Package: XDE

Version: 2.0.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch XDE_2.0.0.tar.gz

StartedAt: 2012-03-24 04:49:59 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 04:53:35 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 215.7 seconds

RetCode: 0

Status:  OK

CheckDir: XDE.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/XDE.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'XDE/DESCRIPTION' ... OK
* this is package 'XDE' version '2.0.0'
* 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 whether package 'XDE' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
computeGOF: no visible binding for global variable 'psi'
* checking Rd files ... NOTE
prepare_Rd: firstMcmc.Rd:14-15: Dropping empty section \details
prepare_Rd: thin.Rd:31-32: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.9-bioc/meat/XDE.Rcheck/XDE/libs/i386/XDE.so':
  Found '__ZSt4cout', possibly from 'std::cout' (C++)
  Found '_exit', possibly from 'exit' (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'XDE' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -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:21: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -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++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c Potential_v2.cpp -o Potential_v2.o
Potential_v2.cpp: In function 'double potentialOmega0(double, double, double)':
Potential_v2.cpp:687: warning: suggest parentheses around assignment used as truth value
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c Random.cpp -o Random.o
Random.cpp: In member function 'int Random::Discrete(const std::vector<double, std::allocator<double> >&)':
Random.cpp:156: 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:433: 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:507: warning: comparison between signed and unsigned integer expressions
Random.cpp:510: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'std::vector<int, std::allocator<int> > Random::Permutation(int)':
Random.cpp:916: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'double Random::lnGamma(double)':
Random.cpp:941: warning: unused variable 'x'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Update_v2.h:8,
                 from Rinterface_v2.cpp:3:
Random.h:19:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:38,
                 from Rinterface_v2.cpp:1:
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:30:1: warning: this is the location of the previous definition
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c Structure.cpp -o Structure.o
In file included from /usr/include/c++/4.0.0/backward/strstream:51,
                 from Structure.cpp:1:
/usr/include/c++/4.0.0/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.
In file included from Structure.cpp:29:
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
In file included from Structure.cpp:30:
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
In file included from ReportProbDelta.h:9,
                 from Structure.cpp:31:
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
In file included from Structure.cpp:31:
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:1102: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1106: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1109: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1121: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1125: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1128: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c Update_v2.cpp -o Update_v2.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -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:220: warning: unused variable 'detPrior'
Utility_v2.cpp:227: warning: unused variable 'detPosterior'
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:302: warning: unused variable 's'
Utility_v2.cpp:327: warning: unused variable 'detPrior'
Utility_v2.cpp:333: warning: unused variable 'detPosterior'
Utility_v2.cpp: In function 'void updateMRF1perfect_onedelta(int, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, double, double, double, Random&)':
Utility_v2.cpp:433: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:455: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:467: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function 'double perfectMRF1_onedelta(int*, int, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, double, double, double, unsigned int*, int)':
Utility_v2.cpp:576: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:620: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function 'void updateMRF2perfect_onedelta(int, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, double, double, Random&)':
Utility_v2.cpp:655: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function 'double perfectMRF2_onedelta(int*, int, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, double, double, unsigned int*, int)':
Utility_v2.cpp:743: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:780: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:784: warning: unused variable 'ngg'
Utility_v2.cpp: In function 'void updateMRF2perfect(int, int, int, int, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, double, double, double, Random&)':
Utility_v2.cpp:813: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function 'double perfectMRF2(int*, int, int, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, double, double, double, unsigned int*, int)':
Utility_v2.cpp:924: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:969: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:974: warning: unused variable 'ngg'
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:13:
Random.h:19:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:38,
                 from diffExpressed_main.cpp:1:
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:30:1: warning: this is the location of the previous definition
In file included from diffExpressed_main.cpp:19:
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
In file included from diffExpressed_main.cpp:28:
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
In file included from diffExpressed_main.cpp:29:
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
In file included from diffExpressed_main.cpp:30:
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
In file included from diffExpressed_main.cpp:38:
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
In file included from UpdateSigma2MH.h:4,
                 from diffExpressed_main.cpp:40:
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
In file included from diffExpressed_main.cpp:40:
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
In file included from diffExpressed_main.cpp:41:
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
In file included from diffExpressed_main.cpp:42:
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
In file included from diffExpressed_main.cpp:43:
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
In file included from diffExpressed_main.cpp:44:
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
In file included from diffExpressed_main.cpp:45:
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
In file included from diffExpressed_main.cpp:140:
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: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:199: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:214: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:221: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:224: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o XDE.so Cholesky.o Matrix.o Potential_v2.o Random.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/XDE.Rcheck/XDE/libs/i386
** 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 'lapply' from package 'base' in package 'XDE'
Creating a generic function for 'nrow' from package 'base' in package 'XDE'
Creating a generic function for 'plot' from package 'graphics' in package 'XDE'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'XDE.Rnw' 
   'XdeParameterClass.Rnw' 
** testing if installed package can be loaded

* DONE (XDE)

name	user	system	elapsed
ExpressionSetList-class	0.075	0.010	0.087
Parameters-class	0.001	0.001	0.002
XdeMcmc-class	0	0	0
XdeParameter-class	0.001	0.001	0.002
burnin	0.000	0.001	0.001
empiricalStart	0.718	0.019	0.747
expressionSetList	0.038	0.002	0.040
firstMcmc	0.441	0.008	0.456
geneCenter	0.136	0.005	0.143
hyperparameters	0.403	0.005	0.413
lastMcmc	0	0	0
output	0.280	0.015	0.305
ssStatistic	1.748	0.064	1.834
studyCenter	0.139	0.003	0.144
symbolsInteresting	0.498	0.020	0.527
xde	0.001	0.000	0.000
xmcmc	0.639	0.035	0.795
xsScores	0.076	0.005	0.083