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This page was generated on 2022-03-18 11:07:41 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for GRENITS on riesling1


To the developers/maintainers of the GRENITS package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRENITS.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 825/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRENITS 1.47.0  (landing page)
Edward Morrissey
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/GRENITS
git_branch: master
git_last_commit: 2443b0d
git_last_commit_date: 2021-10-26 11:59:41 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GRENITS
Version: 1.47.0
Command: rm -rf GRENITS.buildbin-libdir && mkdir GRENITS.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=GRENITS.buildbin-libdir GRENITS_1.47.0.tar.gz
StartedAt: 2022-03-17 21:13:09 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 21:15:30 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 141.0 seconds
RetCode: 0
Status:   OK  
PackageFile: GRENITS_1.47.0.zip
PackageFileSize: 812 KiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GRENITS.buildbin-libdir && mkdir GRENITS.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=GRENITS.buildbin-libdir GRENITS_1.47.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'GRENITS' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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;
                                       ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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;
                                       ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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;
                                       ^~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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;
                                                               ^~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c R_C_interface.cpp -o R_C_interface.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)':
commonFunctions.cc:268:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i = 0; i!=Gamma_fixed.n_cols;i++)
                  ~^~~~~~~~~~~~~~~~~~~~
commonFunctions.cc:378:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-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;
                                                           ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c functionsErrorModel.cc -o functionsErrorModel.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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 of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
       for(int j_loop = 0; j_loop < genes; j_loop++)
                           ~~~~~~~^~~~~~~
updateFunctions_AR1.cc:134:8: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-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 of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-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;
                                                           ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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 of integer expressions of different signedness: 'int' and 'unsigned int' [-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 of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-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 of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
       for(base_k = 0; base_k != M; base_k++)
                       ~~~~~~~^~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o GRENITS.dll tmp.def 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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/meat/GRENITS.buildbin-libdir/00LOCK-GRENITS/00new/GRENITS/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'GRENITS'
    finding HTML links ... done
    LockeData                               html  
    LockeDataError                          html  
    analyse.output                          html  
    defaultParams_gauss                     html  
    defaultParams_linear                    html  
    defaultParams_nonLinear                 html  
    defaultParams_student                   html  
    function_LinearNet                      html  
    function_NonLinearNet                   html  
    function_ReplicatesNet_gauss            html  
    function_ReplicatesNet_student          html  
    plotPriors                              html  
    readChains                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* MD5 sums
packaged installation of 'GRENITS' as GRENITS_1.47.0.zip
* DONE (GRENITS)