Package: XDE

Version: 2.29.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:XDE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings XDE_2.29.0.tar.gz

StartedAt: 2019-04-09 04:20:59 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:23:27 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 148.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: XDE.Rcheck

Warnings: 1

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:XDE.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings XDE_2.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/XDE.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XDE/DESCRIPTION’ ... OK
* this is package ‘XDE’ version ‘2.29.0’
* 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 ‘XDE’ can be installed ... WARNING
Found the following significant warnings:
  Warning: For function ‘dims’, signature ‘Parameters’: argument in method definition changed from (object) to (x)
See ‘/home/biocbuild/bbs-3.9-bioc/meat/XDE.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.3Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/XDE.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 XDE
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘XDE’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Cholesky.cpp -o Cholesky.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Matrix_v2.cpp -o Matrix_v2.o
Matrix_v2.cpp: In function ‘void matrixMult(const std::vector<std::vector<double> >&, const std::vector<double>&, std::vector<double>&)’:
Matrix_v2.cpp:244:7: warning: unused variable ‘k’ [-Wunused-variable]
   int k = 1;
       ^
Matrix_v2.cpp:246:9: warning: unused variable ‘j’ [-Wunused-variable]
   int i,j,r;
         ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Potential_v2.cpp -o Potential_v2.o
Potential_v2.cpp: In function ‘double potentialDDeltaStar_HyperInverseWishart(int, const double*, const double*, const double*, const double*, const double*, int, int, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Potential_v2.cpp:308:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < UBlocks.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:310:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < UBlocks[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:316:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < theGene.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:321:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < Omega[0].size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:322:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < UU[first].size(); j++) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:328:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Omega.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:329:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < oldComponents[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:330:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < UU[first].size(); j++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:335:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < Omega[k].size() - oldComponents[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:336:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < UU[first].size(); j++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:345:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < Omega.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:347:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < theGene[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:356:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Omega.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:364:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaSub.size(); i++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:366:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaSub[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:369:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < USub.size(); i++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:371:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < USub[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Potential_v2.cpp:374:34: warning: statement has no effect [-Wunused-value]
  if (theGene[k][i] == 1) include == 1;
                          ˜˜˜˜˜˜˜˜^˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Random_v2.cpp -o Random_v2.o
Random_v2.cpp: In member function ‘int Random::Discrete(const std::vector<double>&)’:
Random_v2.cpp:159:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < prob.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp: In member function ‘std::vector<std::vector<double> > Random::CorrelationStandardInverseWishartAlternativeParam(int, double)’:
Random_v2.cpp:512:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < w.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:515:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < w[i].size(); j++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp: In member function ‘std::vector<std::vector<std::vector<double> > > Random::HyperInverseWishart(double, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Random_v2.cpp:548:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < D.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:551:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < Sigma[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:557:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < temp.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:558:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < temp[i].size(); j++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:571:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < D.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:585:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DRR.size(); i++) DRR[i].resize(DRR.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:586:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DSS.size(); i++) DSS[i].resize(DSS.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:587:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DRS.size(); i++) DRS[i].resize(DSS.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:588:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DSR.size(); i++) DSR[i].resize(DRR.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:590:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DSS.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:591:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DSS[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:594:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DRR.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:595:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DRR[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:598:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DSR.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:599:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DSR[i].size(); j++) {
