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Package 262/264HostnameOS / ArchBUILDCHECKBUILD BIN
XDE 0.99.2
Robert Scharpf
Snapshot Date: 2008-04-09 00:13:10 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/XDE
Last Changed Rev: 30920 / Revision: 30951
Last Changed Date: 2008-04-08 10:29:34 -0700 (Tue, 08 Apr 2008)
lamb1 Linux (SUSE 10.1) / x86_64 [ OK ] WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  WARNINGS 
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.1) / i386  OK  WARNINGS  OK 
Package: XDE
Version: 0.99.2
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD build XDE
StartedAt: 2008-04-09 03:23:05 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 03:23:43 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 37.5 seconds
RetCode: 0
Status: OK
PackageFile: XDE_0.99.2.tar.gz
PackageFileSize: 694.1 KiB

Command output

* checking for file 'XDE/DESCRIPTION' ... OK
* preparing 'XDE':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* Installing *source* package 'XDE' ...
** libs
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Cholesky.cpp -o Cholesky.o
Cholesky.cpp: In constructor 'Cholesky::Cholesky(const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, int&)':
Cholesky.cpp:18: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:13:
Random.h:17:1: warning: "PI" redefined
In file included from /home/biocbuild/bbs-2.2-bioc/R/include/R.h:44,
                 from diffExpressed_main.cpp:1:
/home/biocbuild/bbs-2.2-bioc/R/include/R_ext/Constants.h:30:1: warning: this is the location of the previous definition
PotentialX.h: In destructor 'virtual PotentialX::~PotentialX()':
PotentialX.h:44: warning: comparison between signed and unsigned integer expressions
PotentialX.h: In member function 'virtual double PotentialX::potential(Random&) const':
PotentialX.h:64: warning: comparison between signed and unsigned integer expressions
PotentialSigma2.h: In destructor 'virtual PotentialSigma2::~PotentialSigma2()':
PotentialSigma2.h:44: warning: comparison between signed and unsigned integer expressions
PotentialSigma2.h: In member function 'virtual double PotentialSigma2::potential(Random&) const':
PotentialSigma2.h:64: warning: comparison between signed and unsigned integer expressions
PotentialPhi.h: In destructor 'virtual PotentialPhi::~PotentialPhi()':
PotentialPhi.h:44: warning: comparison between signed and unsigned integer expressions
PotentialPhi.h: In member function 'virtual double PotentialPhi::potential(Random&) const':
PotentialPhi.h:64: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In constructor 'PotentialSum::PotentialSum(const std::vector<Potential*, std::allocator<Potential*> >&)':
PotentialSum.h:30: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In destructor 'virtual PotentialSum::~PotentialSum()':
PotentialSum.h:41: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In member function 'virtual double PotentialSum::potential(Random&) const':
PotentialSum.h:61: warning: comparison between signed and unsigned integer expressions
UpdateDeltaMH.h: In constructor 'UpdateDeltaMH::UpdateDeltaMH(Structure*, int)':
UpdateDeltaMH.h:47: warning: comparison between signed and unsigned integer expressions
UpdateDeltaMH.h: In destructor 'virtual UpdateDeltaMH::~UpdateDeltaMH()':
UpdateDeltaMH.h:59: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor 'UpdateMultiplicativePositive::UpdateMultiplicativePositive(const std::vector<Potential*, std::allocator<Potential*> >&, const std::vector<double*, std::allocator<double*> >&, double)':
UpdateMultiplicativePositive.h:50: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:53: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor 'UpdateMultiplicativePositive::UpdateMultiplicativePositive(const Potential*, const std::vector<double*, std::allocator<double*> >&, double)':
UpdateMultiplicativePositive.h:76: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor 'UpdateMultiplicativePositive::UpdateMultiplicativePositive(const std::vector<Potential*, std::allocator<Potential*> >&, const std::vector<double*, std::allocator<double*> >&, const std::vector<double*, std::allocator<double*> >&, double)':
UpdateMultiplicativePositive.h:124: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:127: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:130: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor 'UpdateMultiplicativePositive::UpdateMultiplicativePositive(const Potential*, const std::vector<double*, std::allocator<double*> >&, const std::vector<double*, std::allocator<double*> >&, double)':
UpdateMultiplicativePositive.h:159: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:162: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In member function 'virtual int UpdateMultiplicativePositive::update(Random&)':
UpdateMultiplicativePositive.h:213: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In constructor 'UpdateSigma2MH::UpdateSigma2MH(Structure*, double)':
UpdateSigma2MH.h:49: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In destructor 'virtual UpdateSigma2MH::~UpdateSigma2MH()':
UpdateSigma2MH.h:61: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In member function 'virtual void UpdateSigma2MH::setEpsilon(double)':
UpdateSigma2MH.h:71: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In member function 'virtual int UpdateSigma2MH::update(Random&)':
UpdateSigma2MH.h:96: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In constructor 'UpdateTMH::UpdateTMH(Structure*, const Potential*, double)':
