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BioC 3.2: CHECK report for XDE on linux1.bioconductor.org

This page was generated on 2015-10-27 17:24:11 -0400 (Tue, 27 Oct 2015).

Package 1099/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XDE 2.16.0
Robert Scharpf
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/XDE
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: XDE
Version: 2.16.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings XDE_2.16.0.tar.gz
StartedAt: 2015-10-27 09:08:08 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 09:10:20 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 131.6 seconds
RetCode: 0
Status:  OK 
CheckDir: XDE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings XDE_2.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/XDE.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘2.16.0’
* 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 ... NOTE
Found the following hidden files and directories:
  data/.commands.R
  data/.createLogFiles.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘XDE’ can be installed ... [38s/38s] OK
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘graphics’ ‘methods’ ‘genefilter’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘GeneMeta’ ‘RColorBrewer’ ‘genefilter’ ‘siggenes’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': ‘graphics:::pairs’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘pairs’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
$,XdeMcmc: warning in matrix(mcmc, nr = iterations(x), nc =
  length(studyNames(x)), byrow = byrow): partial argument match of 'nr'
  to 'nrow'
$,XdeMcmc: warning in matrix(mcmc, nr = iterations(x), nc =
  length(studyNames(x)), byrow = byrow): partial argument match of 'nc'
  to 'ncol'
$,XdeMcmc: warning in matrix(mcmc, nc = 1, byrow = TRUE): partial
  argument match of 'nc' to 'ncol'
$,XdeMcmc: warning in matrix(mcmc, nc = S * (S - 1)/2, byrow = TRUE):
  partial argument match of 'nc' to 'ncol'
$,XdeMcmc: warning in matrix(mcmc, nc = 18, nr = iterations(x), byrow =
  TRUE): partial argument match of 'nr' to 'nrow'
$,XdeMcmc: warning in matrix(mcmc, nc = 18, nr = iterations(x), byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
.studySplit,ExpressionSet : .local: warning in matrix(1, nr =
  nrow(eset[[1]]), nc = nsplit): partial argument match of 'nr' to
  'nrow'
.studySplit,ExpressionSet : .local: warning in matrix(1, nr =
  nrow(eset[[1]]), nc = nsplit): partial argument match of 'nc' to
  'ncol'
computeGOF: no visible binding for global variable ‘psi’
modelA_B_MIupdates: no visible binding for global variable ‘x’
modelA_B_MIupdates: no visible binding for global variable ‘d’
rupdateBDDeltaStar_HyperInverseWishart: no visible binding for global
  variable ‘phenodata’
ssStatistic : sam.wrapper: no visible global function definition for
  ‘sam’
ssStatistic : z.wrapper: no visible global function definition for
  ‘zScores’
pairs,matrix : panel: no visible global function definition for
  ‘brewer.pal’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [7s/7s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [3s/3s]
 [3s/3s] 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: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/XDE.Rcheck/00check.log’
for details.


XDE.Rcheck/00install.out:

* installing *source* package ‘XDE’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Cholesky.cpp -o Cholesky.o
g++ -I/home/biocbuild/bbs-3.2-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++ -I/home/biocbuild/bbs-3.2-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:308:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < UBlocks.size(); k++) {
                                ^
Potential_v2.cpp:310:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < UBlocks[k].size(); i++)
                                     ^
Potential_v2.cpp:316:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < theGene.size(); k++) 
                                ^
Potential_v2.cpp:321:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < Omega[0].size(); i++)
                                 ^
Potential_v2.cpp:322:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < UU[first].size(); j++) {
                                    ^
Potential_v2.cpp:328:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Omega.size(); k++) {
                              ^
Potential_v2.cpp:329:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < oldComponents[k].size(); i++)
                                           ^
Potential_v2.cpp:330:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < UU[first].size(); j++) {
                                      ^
Potential_v2.cpp:335:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < Omega[k].size() - oldComponents[k].size(); i++)
                                                             ^
Potential_v2.cpp:336:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < UU[first].size(); j++) {
                                      ^
Potential_v2.cpp:345:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < Omega.size(); k++) {
                              ^
Potential_v2.cpp:347:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < theGene[k].size(); i++)
                                     ^
Potential_v2.cpp:356:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Omega.size(); k++) 
                              ^
Potential_v2.cpp:364:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaSub.size(); i++) {
                                     ^
Potential_v2.cpp:366:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaSub[i].size(); j++)
                                   ^
Potential_v2.cpp:369:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < USub.size(); i++) {
                                 ^
Potential_v2.cpp:371:31: 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;
                                  ^
Potential_v2.cpp: In function ‘double potentialOmega0(double, double, double)’:
Potential_v2.cpp:876:19: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
   if (omega0 = 0.0)
                   ^
g++ -I/home/biocbuild/bbs-3.2-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:159:29: 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:512:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < w.size(); i++)
                          ^
Random_v2.cpp:515:33: 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:548:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < D.size(); k++) {
                          ^
Random_v2.cpp:551:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < Sigma[k].size(); i++)
                                   ^
Random_v2.cpp:557:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < temp.size(); i++)
                             ^
Random_v2.cpp:558:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < temp[i].size(); j++)
                                  ^
Random_v2.cpp:571:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < D.size(); k++) {
                          ^