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:608:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaSS.size(); i++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:610:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaSS[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:625:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DRR.size(); i++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:627:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DRR[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:675:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < LDSSInverseT.size(); i++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:677:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < LDSSInverseT[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:693:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DRR.size(); i++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:695:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DSS.size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:705:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < mean.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:706:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < mean[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:726:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaSR.size(); i++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:728:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaSR[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:740:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaRGivenS.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:741:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaRGivenS[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:746:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaSS.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:747:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaSS[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:749:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaRR.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:750:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaRR[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:752:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaSS.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:753:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaRR.size(); j++) {
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:760:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < temp7.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:761:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < temp7[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp: In member function ‘std::vector<double> Random::GaussianGraphicalModel(const std::vector<double>&, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Random_v2.cpp:790:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < UBlocks[k].size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:807:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < vec.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:812:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < vec.size(); i++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:821:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Cov.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:834:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovSS.size(); i++) CovSS[i].resize(CovSS.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:835:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovRR.size(); i++) CovRR[i].resize(CovRR.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:836:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovSR.size(); i++) CovSR[i].resize(CovRS.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:837:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovRS.size(); i++) CovRS[i].resize(CovSR.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:840:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovSS.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:841:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < CovSS[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:844:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovRR.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:845:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < CovRR[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:848:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovSR.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:849:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < CovSR[i].size(); j++) {
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:863:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovRGivenS.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:864:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < CovRGivenS[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:877:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < vec.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:884:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < obs.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:889:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < mean.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:894:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < z.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:899:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < obs.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:901:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < z.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:913:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < vec.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:918:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < z.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:923:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < z.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:928:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < mean.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp: In member function ‘std::vector<std::vector<double> > Random::MatrixVariateNormal(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Random_v2.cpp:948:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < UBlocks.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:950:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < UBlocks[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:966:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j < U[0].size(); j++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:968:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < vec.size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:973:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < vec.size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:976:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j == U[0].size() - 1) first += z.size();
         ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:978:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < z.size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:994:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Omega.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1007:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaSS.size(); i++) OmegaSS[i].resize(OmegaSS.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1008:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaRR.size(); i++) OmegaRR[i].resize(OmegaRR.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1009:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaSR.size(); i++) OmegaSR[i].resize(OmegaRS.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1010:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaRS.size(); i++) OmegaRS[i].resize(OmegaSR.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1012:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaSS.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1013:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaSS[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1016:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaRR.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1017:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaRR[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1020:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaSR.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1021:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaSR[i].size(); j++) {
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1035:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaRGivenS.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1036:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaRGivenS[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1048:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < U[0].size(); j++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1050:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < vec.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1057:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < obs.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1062:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < mean.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1067:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < z.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1070:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (j == U[0].size() - 1) first += z.size();
      ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1072:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < obs.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1074:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < z.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1086:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < U[k].size(); j++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1088:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < vec.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1093:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < vec.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1096:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (j == U[k].size() - 1) first += z.size();
      ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1098:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < z.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1133:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < LT.size(); i++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1135:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < LT[i].size(); j++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1143:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < U.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1144:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < U[i].size(); j++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp: In member function ‘double Random::PotentialHyperInverseWishart(double, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&, const std::vector<std::vector<std::vector<double> > >&)’:
Random_v2.cpp:1183:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < D.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1188:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < D.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1196:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DSS.size(); i++) DSS[i].resize(DSS.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1197:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaSS.size(); i++) SigmaSS[i].resize(SigmaSS.size());
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1199:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DSS.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1200:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DSS[i].size(); j++) {
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp: In member function ‘double Random::PotentialGaussianGraphicalModel(const std::vector<double>&, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&, const std::vector<double>&)’:
Random_v2.cpp:1225:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < UU.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1232:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < UBlocks.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1236:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < Cov[0].size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1240:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Cov.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1241:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < oldComponents[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1244:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < Cov[k].size() - oldComponents[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1251:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < Cov.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1258:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Cov.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1265:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovSub.size(); i++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1267:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < CovSub[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1271:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < USub.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp: In member function ‘double Random::PotentialMatrixVariateNormal(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)’:
Random_v2.cpp:1297:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < XT.size(); i++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1299:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < XT[i].size(); j++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1310:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < temp3.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp: In member function ‘double Random::PotentialMatrixVariateNormal(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&, const std::vector<std::vector<double> >&)’:
Random_v2.cpp:1335:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < UU.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1336:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < UU[i].size(); j++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1343:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < UBlocks.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1345:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < UBlocks[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1350:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < Omega[0].size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1351:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < UU[first].size(); j++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1355:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Omega.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1356:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < oldComponents[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1357:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < UU[first].size(); j++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1360:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < Omega[k].size() - oldComponents[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1361:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < UU[first].size(); j++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1380:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < Omega.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1385:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Omega.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1391:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaSub.size(); i++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1393:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaSub[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1396:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < USub.size(); i++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp:1398:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < USub[i].size(); j++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp: In member function ‘std::vector<int> Random::Permutation(int)’:
Random_v2.cpp:1822:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < perm.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Random_v2.cpp: In member function ‘double Random::lnGamma(double)’:
Random_v2.cpp:1847:10: warning: unused variable ‘x’ [-Wunused-variable]
   double x,y,tt,sum;
          ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Update_v2.h:8:0,
                 from Rinterface_v2.cpp:2:
Random.h:19:0: warning: "PI" redefined
 #define PI         3.14159265
 
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/R.h:85:0,
                 from Rinterface_v2.cpp:1:
/home/biocbuild/bbs-3.9-bioc/R/include/R_ext/Constants.h:36:0: note: this is the location of the previous definition
 #define PI             M_PI
 
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Structure.cpp -o Structure.o
In file included from Structure.cpp:29:0:
ReportPotential.h: In constructor ‘ReportPotential::ReportPotential(const string&, const std::vector<Potential*>&)’:
ReportPotential.h:32:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
ReportPotential.h: In constructor ‘ReportPotential::ReportPotential(double*, const std::vector<Potential*>&)’:
ReportPotential.h:48:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
ReportPotential.h: In member function ‘virtual void ReportPotential::report(const Structure*)’:
ReportPotential.h:69:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < model.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
ReportPotential.h:78:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < model.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from Structure.cpp:30:0:
ReportAcceptance.h: In constructor ‘ReportAcceptance::ReportAcceptance(const string&, const std::vector<Update*>&)’:
ReportAcceptance.h:32:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < update.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ReportAcceptance.h: In constructor ‘ReportAcceptance::ReportAcceptance(double*, const std::vector<Update*>&)’:
ReportAcceptance.h:48:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < update.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ReportAcceptance.h: In member function ‘virtual void ReportAcceptance::report(const Structure*)’:
ReportAcceptance.h:67:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < update.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
ReportAcceptance.h:76:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < update.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from ReportProbDelta.h:9:0,
                 from Structure.cpp:31:
PotentialSum.h: In constructor ‘PotentialSum::PotentialSum(const std::vector<Potential*>&)’:
PotentialSum.h:30:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < term.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
PotentialSum.h: In destructor ‘virtual PotentialSum::˜PotentialSum()’:
PotentialSum.h:41:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < term.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
