BioC 2.8: CHECK report for XDE on gewurz

Package: XDE

Version: 1.12.0

Command: D:\biocbld\bbs-2.8-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch XDE_1.12.0.tar.gz

StartedAt: 2011-10-20 17:12:53 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 17:14:19 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 86.2 seconds

RetCode: 0

Status: WARNINGS

CheckDir: XDE.Rcheck

Warnings: 1

* using log directory 'D:/biocbld/bbs-2.8-bioc/meat/XDE.Rcheck'
* using R version 2.13.2 (2011-09-30)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'XDE/DESCRIPTION' ... OK
* this is package 'XDE' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... 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 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 ... NOTE
'library' or 'require' call not declared from: coda
* 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 examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... WARNING
Package vignette(s) without corresponding PDF:
   XDE.Rnw
   XdeParameterClass.Rnw

* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'D:/biocbld/bbs-2.8-bioc/meat/XDE.Rcheck/00check.log'
for details

* installing *source* package 'XDE' ...
** libs
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c Cholesky.cpp -o Cholesky.o
Cholesky.cpp: In constructor 'Cholesky::Cholesky(const std::vector<std::vector<double> >&, int&)':
Cholesky.cpp:21:21: warning: comparison between signed and unsigned integer expressions
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c Matrix.cpp -o Matrix.o
Matrix.cpp: In function 'void matrixMult(const std::vector<std::vector<double> >&, const std::vector<double>&, std::vector<double>&)':
Matrix.cpp:142:7: warning: unused variable 'k'
Matrix.cpp:144:9: warning: unused variable 'j'
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c Random.cpp -o Random.o
Random.cpp: In member function 'int Random::Discrete(const std::vector<double>&)':
Random.cpp:156:29: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'std::vector<std::vector<double> > Random::InverseWishart(double, const std::vector<std::vector<double> >&)':
Random.cpp:433:26: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'std::vector<std::vector<double> > Random::CorrelationStandardInverseWishart(int, double)':
Random.cpp:507:26: warning: comparison between signed and unsigned integer expressions
Random.cpp:510:33: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'std::vector<int> Random::Permutation(int)':
Random.cpp:916:29: warning: comparison between signed and unsigned integer expressions
Random.cpp: In member function 'double Random::lnGamma(double)':
Random.cpp:941:10: warning: unused variable 'x'
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c Structure.cpp -o Structure.o
In file included from c:/rtools214/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.5.2/backward/strstream:47:0,
                 from Structure.cpp:1:
c:/rtools214/mingw64/lib/gcc/../../x86_64-w64-mingw32/include/c++/4.5.2/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.
In file included from Structure.cpp:29:0:
ReportPotential.h: In constructor 'ReportPotential::ReportPotential(const std::string&, const std::vector<Potential*>&)':
ReportPotential.h:32:30: warning: comparison between signed and unsigned integer expressions
ReportPotential.h: In constructor 'ReportPotential::ReportPotential(double*, const std::vector<Potential*>&)':
ReportPotential.h:48:30: warning: comparison between signed and unsigned integer expressions
ReportPotential.h: In member function 'virtual void ReportPotential::report(const Structure*)':
ReportPotential.h:69:34: warning: comparison between signed and unsigned integer expressions
ReportPotential.h:78:34: warning: comparison between signed and unsigned integer expressions
In file included from Structure.cpp:30:0:
ReportAcceptance.h: In constructor 'ReportAcceptance::ReportAcceptance(const std::string&, const std::vector<Update*>&)':
ReportAcceptance.h:32:31: warning: comparison between signed and unsigned integer expressions
ReportAcceptance.h: In constructor 'ReportAcceptance::ReportAcceptance(double*, const std::vector<Update*>&)':
ReportAcceptance.h:48:31: warning: comparison between signed and unsigned integer expressions
ReportAcceptance.h: In member function 'virtual void ReportAcceptance::report(const Structure*)':
ReportAcceptance.h:67:35: warning: comparison between signed and unsigned integer expressions
ReportAcceptance.h:76:35: warning: comparison between signed and unsigned integer expressions
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
PotentialSum.h: In destructor 'virtual PotentialSum::˜PotentialSum()':
PotentialSum.h:41:29: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In member function 'virtual double PotentialSum::potential(Random&) const':
PotentialSum.h:61:29: warning: comparison between signed and unsigned integer expressions
In file included from Structure.cpp:31:0:
ReportProbDelta.h: In constructor 'ReportProbDelta::ReportProbDelta(const std::string&, Structure*, int)':
