Package: XDE

Version: 2.2.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings XDE_2.2.0.tar.gz

StartedAt: 2012-09-24 04:11:42 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 04:14:55 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 193.1 seconds

RetCode: 0

Status:  OK

CheckDir: XDE.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/XDE.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XDE/DESCRIPTION’ ... OK
* this is package ‘XDE’ version ‘2.2.0’
* 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 ... NOTE
  installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
* 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 ... OK
* 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 ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/XDE.Rcheck/XDE/libs/XDE.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
    Objects: ‘Cholesky.o’, ‘Random_v2.o’, ‘Structure.o’, ‘Update_v2.o’,
      ‘diffExpressed_main.o’
  Found ‘exit’, possibly from ‘exit’ (C)
    Objects: ‘Cholesky.o’, ‘Random_v2.o’, ‘Structure.o’, ‘Update_v2.o’,
      ‘Utility_v2.o’, ‘diffExpressed_main.o’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘Utility_v2.o’

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘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

NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/XDE.Rcheck/00check.log’
for details.

* installing *source* package ‘XDE’ ...
** libs
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Cholesky.cpp -o Cholesky.o
Cholesky.cpp: In constructor ‘Cholesky::Cholesky(const std::vector<std::vector<double> >&, int&)’:
Cholesky.cpp:21:21: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Matrix_v2.cpp -o Matrix_v2.o
Matrix_v2.cpp: In function ‘void matrixMult(const std::vector<std::vector<double> >&, const std::vector<double>&, std::vector<double>&)’:
Matrix_v2.cpp:244:7: warning: unused variable ‘k’
Matrix_v2.cpp:246:9: warning: unused variable ‘j’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Potential_v2.cpp -o Potential_v2.o
Potential_v2.cpp: In function ‘double potentialDDeltaStar_HyperInverseWishart(int, const double*, const double*, const double*, const double*, const double*, int, int, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Potential_v2.cpp:308:32: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:310:37: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:316:32: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:321:33: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:322:36: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:328:30: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:329:43: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:330:38: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:335:61: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:336:38: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:345:30: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:347:37: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:356:30: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:364:37: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:366:35: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:369:33: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:371:31: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:374:38: warning: statement has no effect
Potential_v2.cpp: In function ‘double potentialOmega0(double, double, double)’:
Potential_v2.cpp:876:19: warning: suggest parentheses around assignment used as truth value
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Random_v2.cpp -o Random_v2.o
Random_v2.cpp: In member function ‘int Random::Discrete(const std::vector<double>&)’:
Random_v2.cpp:158:29: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<std::vector<double> > Random::CorrelationStandardInverseWishartAlternativeParam(int, double)’:
Random_v2.cpp:511:26: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:514:33: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<std::vector<std::vector<double> > > Random::HyperInverseWishart(double, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Random_v2.cpp:547:26: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:550:35: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:556:29: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:557:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:570:26: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:584:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:585:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:586:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:587:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:589:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:590:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:593:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:594:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:597:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:598:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:607:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:609:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:624:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:626:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:674:41: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:676:39: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:692:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:694:27: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:704:33: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:705:31: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:725:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:727:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:739:41: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:740:39: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:745:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:746:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:748:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:749:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:751:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:752:31: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:759:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:760:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<double> Random::GaussianGraphicalModel(const std::vector<double>&, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Random_v2.cpp:789:35: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:806:28: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:811:28: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:820:28: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:833:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:834:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:835:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:836:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:839:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:840:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:843:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:844:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:847:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:848:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:862:39: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:863:37: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:876:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:883:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:888:33: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:893:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:898:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:900:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:912:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:917:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:922:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:927:29: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<std::vector<double> > Random::MatrixVariateNormal(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Random_v2.cpp:947:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:949:37: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:965:29: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:967:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:972:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:975:28: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:977:28: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:993:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1006:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1007:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1008:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1009:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1011:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1012:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1015:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1016:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1019:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1020:34: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1034:41: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1035:39: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1047:33: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1049:27: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1056:27: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1061:28: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1066:25: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1069:25: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1071:27: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1073:25: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1085:33: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1087:27: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1092:27: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1095:25: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1097:25: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1132:27: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1134:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1142:26: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1143:31: 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> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&, const std::vector<std::vector<std::vector<double> > >&)’:
Random_v2.cpp:1182:26: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1187:26: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1195:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1196:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1198:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1199:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialGaussianGraphicalModel(const std::vector<double>&, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&, const std::vector<double>&)’:
Random_v2.cpp:1224:27: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1231:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1235:31: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1239:28: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1240:43: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1243:59: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1250:28: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1257:28: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1264:35: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1266:33: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1270:33: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialMatrixVariateNormal(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&)’:
Random_v2.cpp:1296:27: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1298:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1309:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialMatrixVariateNormal(const std::vector<std::vector<double> >&, const std::vector<std::vector<double> >&, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&, const std::vector<std::vector<double> >&)’:
Random_v2.cpp:1334:27: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1335:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1342:32: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1344:37: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1349:33: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1350:36: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1354:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1355:43: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1356:38: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1359:61: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1360:38: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1379:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1384:30: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1390:37: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1392:35: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1395:33: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1397:31: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<int> Random::Permutation(int)’:
Random_v2.cpp:1821:29: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::lnGamma(double)’:
Random_v2.cpp:1846:10: warning: unused variable ‘x’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Update_v2.h:8:0,
                 from Rinterface_v2.cpp:3:
Random.h:19:0: warning: "PI" redefined
/home/biocbuild/bbs-2.10-bioc/R/include/R_ext/Constants.h:30:0: note: this is the location of the previous definition
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Structure.cpp -o Structure.o
In file included from /usr/include/c++/4.5/backward/strstream:47:0,
                 from Structure.cpp:1:
/usr/include/c++/4.5/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
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Update_v2.cpp -o Update_v2.o
Update_v2.cpp: In function ‘void updateOmega_HyperInverseWishart(unsigned int*, int*, std::vector<std::vector<std::vector<double> > >&, int, int, const double*, const double*, const double*, const double*, const double*, double, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Update_v2.cpp:3917:10: 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> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&)’:
Update_v2.cpp:3971:10: warning: unused variable ‘pot’
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Utility_v2.cpp -o Utility_v2.o
Utility_v2.cpp: In function ‘double nuGibbs(double*, int, int, const int*, double, const double*, const double*, const double*, const double*, const double*, const int*, const double*, const int*, const double*, Random&, int)’:
Utility_v2.cpp:221:12: warning: unused variable ‘detPrior’
Utility_v2.cpp:228:12: 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:303:9: warning: unused variable ‘s’
Utility_v2.cpp:328:12: warning: unused variable ‘detPrior’
Utility_v2.cpp:334:12: warning: unused variable ‘detPosterior’
Utility_v2.cpp: In function ‘void updateMRF1perfect_onedelta(int, std::vector<int>&, std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::vector<int> >&, double, double, double, Random&)’:
Utility_v2.cpp:413:39: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:435:39: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:447:46: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘double perfectMRF1_onedelta(int*, int, const std::vector<std::vector<int> >&, const std::vector<double>&, const std::vector<double>&, double, double, double, unsigned int*, int)’:
Utility_v2.cpp:556:26: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:600:41: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘void updateMRF2perfect_onedelta(int, std::vector<int>&, std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::vector<int> >&, double, double, Random&)’:
Utility_v2.cpp:635:37: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘double perfectMRF2_onedelta(int*, int, const std::vector<std::vector<int> >&, const std::vector<double>&, const std::vector<double>&, double, double, unsigned int*, int)’:
Utility_v2.cpp:723:26: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:760:39: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:764:6: warning: unused variable ‘ngg’
Utility_v2.cpp: In function ‘void updateMRF2perfect(int, int, int, int, std::vector<int>&, std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<std::vector<int> >&, double, double, double, Random&)’:
Utility_v2.cpp:793:37: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘double perfectMRF2(int*, int, int, const std::vector<std::vector<int> >&, const std::vector<double>&, const std::vector<double>&, double, double, double, unsigned int*, int)’:
Utility_v2.cpp:904:26: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:949:41: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:954:8: warning: unused variable ‘ngg’
Utility_v2.cpp: In function ‘double OmegaGibbs(double, const std::vector<std::vector<std::vector<double> > >&, const std::vector<int>&, const std::vector<std::vector<int> >&, int, int, const double*, const double*, const double*, const double*, const double*, std::vector<std::vector<std::vector<double> > >&, Random&, int)’:
Utility_v2.cpp:1027:34: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1028:40: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1036:29: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1041:43: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1047:56: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1059:36: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1060:42: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘double DeltaStarGibbs(const std::vector<int>&, const std::vector<std::vector<int> >&, int, int, const int*, double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*, const int*, const double*, const std::vector<std::vector<std::vector<double> > >&, Random&, int)’:
Utility_v2.cpp:1096:33: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1101:33: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1104:43: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1107:45: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1115:33: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1129:30: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1133:45: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1135:59: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1238:33: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1240:32: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1242:34: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1258:36: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1260:43: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1262:45: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1409:34: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1458:43: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1460:43: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1501:45: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1563:29: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1565:37: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1600:30: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1602:29: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1653:29: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1693:28: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1713:33: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1779:31: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘void inverseTransformOmega(const std::vector<std::vector<std::vector<double> > >&, double*)’:
Utility_v2.cpp:1875:41: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1877:46: warning: comparison between signed and unsigned integer expressions
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:13:0:
Random.h:19:0: warning: "PI" redefined
/home/biocbuild/bbs-2.10-bioc/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
g++ -shared -L/usr/local/lib64 -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o -lm -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/XDE.Rcheck/XDE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘pairs’ from package ‘graphics’ in package ‘XDE’
Creating a generic function for ‘plot’ from package ‘graphics’ in package ‘XDE’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘XDE.Rnw’ 
   ‘XdeParameterClass.Rnw’ 
** testing if installed package can be loaded

* DONE (XDE)

name	user	system	elapsed
ExpressionSetList-class	0.052	0.000	0.054
Parameters-class	0.000	0.000	0.002
XdeMcmc-class	0	0	0
XdeParameter-class	0.000	0.000	0.002
burnin	0	0	0
empiricalStart	0.548	0.000	0.550
expressionSetList	0.016	0.008	0.022
firstMcmc	0.196	0.004	0.199
geneCenter	0.096	0.000	0.093
hyperparameters	0.160	0.000	0.161
lastMcmc	0	0	0
output	0.088	0.004	0.092
ssStatistic	1.336	0.012	1.350
studyCenter	0.096	0.004	0.102
symbolsInteresting	0.168	0.008	0.177
xde	0	0	0
xmcmc	0.088	0.008	0.095
xsScores	0.036	0.000	0.034