               
  running build_ext                                                                                                                                                                                   
  customize UnixCCompiler                                                                                                                                                                             
  customize UnixCCompiler using build_ext                                                                                                                                                             
  updating extension 'carmcmc._carmcmc' libraries from ['boost_python', 'boost_filesystem', 'boost_system', 'armadillo', 'carmcmc'] to ['boost_python', 'boost_filesystem', 'boost_system', 'armadillo
', 'carmcmc', 'boost_python', 'boost_filesystem', 'boost_system', 'armadillo']                                                                                                                        
  customize UnixCCompiler                                                                                                                                                                             
  customize UnixCCompiler using build_ext                                                                                                                                                             
  building 'carmcmc._carmcmc' extension                                                                                                                                                               
  compiling C++ sources                                                                                                                                                                               
  C compiler: g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC                                                              
                                                                                                                                                                                                      
  compile options: '-I/opt/conda/include -I/usr/local/include -I/opt/armadillo/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/python
2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c'                                                                                                                               
  extra options: '-O3 -std=c++0x'                                                                                                                                                                     
  g++: ./boost_python_wrapper.cpp                                                                                                                                                                     
  g++: ./carmcmc.cpp                                                                                                                                                                                  
  ./boost_python_wrapper.cpp:12:10: fatal error: boost/python/numeric.hpp: No such file or directory                                                                                                  
   #include <boost/python/numeric.hpp>                                                                                                                                                                
            ^~~~~~~~~~~~~~~~~~~~~~~~~~                                                                                                                                                                
  compilation terminated.                                                                                                                                                                             
  error: Command "g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/opt/conda/include -I/usr/local/include -I/opt/armadill
o/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c ./boos
t_python_wrapper.cpp -o build/temp.linux-x86_64-2.7/boost_python_wrapper.o -MMD -MF build/temp.linux-x86_64-2.7/boost_python_wrapper.o.d -O3 -std=c++0x" failed with exit status 1                    
  ./carmcmc.cpp: In function ‘std::shared_ptr<CAR1> RunCar1Sampler(int, int, std::vector<double>, std::vector<double>, std::vector<double>, int, const std::vector<double>&)’:                        
  ./carmcmc.cpp:43:9: warning: unused variable ‘report_iter’ [-Wunused-variable]                                                                                                                      
       int report_iter = burnin + thin * sample_size;                                                                                                                                                 
           ^~~~~~~~~~~                                                                                                                                                                                
  In file included from ./include/carpack.hpp:24:0,                                                                                                                                                   
                   from ./carmcmc.cpp:27:                                                                                                                                                             
  ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                             
  ./include/kfilter.hpp:256:56:   required from here                                                                                                                                                  
  ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time.n_elem; i++) {                                                                                                                                                        
                         ~^~~~~~~~~~~~                                                                                                                                                                
  ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:   
  ./include/kfilter.hpp:369:62:   required from here                                                                                                                                                  
  ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
  In file included from ./carmcmc.cpp:27:0:                                                                                                                                                           
  ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::basic
_string<char>]’:                                                                                                                                                                                      
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                   
           for (int i=0; i<value_.n_elem; i++) {                                                                                                                                                      
                         ~^~~~~~~~~~~~~~                                                                                                                                                              
  ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:                
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:          
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                   
           for (int i=0; i<value_.n_elem; i++) {                                                                                                                                                      
                         ~^~~~~~~~~~~~~~                                                                                                                                                              
  ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                                          
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  ./include/carpack.hpp: In instantiation of ‘void CARMA_Base<OmegaType>::Save(arma::vec&) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:                       
  ./include/steps.hpp:344:13:   required from ‘void ExchangeStep<ParValueType, ParameterType>::DoStep() [with ParValueType = arma::Col<double>; ParameterType = CARp]’                                
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/carpack.hpp:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  In file included from ./include/carpack.hpp:24:0,                                                                                                                                                   
                   from ./carmcmc.cpp:27:                                                                                                                                                             
  ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:                                                            
  ./include/carpack.hpp:155:13:   required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’              
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
           for (int i=1; i<time_.n_elem; i++) {                                                                                                                                                       
                         ~^~~~~~~~~~~~~                                                                                                                                                               
  ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:                                                                                      
  ./include/carpack.hpp:155:13:   required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’                                        
  ./carmcmc.cpp:177:1:   required from here                                                                                                                                                           
  ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                  
  ----------------------------------------                                                                                                                                                            
  ERROR: Failed building wheel for carmcmc                                                                                                                                                            
  Running setup.py clean for carmcmc                                                                                                                                                                  
Failed to build carmcmc                                                                                                                                                                               
Installing collected packages: carmcmc                                                                                                                                                                
  Running setup.py install for carmcmc: started                                                                                                                                                       
    Running setup.py install for carmcmc: still running...                                                                                                                                            
    Running setup.py install for carmcmc: finished with status 'error'                                                                                                                                
    ERROR: Command errored out with exit status 1:                                                                                                                                                    
     command: /opt/conda/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-ORR7mJ/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-ORR7mJ/setup.py'"'"';f=getat
tr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-QfigSn/inst
all-record.txt --single-version-externally-managed --compile                                                                                                                                          
         cwd: /tmp/pip-req-build-ORR7mJ/                                                                                                                                                              
    Complete output (296 lines):                                                                                                                                                                      
    non-existing path in '.': '/usr/lib64'                                                                                                                                                            
    non-existing path in '.': '/usr/lib64'                                                                                                                                                            
    non-existing path in '.': 'examples'                                                                                                                                                              
    running install                                                                                                                                                                                   
    running build                                                                                                                                                                                     
    running config_cc                                                                                                                                                                                 
    unifing config_cc, config, build_clib, build_ext, build commands --compiler options                                                                                                               
    running config_fc                                                                                                                                                                                 
    unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options                                                                                                              
    running build_src                                                                                                                                                                                 
    build_src                                                                                                                                                                                         
    building library "carmcmc" sources                                                                                                                                                                
    building extension "carmcmc._carmcmc" sources                                                                                                                                                     
    building data_files sources                                                                                                                                                                       
    build_src: building npy-pkg config files                                                                                                                                                          
    running build_clib                                                                                                                                                                                
    customize UnixCCompiler                                                                                                                                                                           
    customize UnixCCompiler using build_clib                                                                                                                                                          
    building 'carmcmc' library                                                                                                                                                                        
    compiling C++ sources                                                                                                                                                                             
    C compiler: g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC                                                            
                                                                                                                                                                                                      