ReportProbDelta.h:53:33: warning: comparison between signed and unsigned integer expressions
ReportProbDelta.h: In constructor 'ReportProbDelta::ReportProbDelta(double*, Structure*, int)':
ReportProbDelta.h:85:33: warning: comparison between signed and unsigned integer expressions
ReportProbDelta.h: In destructor 'virtual ReportProbDelta::˜ReportProbDelta()':
ReportProbDelta.h:96:30: warning: comparison between signed and unsigned integer expressions
Structure.cpp: In member function 'void Structure::setInitialValues(std::string&)':
Structure.cpp:1102:31: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1106:28: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1109:28: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1121:33: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1125:30: warning: comparison between signed and unsigned integer expressions
Structure.cpp:1128:30: warning: comparison between signed and unsigned integer expressions
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:13:0:
Random.h:19:0: warning: "PI" redefined
D:/biocbld/BBS-2˜1.8-B/R/include/R_ext/Constants.h:30:0: note: this is the location of the previous definition
In file included from diffExpressed_main.cpp:19:0:
PotentialX.h: In destructor 'virtual PotentialX::˜PotentialX()':
PotentialX.h:44:30: warning: comparison between signed and unsigned integer expressions
PotentialX.h: In member function 'virtual double PotentialX::potential(Random&) const':
PotentialX.h:64:30: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:28:0:
PotentialSigma2.h: In destructor 'virtual PotentialSigma2::˜PotentialSigma2()':
PotentialSigma2.h:44:30: warning: comparison between signed and unsigned integer expressions
PotentialSigma2.h: In member function 'virtual double PotentialSigma2::potential(Random&) const':
PotentialSigma2.h:64:30: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:29:0:
PotentialPhi.h: In destructor 'virtual PotentialPhi::˜PotentialPhi()':
PotentialPhi.h:44:30: warning: comparison between signed and unsigned integer expressions
PotentialPhi.h: In member function 'virtual double PotentialPhi::potential(Random&) const':
PotentialPhi.h:64:30: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:30:0:
PotentialSum.h: In constructor 'PotentialSum::PotentialSum(const std::vector<Potential*>&)':
PotentialSum.h:30:29: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In destructor 'virtual PotentialSum::˜PotentialSum()':
PotentialSum.h:41:29: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In member function 'virtual double PotentialSum::potential(Random&) const':
PotentialSum.h:61:29: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:38:0:
UpdateDeltaMH.h: In constructor 'UpdateDeltaMH::UpdateDeltaMH(Structure*, int)':
UpdateDeltaMH.h:47:33: warning: comparison between signed and unsigned integer expressions
UpdateDeltaMH.h: In destructor 'virtual UpdateDeltaMH::˜UpdateDeltaMH()':
UpdateDeltaMH.h:59:30: warning: comparison between signed and unsigned integer expressions
In file included from UpdateSigma2MH.h:4:0,
                 from diffExpressed_main.cpp:40:
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
UpdateMultiplicativePositive.h:53:33: warning: comparison between signed and unsigned integer expressions
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
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
UpdateMultiplicativePositive.h:127:34: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:130:34: warning: comparison between signed and unsigned integer expressions
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
UpdateMultiplicativePositive.h:162:34: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In member function 'virtual int UpdateMultiplicativePositive::update(Random&)':
UpdateMultiplicativePositive.h:213:34: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:40:0:
UpdateSigma2MH.h: In constructor 'UpdateSigma2MH::UpdateSigma2MH(Structure*, double)':
UpdateSigma2MH.h:49:28: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In destructor 'virtual UpdateSigma2MH::˜UpdateSigma2MH()':
UpdateSigma2MH.h:61:27: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In member function 'virtual void UpdateSigma2MH::setEpsilon(double)':
UpdateSigma2MH.h:71:27: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In member function 'virtual int UpdateSigma2MH::update(Random&)':
UpdateSigma2MH.h:96:27: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:41:0:
UpdateTMH.h: In constructor 'UpdateTMH::UpdateTMH(Structure*, const Potential*, double)':
UpdateTMH.h:48:33: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In destructor 'virtual UpdateTMH::˜UpdateTMH()':
UpdateTMH.h:60:27: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In member function 'virtual int UpdateTMH::update(Random&)':
UpdateTMH.h:84:27: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:42:0:
UpdateLMH.h: In constructor 'UpdateLMH::UpdateLMH(Structure*, const Potential*, double)':