Random_v2.cpp:585:32: 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:586:32: 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:587:32: 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:588:32: 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:590:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DSS.size(); i++)
                                ^
Random_v2.cpp:591:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DSS[i].size(); j++)
                              ^
Random_v2.cpp:594:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DRR.size(); i++)
                                ^
Random_v2.cpp:595:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DRR[i].size(); j++)
                              ^
Random_v2.cpp:598:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DSR.size(); i++)
                                ^
Random_v2.cpp:599:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DSR[i].size(); j++) {
                              ^
Random_v2.cpp:608:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaSS.size(); i++) {
                                    ^
Random_v2.cpp:610:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaSS[i].size(); j++)
                                  ^
Random_v2.cpp:625:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DRR.size(); i++) {
                                ^
Random_v2.cpp:627:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DRR[i].size(); j++)
                              ^
Random_v2.cpp:675:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < LDSSInverseT.size(); i++) {
                                         ^
Random_v2.cpp:677:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < LDSSInverseT[i].size(); j++)
                                       ^
Random_v2.cpp:693:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DRR.size(); i++) {
                                ^
Random_v2.cpp:695:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < DSS.size(); j++)
                           ^
Random_v2.cpp:705:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < mean.size(); i++)
                                 ^
Random_v2.cpp:706:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < mean[i].size(); j++)
                               ^
Random_v2.cpp:726:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaSR.size(); i++) {
                                    ^
Random_v2.cpp:728:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaSR[i].size(); j++)
                                  ^
Random_v2.cpp:740:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaRGivenS.size(); i++)
                                         ^
Random_v2.cpp:741:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaRGivenS[i].size(); j++)
                                       ^
Random_v2.cpp:746:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaSS.size(); i++)
                                    ^
Random_v2.cpp:747:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaSS[i].size(); j++)
                                  ^
Random_v2.cpp:749:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaRR.size(); i++)
                                    ^
Random_v2.cpp:750:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaRR[i].size(); j++)
                                  ^
Random_v2.cpp:752:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < SigmaSS.size(); i++)
                                    ^
Random_v2.cpp:753:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < SigmaRR.size(); j++) {
                               ^
Random_v2.cpp:760:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < temp7.size(); i++)
                                  ^
Random_v2.cpp:761:32: 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:790:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < UBlocks[k].size(); k++)
                                   ^
Random_v2.cpp:807:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < vec.size(); i++)
                            ^
Random_v2.cpp:812:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < vec.size(); i++) {
                            ^
Random_v2.cpp:821:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Cov.size(); k++) {
                            ^
Random_v2.cpp:834:34: 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:835:34: 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:836:34: 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:837:34: 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:840:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovSS.size(); i++)
                                  ^
Random_v2.cpp:841:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < CovSS[i].size(); j++)
                                ^
Random_v2.cpp:844:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovRR.size(); i++)
                                  ^
Random_v2.cpp:845:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < CovRR[i].size(); j++)
                                ^
Random_v2.cpp:848:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovSR.size(); i++)
                                  ^
Random_v2.cpp:849:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < CovSR[i].size(); j++) {
                                ^
Random_v2.cpp:863:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovRGivenS.size(); i++)
                                       ^
Random_v2.cpp:864:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < CovRGivenS[i].size(); j++)
                                     ^
Random_v2.cpp:877:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < vec.size(); i++)
                                ^
Random_v2.cpp:884:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < obs.size(); i++)
                                ^
Random_v2.cpp:889:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < mean.size(); i++)
                                 ^
Random_v2.cpp:894:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < z.size(); i++)
                              ^
Random_v2.cpp:899:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < obs.size(); i++)
                                ^
Random_v2.cpp:901:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < z.size(); i++)
                              ^
Random_v2.cpp:913:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < vec.size(); i++)
                                ^
Random_v2.cpp:918:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < z.size(); i++)
                              ^
Random_v2.cpp:923:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < z.size(); i++)
                              ^
Random_v2.cpp:928:29: 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:948:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < UBlocks.size(); k++) {
                                ^
Random_v2.cpp:950:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < UBlocks[k].size(); i++)
                                     ^
Random_v2.cpp:966:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (j = 0; j < U[0].size(); j++) {
                             ^
Random_v2.cpp:968:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < vec.size(); i++)