    creating build                                                                                                                                                                                    
    creating build/temp.linux-x86_64-2.7                                                                                                                                                              
    compile options: '-I/opt/conda/include -I/usr/local/include -I/opt/armadillo/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/pyth
on2.7/site-packages/numpy/core/include -c'                                                                                                                                                            
    extra options: '-O3 -std=c++0x'                                                                                                                                                                   
    g++: ./proposals.cpp                                                                                                                                                                              
    g++: ./kfilter.cpp                                                                                                                                                                                
    ./kfilter.cpp: In member function ‘virtual std::pair<double, double> KalmanFilter1::Predict(double)’:                                                                                             
    ./kfilter.cpp:88:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                         
         for (int i=1; i<ipredict; i++) {                                                                                                                                                             
                       ~^~~~~~~~~                                                                                                                                                                     
    ./kfilter.cpp:124:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
         for (int i=ipredict+1; i<time_.n_elem; i++) {                                                                                                                                                
                                ~^~~~~~~~~~~~~                                                                                                                                                        
    ./kfilter.cpp: In member function ‘virtual void KalmanFilterp::Reset()’:                                                                                                                          
    ./kfilter.cpp:147:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
      for (int i=2; i<p_; i++) {                                                                                                                                                                      
                    ~^~~                                                                                                                                                                              
    ./kfilter.cpp:165:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
      for (int i=0; i<p_; i++) {                                                                                                                                                                      
                    ~^~~                                                                                                                                                                              
    ./kfilter.cpp:166:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
       for (int j=i; j<p_; j++) {                                                                                                                                                                     
                     ~^~~                                                                                                                                                                             
    ./kfilter.cpp: In member function ‘virtual std::pair<double, double> KalmanFilterp::Predict(double)’:                                                                                             
    ./kfilter.cpp:232:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
         for (int i=1; i<ipredict; i++) {                                                                                                                                                             
                       ~^~~~~~~~~                                                                                                                                                                     
    ./kfilter.cpp:275:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
         for (int i=ipredict+1; i<time_.n_elem; i++) {                                                                                                                                                
                                ~^~~~~~~~~~~~~                                                                                                                                                        
    In file included from ./kfilter.cpp:10:0:                                                                                                                                                         
    ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                           
    ./include/kfilter.hpp:256:56:   required from here                                                                                                                                                
    ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time.n_elem; i++) {                                                                                                                                                      
                           ~^~~~~~~~~~~~                                                                                                                                                              
    ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’: 
    ./include/kfilter.hpp:369:62:   required from here                                                                                                                                                
    ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
    g++: ./random.cpp                                                                                                                                                                                 
    ./random.cpp: In member function ‘arma::vec RandomGenerator::normal(arma::mat)’:                                                                                                                  
    ./random.cpp:99:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
      for (int i=0; i<z.n_elem; i++) {                                                                                                                                                                
                    ~^~~~~~~~~                                                                                                                                                                        
    g++: ./carpack.cpp                                                                                                                                                                                
    g++: ./carmcmc.cpp                                                                                                                                                                                
    ./carpack.cpp: In member function ‘virtual arma::vec CARp::SetStartingValue(arma::vec)’:                                                                                                          
    ./carpack.cpp:236:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
        if (init.n_elem != (p_+3)) {                                                                                                                                                                  
            ~~~~~~~~~~~~^~~~~~~~~                                                                                                                                                                     
    ./carpack.cpp: In member function ‘arma::vec CARp::StartingAR()’:                                                                                                                                 
    ./carpack.cpp:279:46: warning: ‘typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), const arma::Op<T1, arma::op_sort_vec> >::result arma::sort(const T
1&, arma::uword) [with T1 = arma::Col<double>; typename arma::enable_if2<(arma::is_arma_type<T1>::value && arma::resolves_to_vector<T1>::yes), const arma::Op<T1, arma::op_sort_vec> >::result = const
 arma::Op<arma::Col<double>, arma::op_sort_vec>; arma::uword = long long unsigned int]’ is deprecated [-Wdeprecated-declarations]                                                                     
         lorentz_cent = arma::sort(lorentz_cent, 1);                                                                                                                                                  
                                                  ^                                                                                                                                                   
    In file included from /opt/armadillo/include/armadillo:462:0,                                                                                                                                     
                     from ./carpack.cpp:17:                                                                                                                                                           
    /opt/armadillo/include/armadillo_bits/fn_sort.hpp:74:1: note: declared here                                                                                                                       