UpdateLMH.h:49:33: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In destructor 'virtual UpdateLMH::˜UpdateLMH()':
UpdateLMH.h:61:27: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In member function 'virtual void UpdateLMH::setEpsilon(double)':
UpdateLMH.h:73:27: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In member function 'virtual int UpdateLMH::update(Random&)':
UpdateLMH.h:99:27: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:43:0:
UpdatePhiMH.h: In constructor 'UpdatePhiMH::UpdatePhiMH(Structure*, double)':
UpdatePhiMH.h:45:28: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In destructor 'virtual UpdatePhiMH::˜UpdatePhiMH()':
UpdatePhiMH.h:57:27: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In member function 'virtual void UpdatePhiMH::setEpsilon(double)':
UpdatePhiMH.h:69:27: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In member function 'virtual int UpdatePhiMH::update(Random&)':
UpdatePhiMH.h:96:27: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:44:0:
UpdateThetaMH.h: In constructor 'UpdateThetaMH::UpdateThetaMH(Structure*, const Potential*, double)':
UpdateThetaMH.h:49:33: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In destructor 'virtual UpdateThetaMH::˜UpdateThetaMH()':
UpdateThetaMH.h:61:27: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In member function 'virtual int UpdateThetaMH::update(Random&)':
UpdateThetaMH.h:85:27: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:45:0:
UpdateLambdaMH.h: In constructor 'UpdateLambdaMH::UpdateLambdaMH(Structure*, const Potential*, double)':
UpdateLambdaMH.h:47:33: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In destructor 'virtual UpdateLambdaMH::˜UpdateLambdaMH()':
UpdateLambdaMH.h:59:27: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In member function 'virtual int UpdateLambdaMH::update(Random&)':
UpdateLambdaMH.h:83:27: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:140:0:
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
diffExpressed_main.cpp:199:30: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:214:34: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:221:33: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:224:33: warning: comparison between signed and unsigned integer expressions
x86_64-w64-mingw32-g++ -I"D:/biocbld/BBS-2˜1.8-B/R/include"          -O2 -Wall  -c main.cpp -o main.o
In file included from main.cpp:21:0:
PotentialX.h: In destructor 'virtual PotentialX::˜PotentialX()':
PotentialX.h:44:30: warning: comparison between signed and unsigned integer expressions
PotentialX.h: In member function 'virtual double PotentialX::potential(Random&) const':
PotentialX.h:64:30: warning: comparison between signed and unsigned integer expressions
In file included from main.cpp:30:0:
PotentialSigma2.h: In destructor 'virtual PotentialSigma2::˜PotentialSigma2()':
PotentialSigma2.h:44:30: warning: comparison between signed and unsigned integer expressions
PotentialSigma2.h: In member function 'virtual double PotentialSigma2::potential(Random&) const':
PotentialSigma2.h:64:30: warning: comparison between signed and unsigned integer expressions
In file included from main.cpp:31:0:
PotentialPhi.h: In destructor 'virtual PotentialPhi::˜PotentialPhi()':
PotentialPhi.h:44:30: warning: comparison between signed and unsigned integer expressions
PotentialPhi.h: In member function 'virtual double PotentialPhi::potential(Random&) const':
PotentialPhi.h:64:30: warning: comparison between signed and unsigned integer expressions
In file included from main.cpp:32:0:
PotentialSum.h: In constructor 'PotentialSum::PotentialSum(const std::vector<Potential*>&)':
PotentialSum.h:30:29: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In destructor 'virtual PotentialSum::˜PotentialSum()':
PotentialSum.h:41:29: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In member function 'virtual double PotentialSum::potential(Random&) const':
PotentialSum.h:61:29: warning: comparison between signed and unsigned integer expressions
In file included from main.cpp:40:0:
UpdateDeltaMH.h: In constructor 'UpdateDeltaMH::UpdateDeltaMH(Structure*, int)':
UpdateDeltaMH.h:47:33: warning: comparison between signed and unsigned integer expressions
UpdateDeltaMH.h: In destructor 'virtual UpdateDeltaMH::˜UpdateDeltaMH()':
UpdateDeltaMH.h:59:30: warning: comparison between signed and unsigned integer expressions
In file included from UpdateSigma2MH.h:4:0,
                 from main.cpp:42:
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
UpdateMultiplicativePositive.h:53:33: warning: comparison between signed and unsigned integer expressions
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
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
UpdateMultiplicativePositive.h:127:34: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:130:34: warning: comparison between signed and unsigned integer expressions
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