UpdateTMH.h:48: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In destructor 'virtual UpdateTMH::~UpdateTMH()':
UpdateTMH.h:60: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In member function 'virtual int UpdateTMH::update(Random&)':
UpdateTMH.h:84: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In constructor 'UpdateLMH::UpdateLMH(Structure*, const Potential*, double)':
UpdateLMH.h:49: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In destructor 'virtual UpdateLMH::~UpdateLMH()':
UpdateLMH.h:61: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In member function 'virtual void UpdateLMH::setEpsilon(double)':
UpdateLMH.h:73: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In member function 'virtual int UpdateLMH::update(Random&)':
UpdateLMH.h:99: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In constructor 'UpdatePhiMH::UpdatePhiMH(Structure*, double)':
UpdatePhiMH.h:45: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In destructor 'virtual UpdatePhiMH::~UpdatePhiMH()':
UpdatePhiMH.h:57: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In member function 'virtual void UpdatePhiMH::setEpsilon(double)':
UpdatePhiMH.h:69: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In member function 'virtual int UpdatePhiMH::update(Random&)':
UpdatePhiMH.h:96: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In constructor 'UpdateThetaMH::UpdateThetaMH(Structure*, const Potential*, double)':
UpdateThetaMH.h:49: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In destructor 'virtual UpdateThetaMH::~UpdateThetaMH()':
UpdateThetaMH.h:61: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In member function 'virtual int UpdateThetaMH::update(Random&)':
UpdateThetaMH.h:85: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In constructor 'UpdateLambdaMH::UpdateLambdaMH(Structure*, const Potential*, double)':
UpdateLambdaMH.h:47: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In destructor 'virtual UpdateLambdaMH::~UpdateLambdaMH()':
UpdateLambdaMH.h:59: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In member function 'virtual int UpdateLambdaMH::update(Random&)':
UpdateLambdaMH.h:83: warning: comparison between signed and unsigned integer expressions
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*, 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*, int*)':
PotentialFunction.h:53: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:196: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:211: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:218: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:221: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c main.cpp -o main.o
PotentialX.h: In destructor 'virtual PotentialX::~PotentialX()':
PotentialX.h:44: warning: comparison between signed and unsigned integer expressions
PotentialX.h: In member function 'virtual double PotentialX::potential(Random&) const':
PotentialX.h:64: warning: comparison between signed and unsigned integer expressions
PotentialSigma2.h: In destructor 'virtual PotentialSigma2::~PotentialSigma2()':
PotentialSigma2.h:44: warning: comparison between signed and unsigned integer expressions
PotentialSigma2.h: In member function 'virtual double PotentialSigma2::potential(Random&) const':
PotentialSigma2.h:64: warning: comparison between signed and unsigned integer expressions
PotentialPhi.h: In destructor 'virtual PotentialPhi::~PotentialPhi()':
PotentialPhi.h:44: warning: comparison between signed and unsigned integer expressions
PotentialPhi.h: In member function 'virtual double PotentialPhi::potential(Random&) const':
PotentialPhi.h:64: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In constructor 'PotentialSum::PotentialSum(const std::vector<Potential*, std::allocator<Potential*> >&)':
PotentialSum.h:30: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In destructor 'virtual PotentialSum::~PotentialSum()':
PotentialSum.h:41: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In member function 'virtual double PotentialSum::potential(Random&) const':
PotentialSum.h:61: warning: comparison between signed and unsigned integer expressions
UpdateDeltaMH.h: In constructor 'UpdateDeltaMH::UpdateDeltaMH(Structure*, int)':
UpdateDeltaMH.h:47: warning: comparison between signed and unsigned integer expressions
UpdateDeltaMH.h: In destructor 'virtual UpdateDeltaMH::~UpdateDeltaMH()':
UpdateDeltaMH.h:59: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor 'UpdateMultiplicativePositive::UpdateMultiplicativePositive(const std::vector<Potential*, std::allocator<Potential*> >&, const std::vector<double*, std::allocator<double*> >&, double)':
UpdateMultiplicativePositive.h:50: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:53: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor 'UpdateMultiplicativePositive::UpdateMultiplicativePositive(const Potential*, const std::vector<double*, std::allocator<double*> >&, double)':
UpdateMultiplicativePositive.h:76: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor 'UpdateMultiplicativePositive::UpdateMultiplicativePositive(const std::vector<Potential*, std::allocator<Potential*> >&, const std::vector<double*, std::allocator<double*> >&, const std::vector<double*, std::allocator<double*> >&, double)':