                              ^
Random_v2.cpp:973:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < vec.size(); i++)
                              ^
Random_v2.cpp:976:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     if (j == U[0].size() - 1) first += z.size();
                            ^
Random_v2.cpp:978:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < z.size(); i++)
                            ^
Random_v2.cpp:994:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Omega.size(); k++) {
                              ^
Random_v2.cpp:1007:36: 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:1008:36: 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:1009:36: 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:1010:36: 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:1012:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaSS.size(); i++)
                                    ^
Random_v2.cpp:1013:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaSS[i].size(); j++)
                                  ^
Random_v2.cpp:1016:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaRR.size(); i++)
                                    ^
Random_v2.cpp:1017:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaRR[i].size(); j++)
                                  ^
Random_v2.cpp:1020:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaSR.size(); i++)
                                    ^
Random_v2.cpp:1021:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaSR[i].size(); j++) {
                                  ^
Random_v2.cpp:1035:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaRGivenS.size(); i++)
                                         ^
Random_v2.cpp:1036:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaRGivenS[i].size(); j++)
                                       ^
Random_v2.cpp:1048:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < U[0].size(); j++) {
                                 ^
Random_v2.cpp:1050:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < vec.size(); i++)
                           ^
Random_v2.cpp:1057:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < obs.size(); i++)
                           ^
Random_v2.cpp:1062:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < mean.size(); i++)
                            ^
Random_v2.cpp:1067:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < z.size(); i++)
                         ^
Random_v2.cpp:1070:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (j == U[0].size() - 1) first += z.size();
                         ^
Random_v2.cpp:1072:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < obs.size(); i++)
                           ^
Random_v2.cpp:1074:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < z.size(); i++)
                         ^
Random_v2.cpp:1086:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < U[k].size(); j++) {
                                 ^
Random_v2.cpp:1088:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < vec.size(); i++)
                           ^
Random_v2.cpp:1093:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < vec.size(); i++)
                           ^
Random_v2.cpp:1096:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (j == U[k].size() - 1) first += z.size();
                         ^
Random_v2.cpp:1098:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (i = 0; i < z.size(); i++)
                         ^
Random_v2.cpp:1133:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < LT.size(); i++) {
                           ^
Random_v2.cpp:1135:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < LT[i].size(); j++)
                                ^
Random_v2.cpp:1143:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < U.size(); i++)
                          ^
Random_v2.cpp:1144:31: 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:1183:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < D.size(); k++)
                          ^
Random_v2.cpp:1188:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < D.size(); k++)
                          ^
Random_v2.cpp:1196:32: 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:1197:36: 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:1199:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < DSS.size(); i++)
                                ^
Random_v2.cpp:1200:30: 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:1225:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < UU.size(); i++)
                           ^
Random_v2.cpp:1232:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < UBlocks.size(); k++)
                                ^
Random_v2.cpp:1236:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < Cov[0].size(); i++)
                               ^
Random_v2.cpp:1240:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Cov.size(); k++) {
                            ^
Random_v2.cpp:1241:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < oldComponents[k].size(); i++)
                                           ^
Random_v2.cpp:1244:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < Cov[k].size() - oldComponents[k].size(); i++)
                                                           ^
Random_v2.cpp:1251:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < Cov.size(); k++) {
                            ^
Random_v2.cpp:1258:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Cov.size(); k++) {
                            ^
Random_v2.cpp:1265:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < CovSub.size(); i++) {
                                   ^
Random_v2.cpp:1267:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < CovSub[i].size(); j++)
                                 ^
Random_v2.cpp:1271:33: 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:1297:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < XT.size(); i++) {
                           ^
Random_v2.cpp:1299:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < XT[i].size(); j++)
                                ^
Random_v2.cpp:1310:30: 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:1335:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < UU.size(); i++)
                           ^
Random_v2.cpp:1336:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < UU[i].size(); j++)
                                ^
Random_v2.cpp:1343:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < UBlocks.size(); k++) {
                                ^
Random_v2.cpp:1345:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < UBlocks[k].size(); i++)
                                     ^
Random_v2.cpp:1350:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < Omega[0].size(); i++)
                                 ^
Random_v2.cpp:1351:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (j = 0; j < UU[first].size(); j++)
                                    ^
Random_v2.cpp:1355:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Omega.size(); k++) {
                              ^
Random_v2.cpp:1356:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < oldComponents[k].size(); i++)
