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INSTALL report for birte on malbec1

This page was generated on 2020-04-15 12:09:42 -0400 (Wed, 15 Apr 2020).

Package 183/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
birte 1.22.0
Holger Froehlich
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/birte
Branch: RELEASE_3_10
Last Commit: cadde5e
Last Changed Date: 2019-10-29 13:09:09 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64 [ OK ] ERROR  skipped 
tokay1 Windows Server 2012 R2 Standard / x64  OK  ERROR  skipped  skipped 
merida1 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: birte
Version: 1.22.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL birte
StartedAt: 2020-04-14 18:28:23 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 18:28:51 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 27.1 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL birte
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘birte’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-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<int>*, std::__cxx11::list<int>*, std::__cxx11::list<int>*, std::__cxx11::list<int>*, std::__cxx11::list<int>*, std::__cxx11::list<int>*, double, double, double, double, double, double, double, double, double, double*, double*, double*, double*, double*, double*, int, int, std::__cxx11::list<int>*, std::__cxx11::list<int>*, std::__cxx11::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::__cxx11::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::__cxx11::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:1026:11: warning: ‘delta_loglik’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   log_lik += delta_loglik;
   ~~~~~~~~^~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"/home/biocbuild/bbs-3.10-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-3.10-bioc/R/lib -L/usr/local/lib -o birte.so BayesNetwork.o getStates.o -llapack -lblas -L/home/biocbuild/bbs-3.10-bioc/R/lib -lR
Loading required package: Rcpp
installing to /home/biocbuild/bbs-3.10-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
Warning: Package 'birte' is deprecated and will be removed from Bioconductor
  version 3.11
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'birte' is deprecated and will be removed from Bioconductor
  version 3.11
** testing if installed package keeps a record of temporary installation path
* DONE (birte)