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### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL birte
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘birte’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c BayesNetwork.cpp -o BayesNetwork.o
In file included from BayesNetwork.cpp:26:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
/**
BayesNetwork.cpp: In constructor ‘BayesNetwork::BayesNetwork(int, int, int, int, int, int**, double***, double***, double***, double***, int, int, int, int, int, double*, double*, double*, double*, std::__cxx11::list*, std::__cxx11::list*, std::__cxx11::list*, std::__cxx11::list*, std::__cxx11::list*, std::__cxx11::list*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::__cxx11::list*, std::__cxx11::list*, std::__cxx11::list*, double*, double*, double*, double**, int**, int**, int**, int**, double**, double**, double**)’:
BayesNetwork.cpp:96:8: warning: unused variable ‘j’ [-Wunused-variable]
int i,j,c,r;
^
BayesNetwork.cpp:96:12: warning: unused variable ‘r’ [-Wunused-variable]
int i,j,c,r;
^
BayesNetwork.cpp: In destructor ‘virtual BayesNetwork::~BayesNetwork()’:
BayesNetwork.cpp:221:8: warning: unused variable ‘i’ [-Wunused-variable]
int c,i,j;
^
BayesNetwork.cpp:221:10: warning: unused variable ‘j’ [-Wunused-variable]
int c,i,j;
^
BayesNetwork.cpp: In member function ‘virtual int BayesNetwork::expandDesignMatrix(int, int, int, std::__cxx11::list*, double**, int)’:
BayesNetwork.cpp:357:6: warning: unused variable ‘found’ [-Wunused-variable]
int found, omega_index = 0, i, j;
^~~~~
BayesNetwork.cpp:357:30: warning: unused variable ‘i’ [-Wunused-variable]
int found, omega_index = 0, i, j;
^
BayesNetwork.cpp: In member function ‘virtual int BayesNetwork::shrinkDesignMatrix(int, int, int)’:
BayesNetwork.cpp:383:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
if(p.first == switchid & p.second == mir){
~~~~~~~~^~~~~~~~~~~
BayesNetwork.cpp:380:11: warning: unused variable ‘k’ [-Wunused-variable]
int j=1, k, del=-1; // j startet bei 1, weil die 1. Spalte der Intercept ist
^
BayesNetwork.cpp: In member function ‘virtual void BayesNetwork::updateEvidence2(int, int, int, arma::colvec&)’:
BayesNetwork.cpp:599:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(add != R[c].n_cols){
~~~~^~~~~~~~~~~~~~
BayesNetwork.cpp: In member function ‘virtual double BayesNetwork::swap_states(int**, int, int, std::set*, std::__cxx11::list*, std::set**, double)’:
BayesNetwork.cpp:669:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(swapid1 >= swap_idx[condition].size()) {
~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
BayesNetwork.cpp:665:6: warning: unused variable ‘pos_swaps’ [-Wunused-variable]
int pos_swaps = 0, condition, condition1, condition2, counter;
^~~~~~~~~
BayesNetwork.cpp: In member function ‘virtual void BayesNetwork::MCMC(long int, long int, int, double*)’:
BayesNetwork.cpp:842:6: warning: unused variable ‘mir’ [-Wunused-variable]
int mir, tf;
^~~
BayesNetwork.cpp:842:11: warning: unused variable ‘tf’ [-Wunused-variable]
int mir, tf;
^~
BayesNetwork.cpp:847:7: warning: unused variable ‘eff_samples’ [-Wunused-variable]
long eff_samples = niter / thin + 1;
^~~~~~~~~~~
BayesNetwork.cpp:909:23: warning: unused variable ‘u’ [-Wunused-variable]
double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;
^
BayesNetwork.cpp:909:26: warning: unused variable ‘delta_prior’ [-Wunused-variable]
double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;
^~~~~~~~~~~
BayesNetwork.cpp:909:39: warning: unused variable ‘eps_new’ [-Wunused-variable]
double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;
^~~~~~~
BayesNetwork.cpp:909:48: warning: unused variable ‘eps_old’ [-Wunused-variable]
double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;
^~~~~~~
BayesNetwork.cpp:909:57: warning: unused variable ‘delta_eps’ [-Wunused-variable]
double delta_loglik, u, delta_prior, eps_new, eps_old, delta_eps, best_loglik=-INFINITY;
^~~~~~~~~
BayesNetwork.cpp:910:102: warning: unused variable ‘make_move_eps’ [-Wunused-variable]
int nall_possible_ops, n_Tpos_swaps_total=0, n_Spos_swaps_total=0, n_Qpos_swaps_total=0, make_move, make_move_eps=0, cond=0;
^~~~~~~~~~~~~
BayesNetwork.cpp:910:119: warning: unused variable ‘cond’ [-Wunused-variable]
int nall_possible_ops, n_Tpos_swaps_total=0, n_Spos_swaps_total=0, n_Qpos_swaps_total=0, make_move, make_move_eps=0, cond=0;
^~~~
BayesNetwork.cpp: In member function ‘virtual double BayesNetwork::likelihood()’:
BayesNetwork.cpp:1074:12: warning: unused variable ‘j’ [-Wunused-variable]
int c, i, j, r;
^
BayesNetwork.cpp:1075:9: warning: unused variable ‘bn’ [-Wunused-variable]
double bn;
^~
BayesNetwork.cpp:1078:9: warning: unused variable ‘z’ [-Wunused-variable]
double z;
^
BayesNetwork.cpp: In member function ‘virtual void BayesNetwork::MCMC(long int, long int, int, double*)’:
BayesNetwork.cpp:1026:11: warning: ‘delta_loglik’ may be used uninitialized in this function [-Wmaybe-uninitialized]
log_lik += delta_loglik;
~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I/usr/local/include -fpic -g -O2 -Wall -c getStates.cpp -o getStates.o
In file included from getStates.cpp:24:0:
BayesNetwork.h:203:3: warning: "/*" within comment [-Wcomment]
/**
getStates.cpp: In function ‘SEXPREC* getStates(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
getStates.cpp:349:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if(S2O == NULL | SparentsOfO == NULL)
^
getStates.cpp:366:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if(T2O == NULL | TparentsOfO == NULL)
^
getStates.cpp:384:11: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if(Q2O == NULL | QparentsOfO == NULL)
^
Loading required package: Rcpp
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o birte.so BayesNetwork.o getStates.o -llapack -lblas -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-birte/00new/birte/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (birte)