                                           ^
Random_v2.cpp:1357:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < UU[first].size(); j++)
                                      ^
Random_v2.cpp:1360:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < Omega[k].size() - oldComponents[k].size(); i++)
                                                             ^
Random_v2.cpp:1361:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < UU[first].size(); j++)
                                      ^
Random_v2.cpp:1380:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < Omega.size(); k++)
                              ^
Random_v2.cpp:1385:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < Omega.size(); k++)
                              ^
Random_v2.cpp:1391:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < OmegaSub.size(); i++) {
                                     ^
Random_v2.cpp:1393:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < OmegaSub[i].size(); j++)
                                   ^
Random_v2.cpp:1396:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < USub.size(); i++) {
                                 ^
Random_v2.cpp:1398:31: 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:1822:29: 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++ -I/home/biocbuild/bbs-3.2-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 [enabled by default]
 #define PI         3.14159265
 ^
In file included from /home/biocbuild/bbs-3.2-bioc/R/include/R.h:44:0,
                 from Rinterface_v2.cpp:1:
/home/biocbuild/bbs-3.2-bioc/R/include/R_ext/Constants.h:32:0: note: this is the location of the previous definition
 #define PI             M_PI
 ^
g++ -I/home/biocbuild/bbs-3.2-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:32:30: 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:48:30: 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:69:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < model.size(); i++)
                                  ^
ReportPotential.h:78:34: 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:32:31: 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:48:31: 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:67:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (i = 0; i < update.size(); i++)
                                   ^
ReportAcceptance.h:76:35: 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:30:29: 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:41:29: 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:61:29: 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:53:33: 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:85:33: 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:96:30: 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::string&)’:
Structure.cpp:528:8: warning: unused variable ‘c’ [-Wunused-variable]
   char c;
        ^
Structure.cpp: In member function ‘void Structure::setNumberOfUpdates(std::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::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++ -I/home/biocbuild/bbs-3.2-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++ -I/home/biocbuild/bbs-3.2-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:413:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (gg = 0; gg < neighbour[g].size(); gg++) {
                                       ^
Utility_v2.cpp:435:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (gg = 0; gg < neighbour[g].size(); gg++) {
                                       ^
Utility_v2.cpp:447:46: 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:556:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (b == start.size() - 1) nextSeed = ran.ChangeSeed(dummy);
                          ^
Utility_v2.cpp:600:41: 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:635:37: 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:723:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (b == start.size() - 1) nextSeed = ran.ChangeSeed(dummy);
                          ^
Utility_v2.cpp:760:39: 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:793:37: 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:904:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if (b == start.size() - 1) nextSeed = ran.ChangeSeed(dummy);
                          ^
Utility_v2.cpp:949:41: 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:1027:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (g1 = 0; g1 < DNew[0].size(); g1++)
                                  ^
Utility_v2.cpp:1028:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (g2 = 0; g2 < DNew[0][g1].size(); g2++)
                                        ^
Utility_v2.cpp:1036:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 1; k < DNew.size(); k++) {
                             ^
Utility_v2.cpp:1041:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (g = 0; g < oldComponents[k].size(); g++) {
                                           ^
Utility_v2.cpp:1047:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (g = 0; g < cliqueSize - oldComponents[k].size(); g++) {
                                                        ^
Utility_v2.cpp:1059:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (g1 = 0; g1 < DNew[k].size(); g1++)
                                    ^
Utility_v2.cpp:1060:42: 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:1096:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaInv.size(); k++)
                                 ^
Utility_v2.cpp:1101:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaSep.size(); k++) {
                                 ^
Utility_v2.cpp:1104:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < oldComponents[k].size(); i++) {
                                           ^
Utility_v2.cpp:1107:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (j = 0; j < oldComponents[k].size(); j++) {
                                             ^
Utility_v2.cpp:1115:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaSep.size(); k++) {
                                 ^
Utility_v2.cpp:1129:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < Omega.size(); k++) {
                              ^
Utility_v2.cpp:1133:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (gg = 0; gg < oldComponents[k].size(); gg++)
                                             ^
Utility_v2.cpp:1135:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (gg = oldComponents[k].size(); gg < Omega[k].size(); gg++) {
                                                           ^
Utility_v2.cpp:1238:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaInv.size(); k++) {
                                 ^
Utility_v2.cpp:1240:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (r = 0; r < nr[k].size(); r++) {
                                ^
Utility_v2.cpp:1242:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (s = 0; s < nr[k].size(); s++) {
                                  ^
Utility_v2.cpp:1258:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaSepInv.size(); k++) {
