Package: XDE

Version: 2.32.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:XDE.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings XDE_2.32.0.tar.gz

StartedAt: 2020-04-15 00:28:57 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 00:31:31 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 154.3 seconds

RetCode: 0

Status:  OK

CheckDir: XDE.Rcheck

Warnings: 0

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:XDE.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings XDE_2.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/XDE.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.32.0’
* 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 ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/XDE.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL XDE
###
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* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘XDE’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.10-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-3.10-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-3.10-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-3.10-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-3.10-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-3.10-bioc/R/include/R.h:85:0,
                 from Rinterface_v2.cpp:1:
/home/biocbuild/bbs-3.10-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-3.10-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-3.10-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-3.10-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-3.10-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-3.10-bioc/R/include/R.h:85:0,
                 from diffExpressed_main.cpp:4:
/home/biocbuild/bbs-3.10-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-3.10-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-3.10-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-3.10-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.10-bioc/R/library/00LOCK-XDE/00new/XDE/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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-3.10-bioc/meat/XDE.Rcheck/tests"

$pathToUnitTests
[1] "/home/biocbuild/bbs-3.10-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, 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, 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 2.32.0
------------------- UNIT TEST SUMMARY ---------------------

RUNIT TEST PROTOCOL -- Wed Apr 15 00:31:27 2020 
*********************************************** 
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 
  5.840   0.204   6.140 

name	user	system	elapsed
ExpressionSetList-class	0.024	0.004	0.029
Parameters-class	0.004	0.000	0.002
XdeMcmc-class	0.000	0.000	0.001
XdeParameter-class	0.004	0.000	0.001
burnin	0	0	0
empiricalStart	0.136	0.004	0.157
expressionSetList	0.012	0.004	0.016
firstMcmc	0.156	0.000	0.156
geneCenter	0.068	0.000	0.070
hyperparameters	0.200	0.004	0.201
lastMcmc	0.000	0.000	0.001
output	0.100	0.000	0.098
ssStatistic	0.612	0.000	0.613
studyCenter	0.048	0.000	0.044
symbolsInteresting	0.136	0.000	0.154
xde	0	0	0
xmcmc	0.064	0.012	0.076
xsScores	0.040	0.000	0.039