     sort                                                                                                                                                                                             
     ^~~~                                                                                                                                                                                             
    ./carpack.cpp: In member function ‘virtual bool CARp::CheckPriorBounds(arma::vec)’:                                                                                                               
    ./carpack.cpp:355:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
             for (int i=1; i<lorentz_cent.n_elem; i++) {                                                                                                                                              
                           ~^~~~~~~~~~~~~~~~~~~~                                                                                                                                                      
    ./carpack.cpp: In member function ‘double CARp::Variance(arma::cx_vec, arma::vec, double, double)’:                                                                                               
    ./carpack.cpp:384:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
      for (int k=0; k<alpha_roots.n_elem; k++) {                                                                                                                                                      
                    ~^~~~~~~~~~~~~~~~~~~                                                                                                                                                              
    ./carpack.cpp:387:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
       for (int l=0; l<alpha_roots.n_elem; l++) {                                                                                                                                                     
                     ~^~~~~~~~~~~~~~~~~~~                                                                                                                                                             
    ./carpack.cpp: In member function ‘virtual arma::vec CARMA::SetStartingValue(arma::vec)’:                                                                                                         
    ./carpack.cpp:481:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
        if (init.n_elem != (p_+q_+3)) {                                                                                                                                                               
            ~~~~~~~~~~~~^~~~~~~~~~~~                                                                                                                                                                  
    ./carpack.cpp: In member function ‘virtual arma::vec ZCARMA::SetStartingValue(arma::vec)’:                                                                                                        
    ./carpack.cpp:648:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
        if (init.n_elem != (p_+4)) {                                                                                                                                                                  
            ~~~~~~~~~~~~^~~~~~~~~                                                                                                                                                                     
    ./carpack.cpp: In function ‘arma::vec polycoefs(arma::cx_vec)’:                                                                                                                                   
    ./carpack.cpp:749:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
         for (int i=0; i<roots.n_elem; i++) {                                                                                                                                                         
                       ~^~~~~~~~~~~~~                                                                                                                                                                 
    In file included from ./include/carpack.hpp:24:0,                                                                                                                                                 
                     from ./carpack.cpp:23:                                                                                                                                                           
    ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                           
    ./include/kfilter.hpp:256:56:   required from here                                                                                                                                                
    ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time.n_elem; i++) {                                                                                                                                                      
                           ~^~~~~~~~~~~~                                                                                                                                                              
    ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’: 
    ./include/kfilter.hpp:369:62:   required from here                                                                                                                                                
    ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
    ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:                                                                                    
    ./carpack.cpp:78:23:   required from here                                                                                                                                                         
    ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=1; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    In file included from ./carpack.cpp:23:0:                                                                                                                                                         
    ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                                        
    ./carpack.cpp:90:36:   required from here                                                                                                                                                         
    ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    In file included from ./include/carpack.hpp:24:0,                                                                                                                                                 
                     from ./carpack.cpp:23:                                                                                                                                                           
    ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:                                                          
    ./carpack.cpp:218:27:   required from here                                                                                                                                                        
    ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=1; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    In file included from ./carpack.cpp:23:0:                                                                                                                                                         
    ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:              
    ./carpack.cpp:220:42:   required from here                                                                                                                                                        
    ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::bas
ic_string<char>]’:                                                                                                                                                                                    
    ./carpack.cpp:756:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                 
             for (int i=0; i<value_.n_elem; i++) {                                                                                                                                                    
                           ~^~~~~~~~~~~~~~                                                                                                                                                            
    ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:        
    ./carpack.cpp:756:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                 
    ./carmcmc.cpp: In function ‘std::shared_ptr<CAR1> RunCar1Sampler(int, int, std::vector<double>, std::vector<double>, std::vector<double>, int, const std::vector<double>&)’:                      
    ./carmcmc.cpp:43:9: warning: unused variable ‘report_iter’ [-Wunused-variable]                                                                                                                    
         int report_iter = burnin + thin * sample_size;                                                                                                                                               
             ^~~~~~~~~~~                                                                                                                                                                              
    In file included from ./include/carpack.hpp:24:0,                                                                                                                                                 
                     from ./carmcmc.cpp:27:                                                                                                                                                           
    ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                           
    ./include/kfilter.hpp:256:56:   required from here                                                                                                                                                
    ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time.n_elem; i++) {                                                                                                                                                      
                           ~^~~~~~~~~~~~                                                                                                                                                              
    ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’: 
    ./include/kfilter.hpp:369:62:   required from here                                                                                                                                                
    ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
    In file included from ./carmcmc.cpp:27:0:                                                                                                                                                         
    ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::bas
ic_string<char>]’:                                                                                                                                                                                    
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                 
             for (int i=0; i<value_.n_elem; i++) {                                                                                                                                                    
                           ~^~~~~~~~~~~~~~                                                                                                                                                            
    ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:              
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:        
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                 
             for (int i=0; i<value_.n_elem; i++) {                                                                                                                                                    
                           ~^~~~~~~~~~~~~~                                                                                                                                                            
    ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                                        
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    ./include/carpack.hpp: In instantiation of ‘void CARMA_Base<OmegaType>::Save(arma::vec&) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:                     
    ./include/steps.hpp:344:13:   required from ‘void ExchangeStep<ParValueType, ParameterType>::DoStep() [with ParValueType = arma::Col<double>; ParameterType = CARp]’                              
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    In file included from ./include/carpack.hpp:24:0,                                                                                                                                                 
                     from ./carmcmc.cpp:27:                                                                                                                                                           
    ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:                                                          
    ./include/carpack.hpp:155:13:   required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’            
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=1; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:                                                                                    
    ./include/carpack.hpp:155:13:   required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’                                      
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
    g++: ./steps.cpp                                                                                                                                                                                  
    g++: ./samplers.cpp                                                                                                                                                                               
    ./steps.cpp: In member function ‘virtual void AdaptiveMetro::DoStep()’:                                                                                                                           
    ./steps.cpp:66:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                           
      for (int i=0; i<old_value.n_rows; i++) {                                                                                                                                                        
                    ~^~~~~~~~~~~~~~~~~                                                                                                                                                                
    ./steps.cpp: In function ‘void CholUpdateR1(arma::mat&, arma::vec&, bool)’:                                                                                                                       
    ./steps.cpp:118:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                          
      for (int k=0; k<L.n_rows; k++) {                                                                                                                                                                
                    ~^~~~~~~~~                                                                                                                                                                        
    ./steps.cpp:123:9: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                           
       if (k < L.n_rows-1) {                                                                                                                                                                          
           ~~^~~~~~~~~~~~                                                                                                                                                                             
    ./samplers.cpp: In member function ‘void Sampler::Iterate(int, bool)’:                                                                                                                            
    ./samplers.cpp:41:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
        for(int i = 0; i < steps_.size(); ++i) {                                                                                                                                                      
                       ~~^~~~~~~~~~~~~~~                                                                                                                                                              
    ./samplers.cpp:49:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
        for(int i = 0; i < steps_.size(); ++i) {                                                                                                                                                      
                       ~~^~~~~~~~~~~~~~~                                                                                                                                                              
    ./samplers.cpp: In member function ‘void Sampler::Run(arma::vec)’:                                                                                                                                
    ./samplers.cpp:76:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                        
      bool useInit = (init.n_elem == npar);                                                                                                                                                           
                      ~~~~~~~~~~~~^~~~~~~                                                                                                                                                             
    ar: adding 7 object files to build/temp.linux-x86_64-2.7/libcarmcmc.a                                                                                                                             
    running build_ext                                                                                                                                                                                 
    customize UnixCCompiler                                                                                                                                                                           
    customize UnixCCompiler using build_ext                                                                                                                                                           
    updating extension 'carmcmc._carmcmc' libraries from ['boost_python', 'boost_filesystem', 'boost_system', 'armadillo', 'carmcmc'] to ['boost_python', 'boost_filesystem', 'boost_system', 'armadil
lo', 'carmcmc', 'boost_python', 'boost_filesystem', 'boost_system', 'armadillo']                                                                                                                      
    customize UnixCCompiler                                                                                                                                                                           
    customize UnixCCompiler using build_ext                                                                                                                                                           
    building 'carmcmc._carmcmc' extension                                                                                                                                                             
    compiling C++ sources                                                                                                                                                                             
    C compiler: g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC                                                            
                                                                                                                                                                                                      
