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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:GRENITS.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings GRENITS_1.63.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/GRENITS.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘GRENITS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRENITS’ version ‘1.63.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GRENITS’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.heatMap.ggplot: no visible global function definition for ‘ggplot’
.heatMap.ggplot: no visible global function definition for ‘aes’
.heatMap.ggplot: no visible binding for global variable ‘Var2’
.heatMap.ggplot: no visible binding for global variable ‘Var1’
.heatMap.ggplot: no visible global function definition for ‘geom_tile’
.heatMap.ggplot: no visible binding for global variable ‘value’
.heatMap.ggplot: no visible global function definition for
  ‘scale_fill_gradient’
.heatMap.ggplot: no visible global function definition for ‘theme’
.heatMap.ggplot: no visible global function definition for
  ‘element_blank’
.heatMap.ggplot: no visible global function definition for
  ‘element_text’
.heatMap.ggplot: no visible global function definition for ‘ggtitle’
.heatMap.ggplot: no visible global function definition for ‘labs’
.heatMap.ggplot: no visible global function definition for
  ‘scale_x_discrete’
.heatMap.ggplot: no visible global function definition for
  ‘scale_y_discrete’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘ggplot’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘aes’
.plotDistribParents.LargeMat: no visible binding for global variable
  ‘variable’
.plotDistribParents.LargeMat: no visible binding for global variable
  ‘GeneNames’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘geom_tile’
.plotDistribParents.LargeMat: no visible binding for global variable
  ‘value’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘scale_fill_gradient’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘theme’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘element_blank’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘element_text’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘ggtitle’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘labs’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘scale_x_discrete’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘scale_y_discrete’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘facet_wrap’
Undefined global functions or variables:
  GeneNames Var1 Var2 aes element_blank element_text facet_wrap
  geom_tile ggplot ggtitle labs scale_fill_gradient scale_x_discrete
  scale_y_discrete theme value variable
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... INFO
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ...* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                 user system elapsed
function_NonLinearNet          78.921  0.070  78.999
function_ReplicatesNet_student 29.576  0.089  29.671
function_ReplicatesNet_gauss   22.378  0.079  22.459
analyse.output                 12.714  0.081  12.795
function_LinearNet             11.949  0.060  12.018
readChains                      5.854  0.024   5.970
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/GRENITS.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL GRENITS
###
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘GRENITS’ ...
** this is package ‘GRENITS’ version ‘1.63.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
AR1_Gauss_biocond.cc: In function ‘void Error_Gauss_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)’:
AR1_Gauss_biocond.cc:49:30: warning: unused variable ‘numDiag’ [-Wunused-variable]
   49 |   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]
   49 |   int           num_fixedON, numDiag, p_sqr, free_gammas;
      |                                       ^~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
AR1_Student_biocond.cc: In function ‘void Error_Student_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)’:
AR1_Student_biocond.cc:49:30: warning: unused variable ‘numDiag’ [-Wunused-variable]
   49 |   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]
   49 |   int           num_fixedON, numDiag, p_sqr, free_gammas;
      |                                       ^~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c AR1_biocond.cc -o AR1_biocond.o
AR1_biocond.cc: In function ‘void AR1_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)’:
AR1_biocond.cc:48:30: warning: unused variable ‘numDiag’ [-Wunused-variable]
   48 |   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]
   48 |   int           num_fixedON, numDiag, p_sqr, free_gammas;
      |                                       ^~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c PSplines_biocond.cc -o PSplines_biocond.o
PSplines_biocond.cc: In function ‘void PSplines_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)’:
PSplines_biocond.cc:45:63: warning: unused variable ‘numDiag’ [-Wunused-variable]
   45 |   int                 num_fixedON, nodesSpline, degreeSpline, numDiag, free_gammas;
      |                                                               ^~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c R_C_interface.cpp -o R_C_interface.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -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 arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  268 |   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]
  315 |   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 arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  375 |   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 arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  378 |     for(int j = 0; j!=Gamma_fixed.n_cols;j++)
      |                    ~^~~~~~~~~~~~~~~~~~~~
commonFunctions.cc: In function ‘void updateCoefficients_reg(arma::mat&, const int&, const arma::urowvec&, const arma::mat&, const arma::rowvec&, const arma::ucolvec&)’:
commonFunctions.cc:438:59: warning: unused variable ‘num_on’ [-Wunused-variable]
  438 |   unsigned int                                            num_on;
      |                                                           ^~~~~~
commonFunctions.cc: In function ‘void updateCoefficients(arma::mat&, const int&, const arma::urowvec&, const arma::mat&, const arma::rowvec&)’:
commonFunctions.cc:480:59: warning: unused variable ‘num_on’ [-Wunused-variable]
  480 |   unsigned int                                            num_on;
      |                                                           ^~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
updateFunctions_AR1.cc: In function ‘void updateCoeffAndGibbsVars(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, const arma::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]
  128 |       for(int j_loop = 0; j_loop < genes; j_loop++)
      |                           ~~~~~~~^~~~~~~
updateFunctions_AR1.cc:134:15: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  134 |         if (i != j)
      |             ~~^~~~
updateFunctions_AR1.cc: In function ‘void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::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 arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  186 |       for(int j_loop = 0; j_loop < seq_rnd.n_elem; j_loop++)
      |                           ~~~~~~~^~~~~~~~~~~~~~~~
updateFunctions_AR1.cc: In function ‘void calc_logMVPDF_withLinks(double&, const arma::mat&, const arma::rowvec&, arma::urowvec&)’:
updateFunctions_AR1.cc:264:59: warning: unused variable ‘num_on’ [-Wunused-variable]
  264 |   unsigned int                                            num_on;
      |                                                           ^~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
updateFunctions_Splines.cc: In function ‘void initBasesOn_rowvec(arma::urowvec&, const arma::urowvec&, int, int)’:
updateFunctions_Splines.cc:158:16: warning: variable ‘start_indx’ set but not used [-Wunused-but-set-variable]
  158 |   int       G, start_indx, end_indx;
      |                ^~~~~~~~~~
updateFunctions_Splines.cc:158:28: warning: variable ‘end_indx’ set but not used [-Wunused-but-set-variable]
  158 |   int       G, start_indx, end_indx;
      |                            ^~~~~~~~
updateFunctions_Splines.cc: In function ‘void initBasesOn(arma::urowvec&, const arma::umat&, int, int)’:
updateFunctions_Splines.cc:182:16: warning: variable ‘start_indx’ set but not used [-Wunused-but-set-variable]
  182 |   int       G, start_indx, end_indx;
      |                ^~~~~~~~~~
updateFunctions_Splines.cc:182:28: warning: variable ‘end_indx’ set but not used [-Wunused-but-set-variable]
  182 |   int       G, start_indx, end_indx;
      |                            ^~~~~~~~
updateFunctions_Splines.cc: In function ‘void updateTaus_reg(arma::mat&, arma::colvec&, const arma::mat&, arma::urowvec&, const arma::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]
  296 |     if(i == indxReg)
      |        ~~^~~~~~~~~~
updateFunctions_Splines.cc: In function ‘void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const arma::mat&, const arma::rowvec&, const arma::colvec&, int, int, int, arma::urowvec&, const arma::ucolvec&, const arma::urowvec&, const arma::ucolvec&, const arma::uvec&)’:
updateFunctions_Splines.cc:478:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  478 |   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]
  714 |       for(base_k = 0; base_k != M; base_k++)
      |                       ~~~~~~~^~~~
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-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 -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
installing to /home/biocbuild/bbs-3.23-bioc/R/site-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)