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INSTALL report for GRENITS on malbec2

This page was generated on 2020-10-17 11:54:54 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GRENITS PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 776/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRENITS 1.40.0
Edward Morrissey
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GRENITS
Branch: RELEASE_3_11
Last Commit: 75d149a
Last Changed Date: 2020-04-27 14:26:17 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GRENITS
Version: 1.40.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GRENITS
StartedAt: 2020-10-16 16:13:15 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 16:14:55 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 100.7 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GRENITS
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘GRENITS’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
AR1_Gauss_biocond.cc: In function ‘void Error_Gauss_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)’:
AR1_Gauss_biocond.cc:49:30: warning: unused variable ‘numDiag’ [-Wunused-variable]
   int           num_fixedON, numDiag, p_sqr, free_gammas;
                              ^~~~~~~
AR1_Gauss_biocond.cc:49:39: warning: variable ‘p_sqr’ set but not used [-Wunused-but-set-variable]
   int           num_fixedON, numDiag, p_sqr, free_gammas;
                                       ^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
AR1_Student_biocond.cc: In function ‘void Error_Student_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)’:
AR1_Student_biocond.cc:49:30: warning: unused variable ‘numDiag’ [-Wunused-variable]
   int           num_fixedON, numDiag, p_sqr, free_gammas;
                              ^~~~~~~
AR1_Student_biocond.cc:49:39: warning: variable ‘p_sqr’ set but not used [-Wunused-but-set-variable]
   int           num_fixedON, numDiag, p_sqr, free_gammas;
                                       ^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c AR1_biocond.cc -o AR1_biocond.o
AR1_biocond.cc: In function ‘void AR1_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)’:
AR1_biocond.cc:48:30: warning: unused variable ‘numDiag’ [-Wunused-variable]
   int           num_fixedON, numDiag, p_sqr, free_gammas;
                              ^~~~~~~
AR1_biocond.cc:48:39: warning: variable ‘p_sqr’ set but not used [-Wunused-but-set-variable]
   int           num_fixedON, numDiag, p_sqr, free_gammas;
                                       ^~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c PSplines_biocond.cc -o PSplines_biocond.o
PSplines_biocond.cc: In function ‘void PSplines_c(std::__cxx11::string&, arma::mat&, arma::colvec&, arma::mat&)’:
PSplines_biocond.cc:45:63: warning: unused variable ‘numDiag’ [-Wunused-variable]
   int                 num_fixedON, nodesSpline, degreeSpline, numDiag, free_gammas;
                                                               ^~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c R_C_interface.cpp -o R_C_interface.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc: In function ‘void random_intSequence(arma::ucolvec&)’:
commonFunctions.cc:268:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (int i = 0; i < seq.n_elem; i++)
                   ~~^~~~~~~~~~~~
commonFunctions.cc: In function ‘void estimateRemainingTime(double&, double&, int, int, clock_t&)’:
commonFunctions.cc:315:36: warning: variable ‘so_far_clock’ set but not used [-Wunused-but-set-variable]
   clock_t                          so_far_clock, time_now; //so_far_sec,
                                    ^~~~~~~~~~~~
commonFunctions.cc: In function ‘void processFixedGammas(arma::mat&, int&, int&, arma::umat&, arma::umat&, arma::ucolvec&, arma::umat&, arma::uvec&, arma::uvec&)’:
commonFunctions.cc:375:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 0; i!=Gamma_fixed.n_cols;i++)
                  ~^~~~~~~~~~~~~~~~~~~~
commonFunctions.cc:378:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j = 0; j!=Gamma_fixed.n_cols;j++)
                    ~^~~~~~~~~~~~~~~~~~~~
commonFunctions.cc: In function ‘void updateCoefficients_reg(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&, const ucolvec&)’:
commonFunctions.cc:438:59: warning: unused variable ‘num_on’ [-Wunused-variable]
   unsigned int                                            num_on;
                                                           ^~~~~~
commonFunctions.cc: In function ‘void updateCoefficients(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&)’:
commonFunctions.cc:480:59: warning: unused variable ‘num_on’ [-Wunused-variable]
   unsigned int                                            num_on;
                                                           ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
updateFunctions_AR1.cc: In function ‘void updateCoeffAndGibbsVars(arma::mat&, arma::umat&, const colvec&, const mat&, const mat&, const mat&, const double&, const unsigned int&)’:
updateFunctions_AR1.cc:128:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j_loop = 0; j_loop < genes; j_loop++)
                           ~~~~~~~^~~~~~~
updateFunctions_AR1.cc:134:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (i != j)
      ~~^~~~
updateFunctions_AR1.cc: In function ‘void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const colvec&, const mat&, const mat&, double, const double&, const unsigned int&, arma::umat&, arma::ucolvec&, arma::umat&)’:
updateFunctions_AR1.cc:186:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(int j_loop = 0; j_loop < seq_rnd.n_elem; j_loop++)
                           ~~~~~~~^~~~~~~~~~~~~~~~
updateFunctions_AR1.cc: In function ‘void calc_logMVPDF_withLinks(double&, const mat&, const rowvec&, arma::urowvec&)’:
updateFunctions_AR1.cc:264:59: warning: unused variable ‘num_on’ [-Wunused-variable]
   unsigned int                                            num_on;
                                                           ^~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.11-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
updateFunctions_Splines.cc: In function ‘void initBasesOn_rowvec(arma::urowvec&, const urowvec&, int, int)’:
updateFunctions_Splines.cc:158:16: warning: variable ‘start_indx’ set but not used [-Wunused-but-set-variable]
   int       G, start_indx, end_indx;
                ^~~~~~~~~~
updateFunctions_Splines.cc:158:28: warning: variable ‘end_indx’ set but not used [-Wunused-but-set-variable]
   int       G, start_indx, end_indx;
                            ^~~~~~~~
updateFunctions_Splines.cc: In function ‘void initBasesOn(arma::urowvec&, const umat&, int, int)’:
updateFunctions_Splines.cc:182:16: warning: variable ‘start_indx’ set but not used [-Wunused-but-set-variable]
   int       G, start_indx, end_indx;
                ^~~~~~~~~~
updateFunctions_Splines.cc:182:28: warning: variable ‘end_indx’ set but not used [-Wunused-but-set-variable]
   int       G, start_indx, end_indx;
                            ^~~~~~~~
updateFunctions_Splines.cc: In function ‘void updateTaus_reg(arma::mat&, arma::colvec&, const mat&, arma::urowvec&, const mat&, double, double, int, double, double, double, double, int, double, arma::uvec)’:
updateFunctions_Splines.cc:296:10: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if(i == indxReg)
        ~~^~~~~~~~~~
updateFunctions_Splines.cc: In function ‘void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const mat&, const rowvec&, const colvec&, int, int, int, arma::urowvec&, const ucolvec&, const urowvec&, const ucolvec&, const uvec&)’:
updateFunctions_Splines.cc:478:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int j_loop = 0; j_loop < seq_rnd.n_elem; j_loop++)
                       ~~~~~~~^~~~~~~~~~~~~~~~
updateFunctions_Splines.cc: In function ‘void fixedBasesFromFixedRegs(arma::umat&, arma::umat&, arma::ucolvec&, int)’:
updateFunctions_Splines.cc:714:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for(base_k = 0; base_k != M; base_k++)
                       ~~~~~~~^~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.11-bioc/R/lib -L/usr/local/lib -o GRENITS.so AR1_Gauss_biocond.o AR1_Student_biocond.o AR1_biocond.o PSplines_biocond.o R_C_interface.o ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.11-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.11-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.11-bioc/R/library/00LOCK-GRENITS/00new/GRENITS/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 (GRENITS)