PotentialSum.h: In member function ‘virtual double PotentialSum::potential(Random&) const’:
PotentialSum.h:61:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < term.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
In file included from Structure.cpp:31:0:
ReportProbDelta.h: In constructor ‘ReportProbDelta::ReportProbDelta(const string&, Structure*, int)’:
ReportProbDelta.h:53:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < term.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
ReportProbDelta.h: In constructor ‘ReportProbDelta::ReportProbDelta(double*, Structure*, int)’:
ReportProbDelta.h:85:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < term.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
ReportProbDelta.h: In destructor ‘virtual ReportProbDelta::˜ReportProbDelta()’:
ReportProbDelta.h:96:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Structure.cpp: In member function ‘void Structure::setParameterValues(std::__cxx11::string&)’:
Structure.cpp:528:8: warning: unused variable ‘c’ [-Wunused-variable]
   char c;
        ^
Structure.cpp: In member function ‘void Structure::setNumberOfUpdates(std::__cxx11::string&, std::vector<int>&, std::vector<Update*>&) const’:
Structure.cpp:1642:8: warning: unused variable ‘nRead’ [-Wunused-variable]
    int nRead = sscanf(var1,"%d",&value);
        ^˜˜˜˜
Structure.cpp:1668:12: warning: unused variable ‘nRead’ [-Wunused-variable]
        int nRead = sscanf(var2,"%le",&value);
            ^˜˜˜˜
Structure.cpp:1579:12: warning: unused variable ‘c’ [-Wunused-variable]
       char c;
            ^
Structure.cpp: In member function ‘ReportDiffexpressed* Structure::setReports(std::__cxx11::string&, int&, std::vector<Potential*>&, std::vector<Update*>&, std::vector<Report*>&, int)’:
Structure.cpp:1728:12: warning: unused variable ‘c’ [-Wunused-variable]
       char c;
            ^
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Update_v2.cpp -o Update_v2.o
Update_v2.cpp: In function ‘void updateOmega_HyperInverseWishart(unsigned int*, int*, std::vector<std::vector<std::vector<double> > >&, int, int, const double*, const double*, const double*, const double*, const double*, double, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Update_v2.cpp:3919:10: warning: unused variable ‘pot’ [-Wunused-variable]
   double pot = - OmegaGibbs(df,D,oldClique,oldComponents,Q,G,Delta,
          ^˜˜
Update_v2.cpp: In function ‘void updateDDeltaStar_HyperInverseWishart(unsigned int*, int*, double*, int, int, const int*, const double*, const int*, const double*, const int*, const double*, const double*, const double*, const double*, const double*, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Update_v2.cpp:3973:10: warning: unused variable ‘pot’ [-Wunused-variable]
   double pot = DeltaStarGibbs(oldClique,oldComponents,Q,G,S,newValues,
          ^˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c Utility_v2.cpp -o Utility_v2.o
Utility_v2.cpp: In function ‘double nuGibbs(double*, int, int, const int*, double, const double*, const double*, const double*, const double*, const double*, const int*, const double*, const int*, const double*, Random&, int)’:
Utility_v2.cpp:221:12: warning: unused variable ‘detPrior’ [-Wunused-variable]
     double detPrior = inverse(var,varInv);
            ^˜˜˜˜˜˜˜
Utility_v2.cpp:228:12: warning: unused variable ‘detPosterior’ [-Wunused-variable]
     double detPosterior = 1.0 /inverse(varInv,var);
            ^˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp: In function ‘double DeltaGibbs(int, double*, int, int, const int*, double, const double*, const double*, const double*, const double*, const double*, const int*, const double*, const int*, const double*, Random&, int)’:
Utility_v2.cpp:303:9: warning: unused variable ‘s’ [-Wunused-variable]
     int s;
         ^
Utility_v2.cpp:328:12: warning: unused variable ‘detPrior’ [-Wunused-variable]
     double detPrior = inverse(var,varInv);
            ^˜˜˜˜˜˜˜
Utility_v2.cpp:334:12: warning: unused variable ‘detPosterior’ [-Wunused-variable]
     double detPosterior = 1.0 / inverse(varInv,var);
            ^˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp: In function ‘void updateMRF1perfect_onedelta(int, std::vector<int>&, std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::vector<int> >&, double, double, double, Random&)’:
Utility_v2.cpp:413:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (gg = 0; gg < neighbour[g].size(); gg++) {
                ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:435:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (gg = 0; gg < neighbour[g].size(); gg++) {
                ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:447:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (ggg = 0; ggg < neighbour[gene].size(); ggg++) {
                   ˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp: In function ‘double perfectMRF1_onedelta(int*, int, const std::vector<std::vector<int> >&, const std::vector<double>&, const std::vector<double>&, double, double, double, unsigned int*, int)’:
Utility_v2.cpp:556:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (b == start.size() - 1) nextSeed = ran.ChangeSeed(dummy);
      ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:600:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (gg = 0; gg < neighbour[g].size(); gg++)
                  ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp: In function ‘void updateMRF2perfect_onedelta(int, std::vector<int>&, std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::vector<int> >&, double, double, Random&)’:
Utility_v2.cpp:635:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < neighbour[g].size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp: In function ‘double perfectMRF2_onedelta(int*, int, const std::vector<std::vector<int> >&, const std::vector<double>&, const std::vector<double>&, double, double, unsigned int*, int)’:
Utility_v2.cpp:723:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (b == start.size() - 1) nextSeed = ran.ChangeSeed(dummy);
      ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:760:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (k = 0; k < neighbour[g].size(); k++) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:764:6: warning: unused variable ‘ngg’ [-Wunused-variable]
  int ngg = neighbour[gg].size();
      ^˜˜
Utility_v2.cpp: In function ‘void updateMRF2perfect(int, int, int, int, std::vector<int>&, std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::vector<int> >&, double, double, double, Random&)’:
Utility_v2.cpp:793:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < neighbour[g].size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp: In function ‘double perfectMRF2(int*, int, int, const std::vector<std::vector<int> >&, const std::vector<double>&, const std::vector<double>&, double, double, double, unsigned int*, int)’:
Utility_v2.cpp:904:8: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (b == start.size() - 1) nextSeed = ran.ChangeSeed(dummy);
      ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:949:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (k = 0; k < neighbour[g].size(); k++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:954:8: warning: unused variable ‘ngg’ [-Wunused-variable]
    int ngg = neighbour[gg].size();
        ^˜˜
Utility_v2.cpp: In function ‘double OmegaGibbs(double, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&, int, int, const double*, const double*, const double*, const double*, const double*, std::vector<std::vector<std::vector<double> > >&, Random&, int)’:
Utility_v2.cpp:1027:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (g1 = 0; g1 < DNew[0].size(); g1++)
                ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1028:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (g2 = 0; g2 < DNew[0][g1].size(); g2++)
                  ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1036:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < DNew.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1041:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (g = 0; g < oldComponents[k].size(); g++) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1047:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (g = 0; g < cliqueSize - oldComponents[k].size(); g++) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1059:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (g1 = 0; g1 < DNew[k].size(); g1++)
                  ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1060:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (g2 = 0; g2 < DNew[k][g1].size(); g2++)
                    ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp: In function ‘double DeltaStarGibbs(const std::vector<int>&, const std::vector<std::vector<int> >&, int, int, const int*, double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*, const int*, const double*, const std::vector<std::vector<std::vector<double> > >&, Random&, int)’:
Utility_v2.cpp:1096:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaInv.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1101:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaSep.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1104:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < oldComponents[k].size(); i++) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1107:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < oldComponents[k].size(); j++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1115:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaSep.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1129:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < Omega.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1133:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (gg = 0; gg < oldComponents[k].size(); gg++)
                  ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1135:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (gg = oldComponents[k].size(); gg < Omega[k].size(); gg++) {
                                        ˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1238:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaInv.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1240:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (r = 0; r < nr[k].size(); r++) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1242:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (s = 0; s < nr[k].size(); s++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1258:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaSepInv.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1260:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (r = 0; r < oldComponents[k].size(); r++) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1262:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (s = 0; s < oldComponents[k].size(); s++) {
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1409:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (index = 0; index < L.size(); index++)
                   ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1458:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < VinvSparseReversed.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1460:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < VinvSparseReversed.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1463:33: warning: variable ‘itextra’ set but not used [-Wunused-but-set-variable]
       map<int,double>::iterator itextra = VinvSparse[k].end();
                                 ^˜˜˜˜˜˜
Utility_v2.cpp:1501:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (index = 0; index < cholReversed.size(); index++)
                   ˜˜˜˜˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1563:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < chol.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1565:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < cholReversed.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1600:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < cholT.size(); k++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1602:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < chol.size(); i++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1653:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < mean.size(); i++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1693:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (k = 0; k < z.size(); k++)
                 ˜˜^˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1713:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < sample.size(); i++) {
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1779:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < sample.size(); i++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp: In function ‘void inverseTransformOmega(const std::vector<std::vector<std::vector<double> > >&, double*)’:
Utility_v2.cpp:1875:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaTransformed.size(); k++) {
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