    compile options: '-I/opt/conda/include -I/usr/local/include -I/opt/armadillo/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/pyth
on2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c'                                                                                                                             
    extra options: '-O3 -std=c++0x'                                                                                                                                                                   
    g++: ./boost_python_wrapper.cpp                                                                                                                                                                   
    g++: ./carmcmc.cpp                                                                                                                                                                                
    ./boost_python_wrapper.cpp:12:10: fatal error: boost/python/numeric.hpp: No such file or directory                                                                                                
     #include <boost/python/numeric.hpp>                                                                                                                                                              
              ^~~~~~~~~~~~~~~~~~~~~~~~~~                                                                                                                                                              
    compilation terminated.                                                                                                                                                                           
    error: Command "g++ -pthread -B /opt/conda/compiler_compat -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/opt/conda/include -I/usr/local/include -I/opt/armadi
llo/include -I/usr/include/ -I./include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c ./bo
ost_python_wrapper.cpp -o build/temp.linux-x86_64-2.7/boost_python_wrapper.o -MMD -MF build/temp.linux-x86_64-2.7/boost_python_wrapper.o.d -O3 -std=c++0x" failed with exit status 1                  
    ./carmcmc.cpp: In function ‘std::shared_ptr<CAR1> RunCar1Sampler(int, int, std::vector<double>, std::vector<double>, std::vector<double>, int, const std::vector<double>&)’:                      
    ./carmcmc.cpp:43:9: warning: unused variable ‘report_iter’ [-Wunused-variable]                                                                                                                    
         int report_iter = burnin + thin * sample_size;                                                                                                                                               
             ^~~~~~~~~~~                                                                                                                                                                              
    In file included from ./include/carpack.hpp:24:0,                                                                                                                                                 
                     from ./carmcmc.cpp:27:                                                                                                                                                           
    ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                           
    ./include/kfilter.hpp:256:56:   required from here                                                                                                                                                
    ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time.n_elem; i++) {                                                                                                                                                      
                           ~^~~~~~~~~~~~                                                                                                                                                              
    ./include/kfilter.hpp: In instantiation of ‘std::vector<double> KalmanFilter<OmegaType>::Simulate(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’: 
    ./include/kfilter.hpp:369:62:   required from here                                                                                                                                                
    ./include/kfilter.hpp:150:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
    In file included from ./carmcmc.cpp:27:0:                                                                                                                                                         
    ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = arma::Col<std::complex<double> >; std::__cxx11::string = std::__cxx11::bas
ic_string<char>]’:                                                                                                                                                                                    
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                 
             for (int i=0; i<value_.n_elem; i++) {                                                                                                                                                    
                           ~^~~~~~~~~~~~~~                                                                                                                                                            
    ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:              
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    ./include/carpack.hpp: In instantiation of ‘std::__cxx11::string CARMA_Base<OmegaType>::StringValue() [with OmegaType = double; std::__cxx11::string = std::__cxx11::basic_string<char>]’:        
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:81:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                 
             for (int i=0; i<value_.n_elem; i++) {                                                                                                                                                    
                           ~^~~~~~~~~~~~~~                                                                                                                                                            
    ./include/carpack.hpp: In instantiation of ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’:                                        
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:168:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    ./include/carpack.hpp: In instantiation of ‘void CARMA_Base<OmegaType>::Save(arma::vec&) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’:                     
    ./include/steps.hpp:344:13:   required from ‘void ExchangeStep<ParValueType, ParameterType>::DoStep() [with ParValueType = arma::Col<double>; ParameterType = CARp]’                              
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/carpack.hpp:102:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=0; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    In file included from ./include/carpack.hpp:24:0,                                                                                                                                                 
                     from ./carmcmc.cpp:27:                                                                                                                                                           
    ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = arma::Col<std::complex<double> >]’:                                                          
    ./include/carpack.hpp:155:13:   required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = arma::Col<std::complex<double> >; arma::vec = arma::Col<double>]’            
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
             for (int i=1; i<time_.n_elem; i++) {                                                                                                                                                     
                           ~^~~~~~~~~~~~~                                                                                                                                                             
    ./include/kfilter.hpp: In instantiation of ‘void KalmanFilter<OmegaType>::Filter() [with OmegaType = double]’:                                                                                    
    ./include/carpack.hpp:155:13:   required from ‘double CARMA_Base<OmegaType>::LogDensity(arma::vec) [with OmegaType = double; arma::vec = arma::Col<double>]’                                      
    ./carmcmc.cpp:177:1:   required from here                                                                                                                                                         
    ./include/kfilter.hpp:129:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]                                                                                
    ----------------------------------------                                                                                                                                                          
ERROR: Command errored out with exit status 1: /opt/conda/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-ORR7mJ/setup.py'"'"'; __file__='"'"'/tmp/pip-req-b
uild-ORR7mJ/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --r
ecord /tmp/pip-record-QfigSn/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.                                                                 
The command '/bin/bash -c cd carma_pack/src/ && pip install .' returned a non-zero code: 1                                                                                                            

