BioC 3.3: CHECK report for XDE on zin2

Package: XDE

Version: 2.18.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings XDE_2.18.0.tar.gz

StartedAt: 2016-10-13 07:50:39 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 07:53:04 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 145.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: XDE.Rcheck

Warnings: 1

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###
### Running command:
###
###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings XDE_2.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/XDE.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.18.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  8.1Mb
  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: warning in matrix(1, nr = nrow(eset[[1]]),
  nc = nsplit): partial argument match of 'nr' to 'nrow'
.studySplit,ExpressionSet: warning in matrix(1, nr = nrow(eset[[1]]),
  nc = nsplit): partial argument match of 'nc' to 'ncol'
.goodnessOfFit: no visible global function definition for ‘pchisq’
.onAttach: no visible global function definition for
  ‘packageDescription’
Parameters: no visible global function definition for ‘rgamma’
Parameters: no visible global function definition for ‘rbinom’
computeGOF: no visible global function definition for ‘qnorm’
computeGOF: no visible binding for global variable ‘psi’
computeGOF: no visible global function definition for ‘pchisq’
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’
show,Parameters: no visible global function definition for ‘head’
show,Parameters: no visible global function definition for ‘tail’
Undefined global functions or variables:
  brewer.pal d head packageDescription pchisq phenodata psi qnorm
  rbinom rgamma sam tail x zScores
Consider adding
  importFrom("stats", "pchisq", "qnorm", "rbinom", "rgamma")
  importFrom("utils", "head", "packageDescription", "tail")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'ExpressionSetList,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/XDE.Rcheck/00check.log’
for details.

* installing *source* package ‘XDE’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Cholesky.cpp -o Cholesky.o
g++ -I/home/biocbuild/bbs-3.3-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-3.3-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-3.3-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-3.3-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-3.3-bioc/R/include/R.h:69:0,
                 from Rinterface_v2.cpp:1:
/home/biocbuild/bbs-3.3-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-3.3-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-3.3-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-3.3-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-3.3-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-3.3-bioc/R/include/R.h:69:0,
                 from diffExpressed_main.cpp:4:
/home/biocbuild/bbs-3.3-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-3.3-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-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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)

name	user	system	elapsed
ExpressionSetList-class	0.034	0.000	0.034
Parameters-class	0.002	0.000	0.002
XdeMcmc-class	0.001	0.000	0.000
XdeParameter-class	0.001	0.000	0.002
burnin	0.001	0.000	0.001
empiricalStart	0.376	0.000	0.383
expressionSetList	0.016	0.000	0.018
firstMcmc	0.187	0.009	0.195
geneCenter	0.06	0.00	0.06
hyperparameters	0.180	0.003	0.185
lastMcmc	0.001	0.000	0.001
output	0.080	0.004	0.084
ssStatistic	0.727	0.016	0.743
studyCenter	0.058	0.000	0.058
symbolsInteresting	0.159	0.000	0.160
xde	0.000	0.000	0.001
xmcmc	0.084	0.004	0.090
xsScores	0.028	0.000	0.028