UpdateMultiplicativePositive.h:124: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:127: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:130: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor 'UpdateMultiplicativePositive::UpdateMultiplicativePositive(const Potential*, const std::vector<double*, std::allocator<double*> >&, const std::vector<double*, std::allocator<double*> >&, double)':
UpdateMultiplicativePositive.h:159: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:162: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In member function 'virtual int UpdateMultiplicativePositive::update(Random&)':
UpdateMultiplicativePositive.h:213: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In constructor 'UpdateSigma2MH::UpdateSigma2MH(Structure*, double)':
UpdateSigma2MH.h:49: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In destructor 'virtual UpdateSigma2MH::~UpdateSigma2MH()':
UpdateSigma2MH.h:61: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In member function 'virtual void UpdateSigma2MH::setEpsilon(double)':
UpdateSigma2MH.h:71: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In member function 'virtual int UpdateSigma2MH::update(Random&)':
UpdateSigma2MH.h:96: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In constructor 'UpdateTMH::UpdateTMH(Structure*, const Potential*, double)':
UpdateTMH.h:48: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In destructor 'virtual UpdateTMH::~UpdateTMH()':
UpdateTMH.h:60: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In member function 'virtual int UpdateTMH::update(Random&)':
UpdateTMH.h:84: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In constructor 'UpdateLMH::UpdateLMH(Structure*, const Potential*, double)':
UpdateLMH.h:49: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In destructor 'virtual UpdateLMH::~UpdateLMH()':
UpdateLMH.h:61: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In member function 'virtual void UpdateLMH::setEpsilon(double)':
UpdateLMH.h:73: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In member function 'virtual int UpdateLMH::update(Random&)':
UpdateLMH.h:99: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In constructor 'UpdatePhiMH::UpdatePhiMH(Structure*, double)':
UpdatePhiMH.h:45: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In destructor 'virtual UpdatePhiMH::~UpdatePhiMH()':
UpdatePhiMH.h:57: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In member function 'virtual void UpdatePhiMH::setEpsilon(double)':
UpdatePhiMH.h:69: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In member function 'virtual int UpdatePhiMH::update(Random&)':
UpdatePhiMH.h:96: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In constructor 'UpdateThetaMH::UpdateThetaMH(Structure*, const Potential*, double)':
UpdateThetaMH.h:49: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In destructor 'virtual UpdateThetaMH::~UpdateThetaMH()':
UpdateThetaMH.h:61: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In member function 'virtual int UpdateThetaMH::update(Random&)':
UpdateThetaMH.h:85: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In constructor 'UpdateLambdaMH::UpdateLambdaMH(Structure*, const Potential*, double)':
UpdateLambdaMH.h:47: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In destructor 'virtual UpdateLambdaMH::~UpdateLambdaMH()':
UpdateLambdaMH.h:59: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In member function 'virtual int UpdateLambdaMH::update(Random&)':
UpdateLambdaMH.h:83: warning: comparison between signed and unsigned integer expressions
main.cpp: In function 'int main(int, char**)':
main.cpp:160: warning: comparison between signed and unsigned integer expressions
main.cpp:370: warning: comparison between signed and unsigned integer expressions
main.cpp:384: warning: comparison between signed and unsigned integer expressions
main.cpp:389: warning: comparison between signed and unsigned integer expressions
main.cpp:392: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Matrix.cpp -o Matrix.o
Matrix.cpp: In function 'void matrixMult(const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)':
Matrix.cpp:142: warning: unused variable 'k'
Matrix.cpp:144: warning: unused variable 'j'
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Random.cpp -o Random.o
Random.cpp: In constructor 'Random::Random(unsigned int)':
Random.cpp:11: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'double Random::Unif01()':
Random.cpp:49: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'int Random::Discrete(const std::vector<double, std::allocator<double> >&)':
Random.cpp:144: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > Random::InverseWishart(double, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&)':
Random.cpp:421: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > Random::CorrelationStandardInverseWishart(int, double)':
Random.cpp:495: warning: comparison between signed and unsigned integer expressions
Random.cpp:498: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'std::vector<int, std::allocator<int> > Random::Permutation(int)':
Random.cpp:904: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'double Random::lnGamma(double)':
Random.cpp:929: warning: unused variable 'x'
g++ -I/home/biocbuild/bbs-2.2-bioc/R/include -I/home/biocbuild/bbs-2.2-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c Structure.cpp -o Structure.o
In file included from /usr/include/c++/4.1.0/backward/strstream:51,
                 from Structure.cpp:1:
/usr/include/c++/4.1.0/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