[AstroVPK]

carmcmc is a package written by Brandon Kelly (https://arxiv.org/abs/1402.5978) and outside my control. It is included here purely to allowusers to compare results returned by his code to this package. It is completely optional and you can safely skip it.

[philastrophist]

Ok, cool. I've skipped that. But now I get the below. I'm not even sure where the error is....

Cloning into 'kali'...
notice: kali tools have been set up.
/opt/conda/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /kali/src/CARMATask_cython.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
/opt/conda/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /kali/src/MBHBTask_cython.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
/opt/conda/lib/python2.7/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /kali/src/rand.pyx
  tree = Parsing.p_module(s, pxd, full_module_name)
Compiling /kali/src/rand.pyx because it changed.
Compiling /kali/src/CARMATask_cython.pyx because it changed.
Compiling /kali/src/MBHBTask_cython.pyx because it changed.
[1/3] Cythonizing /kali/src/CARMATask_cython.pyx
[2/3] Cythonizing /kali/src/MBHBTask_cython.pyx
[3/3] Cythonizing /kali/src/rand.pyx
running build_ext
building 'rand' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/kali
creating build/temp.linux-x86_64-2.7/kali/src
g++ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/kali/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c /kali/src/rand.cpp -o build/temp.linux-x86_64-2.7/kali/src/rand.o -O3 -std=c++11 -I$MKLROOT/include -limf -fopenmp -fopenmp-simd
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:0,
                 from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /kali/src/rand.cpp:658:
/opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
g++ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/kali/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c /kali/src/rdrand.cpp -o build/temp.linux-x86_64-2.7/kali/src/rdrand.o -O3 -std=c++11 -I$MKLROOT/include -limf -fopenmp -fopenmp-simd
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
g++ -pthread -shared -B /opt/conda/compiler_compat -L/opt/conda/lib -Wl,-rpath=/opt/conda/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/kali/src/rand.o build/temp.linux-x86_64-2.7/kali/src/rdrand.o -L$MKLROOT/lib/inte -L/opt/conda/lib -Wl,-R$MKLROOT/lib/inte -lpython2.7 -o lib/rand.so -L$MKLROOT/lib/intel64 -lmkl_rt -lpthread -lm -ldl -lgomp -lnlopt
building 'LCTools_cython' extension
g++ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/kali/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c /kali/src/LCTools_cython.cpp -o build/temp.linux-x86_64-2.7/kali/src/LCTools_cython.o -O3 -std=c++11 -I$MKLROOT/include -limf -fopenmp -fopenmp-simd
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
In file included from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:0,
                 from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                 from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /kali/src/LCTools_cython.cpp:339:
/opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
 #warning "Using deprecated NumPy API, disable it with " \
  ^~~~~~~
In file included from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:21:0,
                 from /opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from /kali/src/LCTools_cython.cpp:339:
/opt/conda/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463:1: warning: ‘int _import_array()’ defined but not used [-Wunused-function]
 _import_array(void)
 ^~~~~~~~~~~~~
g++ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/kali/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c /kali/src/LC.cpp -o build/temp.linux-x86_64-2.7/kali/src/LC.o -O3 -std=c++11 -I$MKLROOT/include -limf -fopenmp -fopenmp-simd
cc1plus: warning: command line option ‘-Wstrict-prototypes’ is valid for C/ObjC but not for C++
/kali/src/LC.cpp:13:10: fatal error: mkl.h: No such file or directory
 #include <mkl.h>
          ^~~~~~~
compilation terminated.
error: command 'g++' failed with exit status 1