                                    ^
Utility_v2.cpp:1260:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (r = 0; r < oldComponents[k].size(); r++) {
                                           ^
Utility_v2.cpp:1262:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
       for (s = 0; s < oldComponents[k].size(); s++) {
                                             ^
Utility_v2.cpp:1409:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (index = 0; index < L.size(); index++)
                                  ^
Utility_v2.cpp:1458:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < VinvSparseReversed.size(); k++)
                                           ^
Utility_v2.cpp:1460:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < VinvSparseReversed.size(); k++) {
                                           ^
Utility_v2.cpp:1501:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (index = 0; index < cholReversed.size(); index++)
                                             ^
Utility_v2.cpp:1563:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < chol.size(); k++)
                             ^
Utility_v2.cpp:1565:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < cholReversed.size(); k++) {
                                     ^
Utility_v2.cpp:1600:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < cholT.size(); k++)
                              ^
Utility_v2.cpp:1602:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < chol.size(); i++) {
                             ^
Utility_v2.cpp:1653:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < mean.size(); i++) {
                             ^
Utility_v2.cpp:1693:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (k = 0; k < z.size(); k++)
                            ^
Utility_v2.cpp:1713:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < sample.size(); i++) {
                                 ^
Utility_v2.cpp:1779:31: 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:1875:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (k = 0; k < OmegaTransformed.size(); k++) {
                                         ^
Utility_v2.cpp:1877:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < OmegaTransformed[k].size(); i++)
                                              ^
g++ -I/home/biocbuild/bbs-3.2-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 [enabled by default]
 #define PI         3.14159265
 ^
In file included from /home/biocbuild/bbs-3.2-bioc/R/include/R.h:44:0,
                 from diffExpressed_main.cpp:4:
/home/biocbuild/bbs-3.2-bioc/R/include/R_ext/Constants.h:32:0: 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:44:30: 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:64:30: 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:44:30: 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:64:30: 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:44:30: 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:64:30: 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:30:29: 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:41:29: 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:61:29: 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:47:33: 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:59:30: 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:50:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
                              ^
UpdateMultiplicativePositive.h:53:33: 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:76:33: 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:124:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < model.size(); i++)
                              ^
UpdateMultiplicativePositive.h:127:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < variable1.size(); i++)
                                  ^
UpdateMultiplicativePositive.h:130:34: 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:159:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < variable1.size(); i++)
                                  ^
UpdateMultiplicativePositive.h:162:34: 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:213:34: 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:49:28: 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:61:27: 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:71:27: 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:96:27: 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:48:33: 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:60:27: 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:84:27: 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:49:33: 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:61:27: 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:73:27: 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:99:27: 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:45:28: 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:57:27: 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:69:27: 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:96:27: 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:49:33: 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:61:27: 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:85:27: 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:47:33: 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:59:27: 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:83:27: 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:55:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
 for (i = 0; i < term.size(); i++)
                           ^
diffExpressed_main.cpp:202:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (k = 0; k < update.size(); k++)
                              ^
diffExpressed_main.cpp:217:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
      for (k = 0; k < report.size(); k++)
                                  ^
diffExpressed_main.cpp:224:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < report.size(); i++)
                                 ^
diffExpressed_main.cpp:227:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (i = 0; i < update.size(); i++)
                                 ^
g++ -shared -L/home/biocbuild/bbs-3.2-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 -lm -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.2-bioc/meat/XDE.Rcheck/XDE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘pairs’ from package ‘graphics’ in package ‘XDE’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘XDE’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (XDE)

XDE.Rcheck/XDE-Ex.timings:

nameusersystemelapsed
ExpressionSetList-class0.0420.0040.045
Parameters-class0.0020.0000.002
XdeMcmc-class0.0010.0000.001
XdeParameter-class0.0010.0030.003
burnin0.0000.0000.001
empiricalStart0.2340.0120.246
expressionSetList0.0250.0000.025
firstMcmc0.2370.0000.237
geneCenter0.0770.0000.077
hyperparameters0.2060.0040.210
lastMcmc0.0000.0040.001
output0.1140.0040.120
ssStatistic1.0070.0001.022
studyCenter0.0780.0000.078
symbolsInteresting0.2330.0000.233
xde000
xmcmc0.3160.0040.335
xsScores0.0360.0000.040