UpdateMultiplicativePositive.h:162:34: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In member function 'virtual int UpdateMultiplicativePositive::update(Random&)':
UpdateMultiplicativePositive.h:213:34: warning: comparison between signed and unsigned integer expressions
In file included from main.cpp:42:0:
UpdateSigma2MH.h: In constructor 'UpdateSigma2MH::UpdateSigma2MH(Structure*, double)':
UpdateSigma2MH.h:49:28: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In destructor 'virtual UpdateSigma2MH::˜UpdateSigma2MH()':
UpdateSigma2MH.h:61:27: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In member function 'virtual void UpdateSigma2MH::setEpsilon(double)':
UpdateSigma2MH.h:71:27: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In member function 'virtual int UpdateSigma2MH::update(Random&)':
UpdateSigma2MH.h:96:27: warning: comparison between signed and unsigned integer expressions
In file included from main.cpp:43:0:
UpdateTMH.h: In constructor 'UpdateTMH::UpdateTMH(Structure*, const Potential*, double)':
UpdateTMH.h:48:33: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In destructor 'virtual UpdateTMH::˜UpdateTMH()':
UpdateTMH.h:60:27: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In member function 'virtual int UpdateTMH::update(Random&)':
UpdateTMH.h:84:27: warning: comparison between signed and unsigned integer expressions
In file included from main.cpp:44:0:
UpdateLMH.h: In constructor 'UpdateLMH::UpdateLMH(Structure*, const Potential*, double)':
UpdateLMH.h:49:33: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In destructor 'virtual UpdateLMH::˜UpdateLMH()':
UpdateLMH.h:61:27: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In member function 'virtual void UpdateLMH::setEpsilon(double)':
UpdateLMH.h:73:27: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In member function 'virtual int UpdateLMH::update(Random&)':
UpdateLMH.h:99:27: warning: comparison between signed and unsigned integer expressions
In file included from main.cpp:45:0:
UpdatePhiMH.h: In constructor 'UpdatePhiMH::UpdatePhiMH(Structure*, double)':
UpdatePhiMH.h:45:28: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In destructor 'virtual UpdatePhiMH::˜UpdatePhiMH()':
UpdatePhiMH.h:57:27: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In member function 'virtual void UpdatePhiMH::setEpsilon(double)':
UpdatePhiMH.h:69:27: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In member function 'virtual int UpdatePhiMH::update(Random&)':
UpdatePhiMH.h:96:27: warning: comparison between signed and unsigned integer expressions
In file included from main.cpp:46:0:
UpdateThetaMH.h: In constructor 'UpdateThetaMH::UpdateThetaMH(Structure*, const Potential*, double)':
UpdateThetaMH.h:49:33: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In destructor 'virtual UpdateThetaMH::˜UpdateThetaMH()':
UpdateThetaMH.h:61:27: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In member function 'virtual int UpdateThetaMH::update(Random&)':
UpdateThetaMH.h:85:27: warning: comparison between signed and unsigned integer expressions
In file included from main.cpp:47:0:
UpdateLambdaMH.h: In constructor 'UpdateLambdaMH::UpdateLambdaMH(Structure*, const Potential*, double)':
UpdateLambdaMH.h:47:33: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In destructor 'virtual UpdateLambdaMH::˜UpdateLambdaMH()':
UpdateLambdaMH.h:59:27: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In member function 'virtual int UpdateLambdaMH::update(Random&)':
UpdateLambdaMH.h:83:27: warning: comparison between signed and unsigned integer expressions
main.cpp: In function 'int main(int, char**)':
main.cpp:163:29: warning: comparison between signed and unsigned integer expressions
main.cpp:387:35: warning: comparison between signed and unsigned integer expressions
main.cpp:401:32: warning: comparison between signed and unsigned integer expressions
main.cpp:406:31: warning: comparison between signed and unsigned integer expressions
main.cpp:409:31: warning: comparison between signed and unsigned integer expressions
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o XDE.dll tmp.def Cholesky.o Matrix.o Random.o Structure.o diffExpressed_main.o main.o -lm -LD:/biocbld/BBS-2˜1.8-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.8-bioc/meat/XDE.Rcheck/XDE/libs/x64
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for "pairs" in "XDE"
Creating a new generic function for "lapply" in "XDE"
Creating a new generic function for "nrow" in "XDE"
Creating a new generic function for "plot" in "XDE"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (XDE)

name	user	system	elapsed
ExpressionSetList-class	0.03	0.00	0.03
XdeMcmc-class	0	0	0
XdeParameter-class	0	0	0
burnin	0	0	0
empiricalStart	0.39	0.02	0.44
expressionSetList	0.00	0.01	0.01
firstMcmc	0.23	0.00	0.24
geneCenter	0.13	0.00	0.12
hyperparameters	0.20	0.00	0.21
lastMcmc	0	0	0
output	0.14	0.00	0.14
ssStatistic	1.47	0.00	1.46
studyCenter	0.10	0.00	0.09
symbolsInteresting	0.51	0.00	0.52
xde	0	0	0
xmcmc	0.36	0.02	0.55
xsScores	0.05	0.00	0.04

Summary

Command output