[AstroVPK]

Here's the error -
/kali/src/LC.cpp:13:10: fatal error: mkl.h: No such file or directory
You're missing MKL - either it isn't installed or the headers are not in one of the standard places. Generally speaking, MKL is a great library to use if you're on an Intel platform. Everything still works on AMD platforms but other libraries exist that potentially faster.

[philastrophist]

Thanks! I added a call to compilevars.sh and it appears to stop that message.

Ok this is relevant to your package now, running python setup.py build_ext gives me a new message:

DOCKERFILE

FROM ubuntu
SHELL ["/bin/bash", "-c"]
ENV LANG=C.UTF-8 LC_ALL=C.UTF-8
ENV PATH /opt/conda/bin:$PATH
ENV TINI_VERSION v0.16.1

RUN apt-get update --fix-missing && \
    apt-get install -y wget bzip2 ca-certificates curl git build-essential cmake libgtk2.0-common \
    				   libpango-1.0.0 libasound2-dev xserver-xorg cpio && \
    apt-get clean && \
    rm -rf /var/lib/apt/lists/*

RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh -O ~/miniconda.sh && \
    /bin/bash ~/miniconda.sh -b -p /opt/conda && \
    rm ~/miniconda.sh && \
    /opt/conda/bin/conda clean -tipsy && \
    ln -s /opt/conda/etc/profile.d/conda.sh /etc/profile.d/conda.sh && \
    echo ". /opt/conda/etc/profile.d/conda.sh" >> ~/.bashrc && \
    echo "conda activate base" >> ~/.bashrc

ADD https://github.com/krallin/tini/releases/download/${TINI_VERSION}/tini /usr/bin/tini
RUN chmod +x /usr/bin/tini

COPY parallel_studio_xe_2019_update5_cluster_edition_online.tgz .
COPY mysilent.cfg .
RUN echo "ACTIVATION_SERIAL_NUMBER=$SERIAL_NUMBER"  && echo "ACTIVATION_SERIAL_NUMBER=$SERIAL_NUMBER" >> mysilent.cfg
RUN tar -xvzf parallel_studio_xe_2019_update5_cluster_edition_online.tgz && \
	cd parallel_studio_xe_2019_update5_cluster_edition_online && \
	./install.sh --silent ../mysilent.cfg --cli-mode && \
 	echo "source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64" >> ~/.bashrc 
RUN cd ~

RUN conda install mkl
RUN wget https://github.com/stevengj/nlopt/archive/v2.6.1.tar.gz  -O nlopt.tar.gz 
RUN tar -xvzf nlopt.tar.gz && cd nlopt-2.6.1/ && cmake . && make && make install && ldconfig && cd ..