ReportPotential.h: In constructor 'ReportPotential::ReportPotential(const std::string&, const std::vector<Potential*, std::allocator<Potential*> >&)':
ReportPotential.h:32: warning: comparison between signed and unsigned integer expressions
ReportPotential.h: In constructor 'ReportPotential::ReportPotential(double*, const std::vector<Potential*, std::allocator<Potential*> >&)':
ReportPotential.h:48: warning: comparison between signed and unsigned integer expressions
ReportPotential.h: In member function 'virtual void ReportPotential::report(const Structure*)':
ReportPotential.h:69: warning: comparison between signed and unsigned integer expressions
ReportPotential.h:78: warning: comparison between signed and unsigned integer expressions
ReportAcceptance.h: In constructor 'ReportAcceptance::ReportAcceptance(const std::string&, const std::vector<Update*, std::allocator<Update*> >&)':
ReportAcceptance.h:32: warning: comparison between signed and unsigned integer expressions
ReportAcceptance.h: In constructor 'ReportAcceptance::ReportAcceptance(double*, const std::vector<Update*, std::allocator<Update*> >&)':
ReportAcceptance.h:48: warning: comparison between signed and unsigned integer expressions
ReportAcceptance.h: In member function 'virtual void ReportAcceptance::report(const Structure*)':
ReportAcceptance.h:67: warning: comparison between signed and unsigned integer expressions
ReportAcceptance.h:76: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In constructor 'PotentialSum::PotentialSum(const std::vector<Potential*, std::allocator<Potential*> >&)':
PotentialSum.h:30: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In destructor 'virtual PotentialSum::~PotentialSum()':
PotentialSum.h:41: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In member function 'virtual double PotentialSum::potential(Random&) const':
PotentialSum.h:61: warning: comparison between signed and unsigned integer expressions
ReportProbDelta.h: In constructor 'ReportProbDelta::ReportProbDelta(const std::string&, Structure*, int)':
ReportProbDelta.h:53: warning: comparison between signed and unsigned integer expressions
ReportProbDelta.h: In constructor 'ReportProbDelta::ReportProbDelta(double*, Structure*, int)':
ReportProbDelta.h:85: warning: comparison between signed and unsigned integer expressions
ReportProbDelta.h: In destructor 'virtual ReportProbDelta::~ReportProbDelta()':
ReportProbDelta.h:96: warning: comparison between signed and unsigned integer expressions
Structure.cpp: In member function 'void Structure::setInitialValues(std::string&)':
Structure.cpp:1095: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1099: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1102: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1114: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1118: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1121: warning: comparison between signed and unsigned integer expressions
g++ -shared -L/usr/local/lib64 -o XDE.so Cholesky.o diffExpressed_main.o main.o Matrix.o Random.o Structure.o -lm  -L/home/biocbuild/bbs-2.2-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

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

Creating a new generic function for "pairs" in "XDE"
Creating a new generic function for "nrow" in "XDE"
Creating a new generic function for "plot" in "XDE"
** help
Note: removing empty section \details
Note: removing empty section \examples
 >>> Building/Updating help pages for package 'XDE'
     Formats: text html latex example 
  ExpressionSetList-class           text    html    latex   example
  XdeMcmc-class                     text    html    latex   example
  XdeParameter-class                text    html    latex   example
  burnin                            text    html    latex   example
  calculatePosteriorAvg             text    html    latex
  empiricalStart                    text    html    latex
  expressionSetList                 text    html    latex   example
  firstMcmc                         text    html    latex   example
  geneCenter                        text    html    latex   example
  hyperparameters                   text    html    latex   example
  iterations                        text    html    latex
  lastMcmc                          text    html    latex   example
  output                            text    html    latex   example
  pairs                             text    html    latex
  posteriorAvg                      text    html    latex
  seed                              text    html    latex
  ssStatistic                       text    html    latex   example
  standardizeSamples                text    html    latex
  studyCenter                       text    html    latex   example
  symbolsInteresting                text    html    latex   example
  thin                              text    html    latex
  tuning                            text    html    latex
  updates                           text    html    latex
  xde                               text    html    latex   example
  xmcmc                             text    html    latex   example
  xsScores                          text    html    latex   example
  zeroNu                            text    html    latex
** building package indices ...
* DONE (XDE)
* creating vignettes ... OK
* cleaning src
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'XDE_0.99.2.tar.gz'