Package: GRENITS

Version: 1.36.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GRENITS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GRENITS_1.36.0.tar.gz

StartedAt: 2019-10-16 02:11:48 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:16:54 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 305.3 seconds

RetCode: 0

Status:  OK

CheckDir: GRENITS.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:GRENITS.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings GRENITS_1.36.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/GRENITS.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRENITS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRENITS’ version ‘1.36.0’
* 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
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
* 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 R 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 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
function_NonLinearNet          120.871  0.112 121.601
function_ReplicatesNet_student  46.107  0.160  46.385
function_ReplicatesNet_gauss    39.298  0.119  47.973
analyse.output                  22.292  0.119  22.673
function_LinearNet              22.229  0.048  22.532
readChains                       7.273  0.040   7.315
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/GRENITS.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL GRENITS
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘GRENITS’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.9-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-3.9-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-3.9-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.9-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-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)

name	user	system	elapsed
analyse.output	22.292	0.119	22.673
defaultParams_gauss	0.020	0.000	0.021
defaultParams_linear	0.023	0.000	0.023
defaultParams_nonLinear	0.137	0.000	0.136
defaultParams_student	0.048	0.000	0.048
function_LinearNet	22.229	0.048	22.532
function_NonLinearNet	120.871	0.112	121.601
function_ReplicatesNet_gauss	39.298	0.119	47.973
function_ReplicatesNet_student	46.107	0.160	46.385
plotPriors	0.148	0.000	0.148
readChains	7.273	0.040	7.315