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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/birte_1.16.0.tar.gz && rm -rf birte.buildbin-libdir && mkdir birte.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=birte.buildbin-libdir birte_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL birte_1.16.0.zip && rm birte_1.16.0.tar.gz birte_1.16.0.zip
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install for i386
* installing *source* package 'birte' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::list<int>*, std::list<int>*, std::list<int>*, 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::list<int>*, 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<int>*, std::list<int>*, std::set<int>**, 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:1026:26: warning: 'delta_loglik' may be used uninitialized in this function [-Wmaybe-uninitialized]
log_lik += delta_loglik;
^
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o birte.dll tmp.def BayesNetwork.o getStates.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/birte.buildbin-libdir/birte/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'birte'
finding HTML links ... done
EColiNetwork html
EColiOxygen html
TFexpr html
birteFitRidge html
finding level-2 HTML links ... done
birtePredict html
birteRun html
estimateNetwork html
getPotentialSwaps html
humanNetwork html
limmaAnalysis html
plotConvergence html
proposeInteractions html
simplify html
simulateData html
suggestThreshold html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'birte' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, std::list<int>*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::list<int>*, std::list<int>*, std::list<int>*, 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::list<int>*, 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<int>*, std::list<int>*, std::set<int>**, 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:1026:26: warning: 'delta_loglik' may be used uninitialized in this function [-Wmaybe-uninitialized]
log_lik += delta_loglik;
^
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -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
Loading required package: Rcpp
Loading required package: Rcpp
Loading required package: Rcpp
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o birte.dll tmp.def BayesNetwork.o getStates.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/birte.buildbin-libdir/birte/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'birte' as birte_1.16.0.zip
* DONE (birte)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'birte' successfully unpacked and MD5 sums checked
In R CMD INSTALL