RUN conda update --all && conda install cython future pytest
RUN conda install numpy matplotlib scipy
RUN pip install gatspy multi_key_dict fitsio==0.9.8

# carma_pack
# RUN wget http://sourceforge.net/projects/boost/files/boost/1.54.0/boost_1_54_0.tar.bz2 && tar --bzip2 -xf boost_1_54_0.tar.bz2
# RUN cd boost_1_54_0 && ./bootstrap.sh && sed -i 's/explicit yield_sources ;/explicit allocator_sources ;/g' libs/coroutine/build/Jamfile.v2
# RUN cd boost_1_54_0 && ./b2 install

RUN wget http://sourceforge.net/projects/arma/files/armadillo-9.700.3.tar.xz && \
	tar -xf armadillo-9.700.3.tar.xz && cd armadillo-9.700.3 && \
	cmake -DCMAKE_INSTALL_PREFIX=/opt/armadillo -DBOOST_ROOT=$BOOST_DIR/  .  && \
	make install && cd ~

RUN apt-get update && apt-get install -y libboost-all-dev

RUN echo "export ARMADILLO_DIR=/opt/armadillo" >> ~/.bashrc
ENV ARMADILLO_DIR "/opt/armadillo"

RUN echo "export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}" >> ~/.bashrc
ENV LD_LIBRARY_PATH "/usr/local/lib:${LD_LIBRARY_PATH}"

RUN echo "export LD_LIBRARY_PATH=/opt/armadillo/lib:${LD_LIBRARY_PATH}" >> ~/.bashrc
ENV LD_LIBRARY_PATH "/opt/armadillo/lib:${LD_LIBRARY_PATH}"

RUN echo "export BOOST_DIR=/usr/local" >> ~/.bashrc
ENV BOOST_DIR "/usr/local"

ENV NUMPY_DIR "/opt/conda"

# COPY l_mkl_2019.5.281_online.tgz .
# RUN tar -xvzf l_mkl_2019.5.281_online.tgz && cd l_mkl_2019.5.281_online && ls
# RUN git clone https://github.com/brandonckelly/carma_pack.git
# RUN cd carma_pack/src/ && pip install .
RUN pip install acor
RUN echo "source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64" >> ~/.bashrc
RUN echo "source /opt/intel/mkl/bin/mklvars.sh intel64" >> ~/.bashrc
RUN git clone https://github.com/AstroVPK/kali.git 
ENV GXX_INCLUDE "/usr/lib/gcc/x86_64-pc-linux-gnu/6.4.1/include/c++"

RUN source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64 && \
	source /opt/intel/mkl/bin/mklvars.sh intel64 && \
	cd kali && source ./bin/setup.sh && python setup.py build_ext 
RUN echo "source ~/kali/bin/setup.sh" >> ~/.bashrc
RUN pytest tests && cd ~

ENTRYPOINT [ "/usr/bin/tini", "--" ]
CMD [ "/bin/bash" ]

ERROR MESSAGE

Compiling /kali/src/rand.pyx because it changed.
Compiling /kali/src/CARMATask_cython.pyx because it changed.
Compiling /kali/src/MBHBTask_cython.pyx because it changed.
[1/3] Cythonizing /kali/src/CARMATask_cython.pyx
[2/3] Cythonizing /kali/src/MBHBTask_cython.pyx
[3/3] Cythonizing /kali/src/rand.pyx
running build_ext
building 'rand' extension
creating build
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/kali
creating build/temp.linux-x86_64-2.7/kali/src
icpc -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/kali/include -I/opt/conda/lib/python2.7/site-packages/numpy/core/include -I/opt/conda/include/python2.7 -c /kali/src/rand.cpp -o build/temp.linux-x86_64-2.7/kali/src/rand.o -O3 -xHost -ip -parallel -funroll-loops -fno-alias -fno-fnalias -fargument-noalias -fstrict-aliasing -ansi-alias -fno-stack-protector-all -Wall -gxx-name=g++-4.8 -std=c++11 -falign-functions -I$MKLROOT/include -limf -qopenmp -qopenmp-simd -qopt-report=5 -qopt-report-phase=all
icpc: error #10417: Problem setting up the Intel(R) Compiler compilation environment.  Requires 'install path' setting gathered from 'g++-4.8'
error: command 'icpc' failed with exit status 1
The command '/bin/bash -c source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64 &&        source /opt/intel/mkl/bin/mklvars.sh intel64 &&         cd kali && source ./bin/setup.sh && python setup.py build_ext' returned a non-zero code: 1

[philastrophist]

I see that there is a branch for the Dockerfile, but it is a bit out of date now. I'll try it out and see what happens.