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###
### Running command:
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### rm -rf XDE.buildbin-libdir && mkdir XDE.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XDE_2.12.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R XDE.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=XDE.buildbin-libdir XDE_2.12.0.tar.gz'
>>>>>>>
* installing *source* package ‘XDE’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c Cholesky.cpp -o Cholesky.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c Matrix_v2.cpp -o Matrix_v2.o
Matrix_v2.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_v2.cpp:244: warning: unused variable ‘k’
Matrix_v2.cpp:246: warning: unused variable ‘j’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -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, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Potential_v2.cpp:308: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:310: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:316: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:321: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:322: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:328: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:329: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:330: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:335: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:336: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:345: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:347: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:356: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:364: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:366: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:369: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:371: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:374: warning: statement has no effect
Potential_v2.cpp: In function ‘double potentialOmega0(double, double, double)’:
Potential_v2.cpp:876: warning: suggest parentheses around assignment used as truth value
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c Random_v2.cpp -o Random_v2.o
Random_v2.cpp: In member function ‘int Random::Discrete(const std::vector<double, std::allocator<double> >&)’:
Random_v2.cpp:159: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > Random::CorrelationStandardInverseWishartAlternativeParam(int, double)’:
Random_v2.cpp:512: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:515: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > > Random::HyperInverseWishart(double, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Random_v2.cpp:548: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:551: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:557: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:558: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:571: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:585: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:586: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:587: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:588: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:590: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:591: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:594: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:595: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:598: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:599: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:608: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:610: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:625: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:627: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:675: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:677: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:693: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:695: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:705: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:706: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:726: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:728: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:740: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:741: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:746: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:747: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:749: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:750: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:752: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:753: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:760: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:761: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<double, std::allocator<double> > Random::GaussianGraphicalModel(const std::vector<double, std::allocator<double> >&, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Random_v2.cpp:790: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:807: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:812: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:821: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:834: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:835: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:836: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:837: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:840: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:841: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:844: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:845: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:848: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:849: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:863: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:864: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:877: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:884: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:889: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:894: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:899: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:901: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:913: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:918: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:923: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:928: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > Random::MatrixVariateNormal(const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Random_v2.cpp:948: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:950: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:966: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:968: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:973: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:976: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:978: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:994: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1007: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1008: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1009: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1010: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1012: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1013: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1016: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1017: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1020: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1021: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1035: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1036: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1048: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1050: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1057: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1062: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1067: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1070: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1072: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1074: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1086: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1088: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1093: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1096: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1098: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1133: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1135: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1143: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1144: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialHyperInverseWishart(double, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&)’:
Random_v2.cpp:1183: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1188: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1196: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1197: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1199: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1200: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialGaussianGraphicalModel(const std::vector<double, std::allocator<double> >&, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<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> >&)’:
Random_v2.cpp:1225: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1232: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1236: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1240: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1241: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1244: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1251: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1258: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1265: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1267: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1271: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialMatrixVariateNormal(const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&)’:
Random_v2.cpp:1297: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1299: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1310: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialMatrixVariateNormal(const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&)’:
Random_v2.cpp:1335: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1336: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1343: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1345: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1350: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1351: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1355: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1356: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1357: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1360: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1361: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1380: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1385: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1391: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1393: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1396: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1398: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<int, std::allocator<int> > Random::Permutation(int)’:
Random_v2.cpp:1822: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::lnGamma(double)’:
Random_v2.cpp:1847: warning: unused variable ‘x’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Update_v2.h:8,
from Rinterface_v2.cpp:2:
Random.h:19:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:44,
from Rinterface_v2.cpp:1:
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:32:1: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c Structure.cpp -o Structure.o
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::setParameterValues(std::string&)’:
Structure.cpp:528: warning: unused variable ‘c’
Structure.cpp: In member function ‘void Structure::setNumberOfUpdates(std::string&, std::vector<int, std::allocator<int> >&, std::vector<Update*, std::allocator<Update*> >&) const’:
Structure.cpp:1642: warning: unused variable ‘nRead’
Structure.cpp:1668: warning: unused variable ‘nRead’
Structure.cpp:1579: warning: unused variable ‘c’
Structure.cpp: In member function ‘ReportDiffexpressed* Structure::setReports(std::string&, int&, std::vector<Potential*, std::allocator<Potential*> >&, std::vector<Update*, std::allocator<Update*> >&, std::vector<Report*, std::allocator<Report*> >&, int)’:
Structure.cpp:1728: warning: unused variable ‘c’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -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, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, int, int, const double*, const double*, const double*, const double*, const double*, double, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Update_v2.cpp:3919: warning: unused variable ‘pot’
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, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Update_v2.cpp:3973: warning: unused variable ‘pot’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -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: warning: unused variable ‘detPrior’
Utility_v2.cpp:228: 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:303: warning: unused variable ‘s’
Utility_v2.cpp:328: warning: unused variable ‘detPrior’
Utility_v2.cpp:334: 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:413: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:435: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:447: 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:556: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:600: 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:635: 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:723: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:760: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:764: 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:793: 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:904: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:949: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:954: warning: unused variable ‘ngg’
Utility_v2.cpp: In function ‘double OmegaGibbs(double, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, int, int, const double*, const double*, const double*, const double*, const double*, std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, Random&, int)’:
Utility_v2.cpp:1027: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1028: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1036: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1041: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1047: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1059: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1060: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘double DeltaStarGibbs(const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<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, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, Random&, int)’:
Utility_v2.cpp:1096: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1101: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1104: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1107: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1115: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1129: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1133: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1135: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1238: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1240: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1242: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1258: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1260: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1262: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1409: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1458: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1460: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1501: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1563: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1565: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1600: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1602: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1653: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1693: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1713: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1779: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘void inverseTransformOmega(const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, double*)’:
Utility_v2.cpp:1875: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1877: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:16:
Random.h:19:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:44,
from diffExpressed_main.cpp:4:
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:32:1: warning: this is the location of the previous definition
In file included from diffExpressed_main.cpp:22:
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:31:
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:32:
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:33:
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:41:
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:43:
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:43:
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:44:
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:45:
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:46:
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:47:
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:48:
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:143:
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:202: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:217: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:224: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:227: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.0-bioc/meat/XDE.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR XDE.buildbin-libdir/XDE/libs//XDE.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgcc_s.1.dylib" "XDE.buildbin-libdir/XDE/libs//XDE.so"
install_name_tool -change "/usr/local/lib/libgfortran.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libgfortran.2.dylib" "XDE.buildbin-libdir/XDE/libs//XDE.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.5.2.dylib" "XDE.buildbin-libdir/XDE/libs//XDE.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libreadline.dylib" "XDE.buildbin-libdir/XDE/libs//XDE.so"