Utility_v2.cpp:1877:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < OmegaTransformed[k].size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:16:0:
Random.h:19:0: warning: "PI" redefined
 #define PI         3.14159265
 
In file included from /home/biocbuild/bbs-3.9-bioc/R/include/R.h:85:0,
                 from diffExpressed_main.cpp:4:
/home/biocbuild/bbs-3.9-bioc/R/include/R_ext/Constants.h:36:0: note: this is the location of the previous definition
 #define PI             M_PI
 
In file included from diffExpressed_main.cpp:22:0:
PotentialX.h: In destructor ‘virtual PotentialX::˜PotentialX()’:
PotentialX.h:44:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
PotentialX.h: In member function ‘virtual double PotentialX::potential(Random&) const’:
PotentialX.h:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:31:0:
PotentialSigma2.h: In destructor ‘virtual PotentialSigma2::˜PotentialSigma2()’:
PotentialSigma2.h:44:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
PotentialSigma2.h: In member function ‘virtual double PotentialSigma2::potential(Random&) const’:
PotentialSigma2.h:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:32:0:
PotentialPhi.h: In destructor ‘virtual PotentialPhi::˜PotentialPhi()’:
PotentialPhi.h:44:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
PotentialPhi.h: In member function ‘virtual double PotentialPhi::potential(Random&) const’:
PotentialPhi.h:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:33:0:
PotentialSum.h: In constructor ‘PotentialSum::PotentialSum(const std::vector<Potential*>&)’:
PotentialSum.h:30:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < term.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
PotentialSum.h: In destructor ‘virtual PotentialSum::˜PotentialSum()’:
PotentialSum.h:41:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < term.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
PotentialSum.h: In member function ‘virtual double PotentialSum::potential(Random&) const’:
PotentialSum.h:61:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < term.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:41:0:
UpdateDeltaMH.h: In constructor ‘UpdateDeltaMH::UpdateDeltaMH(Structure*, int)’:
UpdateDeltaMH.h:47:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < term.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
UpdateDeltaMH.h: In destructor ‘virtual UpdateDeltaMH::˜UpdateDeltaMH()’:
UpdateDeltaMH.h:59:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from UpdateSigma2MH.h:4:0,
                 from diffExpressed_main.cpp:43:
UpdateMultiplicativePositive.h: In constructor ‘UpdateMultiplicativePositive::UpdateMultiplicativePositive(const std::vector<Potential*>&, const std::vector<double*>&, double)’:
UpdateMultiplicativePositive.h:50:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
UpdateMultiplicativePositive.h:53:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < variable.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
UpdateMultiplicativePositive.h: In constructor ‘UpdateMultiplicativePositive::UpdateMultiplicativePositive(const Potential*, const std::vector<double*>&, double)’:
UpdateMultiplicativePositive.h:76:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < variable.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
UpdateMultiplicativePositive.h: In constructor ‘UpdateMultiplicativePositive::UpdateMultiplicativePositive(const std::vector<Potential*>&, const std::vector<double*>&, const std::vector<double*>&, double)’:
UpdateMultiplicativePositive.h:124:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜
UpdateMultiplicativePositive.h:127:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < variable1.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
UpdateMultiplicativePositive.h:130:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < variable2.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
UpdateMultiplicativePositive.h: In constructor ‘UpdateMultiplicativePositive::UpdateMultiplicativePositive(const Potential*, const std::vector<double*>&, const std::vector<double*>&, double)’:
UpdateMultiplicativePositive.h:159:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < variable1.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
UpdateMultiplicativePositive.h:162:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < variable2.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
UpdateMultiplicativePositive.h: In member function ‘virtual int UpdateMultiplicativePositive::update(Random&)’:
UpdateMultiplicativePositive.h:213:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < variable1.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:43:0:
UpdateSigma2MH.h: In constructor ‘UpdateSigma2MH::UpdateSigma2MH(Structure*, double)’:
UpdateSigma2MH.h:49:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < term.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
UpdateSigma2MH.h: In destructor ‘virtual UpdateSigma2MH::˜UpdateSigma2MH()’:
UpdateSigma2MH.h:61:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
UpdateSigma2MH.h: In member function ‘virtual void UpdateSigma2MH::setEpsilon(double)’:
UpdateSigma2MH.h:71:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
UpdateSigma2MH.h: In member function ‘virtual int UpdateSigma2MH::update(Random&)’:
UpdateSigma2MH.h:96:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:44:0:
UpdateTMH.h: In constructor ‘UpdateTMH::UpdateTMH(Structure*, const Potential*, double)’:
UpdateTMH.h:48:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < term.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
UpdateTMH.h: In destructor ‘virtual UpdateTMH::˜UpdateTMH()’:
UpdateTMH.h:60:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
UpdateTMH.h: In member function ‘virtual int UpdateTMH::update(Random&)’:
UpdateTMH.h:84:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:45:0:
UpdateLMH.h: In constructor ‘UpdateLMH::UpdateLMH(Structure*, const Potential*, double)’:
UpdateLMH.h:49:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < term.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
UpdateLMH.h: In destructor ‘virtual UpdateLMH::˜UpdateLMH()’:
UpdateLMH.h:61:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
UpdateLMH.h: In member function ‘virtual void UpdateLMH::setEpsilon(double)’:
UpdateLMH.h:73:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
UpdateLMH.h: In member function ‘virtual int UpdateLMH::update(Random&)’:
UpdateLMH.h:99:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:46:0:
UpdatePhiMH.h: In constructor ‘UpdatePhiMH::UpdatePhiMH(Structure*, double)’:
UpdatePhiMH.h:45:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < term.size(); i++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
UpdatePhiMH.h: In destructor ‘virtual UpdatePhiMH::˜UpdatePhiMH()’:
UpdatePhiMH.h:57:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
UpdatePhiMH.h: In member function ‘virtual void UpdatePhiMH::setEpsilon(double)’:
UpdatePhiMH.h:69:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
UpdatePhiMH.h: In member function ‘virtual int UpdatePhiMH::update(Random&)’:
UpdatePhiMH.h:96:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:47:0:
UpdateThetaMH.h: In constructor ‘UpdateThetaMH::UpdateThetaMH(Structure*, const Potential*, double)’:
UpdateThetaMH.h:49:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < term.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
UpdateThetaMH.h: In destructor ‘virtual UpdateThetaMH::˜UpdateThetaMH()’:
UpdateThetaMH.h:61:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
UpdateThetaMH.h: In member function ‘virtual int UpdateThetaMH::update(Random&)’:
UpdateThetaMH.h:85:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:48:0:
UpdateLambdaMH.h: In constructor ‘UpdateLambdaMH::UpdateLambdaMH(Structure*, const Potential*, double)’:
UpdateLambdaMH.h:47:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < term.size(); i++)
                   ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
UpdateLambdaMH.h: In destructor ‘virtual UpdateLambdaMH::˜UpdateLambdaMH()’:
UpdateLambdaMH.h:59:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
UpdateLambdaMH.h: In member function ‘virtual int UpdateLambdaMH::update(Random&)’:
UpdateLambdaMH.h:83:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < up.size(); i++)
               ˜˜^˜˜˜˜˜˜˜˜˜˜
In file included from diffExpressed_main.cpp:143:0:
PotentialFunction.h: In function ‘void xdeLIN_main(int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, int*, char**, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*)’:
PotentialFunction.h:55:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 for (i = 0; i < term.size(); i++)
             ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜
PotentialFunction.h:55:1: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation]
 for (i = 0; i < term.size(); i++)
 ^˜˜
PotentialFunction.h:62:6: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’
      vector<Update *> update;
      ^˜˜˜˜˜
diffExpressed_main.cpp:202:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (k = 0; k < update.size(); k++)
              ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
diffExpressed_main.cpp:217:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (k = 0; k < report.size(); k++)
                  ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
diffExpressed_main.cpp:224:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < report.size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
diffExpressed_main.cpp:227:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < update.size(); i++)
                 ˜˜^˜˜˜˜˜˜˜˜˜˜˜˜˜˜
gcc -I"/home/biocbuild/bbs-3.9-bioc/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2  -Wall -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.9-bioc/R/lib -L/usr/local/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o registerDynamicSymbol.o -lm -L/home/biocbuild/bbs-3.9-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.9-bioc/R/library/00LOCK-XDE/00new/XDE/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: For function ‘dims’, signature ‘Parameters’: argument in method definition changed from (object) to (x)
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘XDE.Rnw’ 
   ‘XdeParameterClass.Rnw’ 
** 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 (XDE)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## from xmapcore package
> if( require( "RUnit", quietly=TRUE ) ) {
+ 	pkg <- "XDE"
+ 
+ 	if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
+ 		path <- file.path( getwd(), "..", "inst", "unitTests" )
+ 	} else {
+ 		path <- system.file( package=pkg, "unitTests" )
+ 	}
+ 
+ 	cat( "\nRunning unit tests\n" )
+ 	print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
+ 	library( package=pkg, character.only=TRUE )
+ 
+ 	##xmap.clear.cache()
+ 
+ 	##Fail on warnings
+ 	options( warn=2 )
+ 
+ 	## Get the pattern (if there is one?)
+ 	patt <- Sys.getenv( "RUNITFILEPATTERN" )
+ 	if( is.null( patt ) || nchar( patt ) == 0 ) {
+ 		testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ 					     dirs=path,
+ 					     testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
+ 	} else {
+ 		##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
+ 		testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
+ 					     testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
+ 					     dirs=path )
+ 	}
+ 	tests <- runTestSuite( testSuite )
+ 
+ 	pathReport <- file.path( path, "report" )
+ 
+ 	cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
+ 	printTextProtocol( tests, showDetails=FALSE )
+ 	printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
+ 	printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )
+ 
+ 	printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )
+ 
+ 	tmp <- getErrors( tests )
+ 	if( tmp$nFail > 0 | tmp$nErr > 0 ){
+ 		stop( paste( "\n\nunit testing failed (#test failures: ", tmp$nFail, ", #R errors: ",  tmp$nErr, ")\n\n", sep=""))
+ 	}
+ } else {
+ 	warning( "cannot run unit tests -- package RUnit is not available" )
+ }

Running unit tests
$pkg
[1] "XDE"

$getwd
[1] "/home/biocbuild/bbs-3.9-bioc/meat/XDE.Rcheck/tests"

$pathToUnitTests
[1] "/home/biocbuild/bbs-3.9-bioc/R/library/XDE/unitTests"

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to XDE version 2.29.0
------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Tue Apr  9 04:23:23 2019 
*********************************************** 
Number of test functions: 0 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
XDE unit testing - 0 test functions, 0 errors, 0 failures
> 
> proc.time()
   user  system elapsed 
  6.486   0.198   6.685 

name	user	system	elapsed
ExpressionSetList-class	0.029	0.000	0.029
Parameters-class	0.001	0.000	0.001
XdeMcmc-class	0	0	0
XdeParameter-class	0.001	0.000	0.001
burnin	0.000	0.000	0.001
empiricalStart	0.146	0.016	0.177
expressionSetList	0.018	0.000	0.018
firstMcmc	0.171	0.008	0.178
geneCenter	0.043	0.004	0.047
hyperparameters	0.112	0.008	0.120
lastMcmc	0	0	0
output	0.074	0.000	0.073
ssStatistic	0.598	0.032	0.630
studyCenter	0.044	0.000	0.044
symbolsInteresting	0.138	0.000	0.152
xde	0	0	0
xmcmc	0.070	0.004	0.074
xsScores	0.041	0.000	0.041