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BioC 2.12: CHECK report for XDE on george2

This page was generated on 2013-10-09 09:37:26 -0700 (Wed, 09 Oct 2013).

Package 666/671HostnameOS / ArchBUILDCHECKBUILD BIN
XDE 2.6.0
Robert Scharpf
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/XDE
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: XDE
Version: 2.6.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings XDE_2.6.0.tar.gz
StartedAt: 2013-10-09 05:31:57 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 05:36:37 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 280.6 seconds
RetCode: 0
Status:  OK 
CheckDir: XDE.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/XDE.Rcheck’
* using R version 3.0.1 (2013-05-16)
* 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 ‘2.6.0’
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
  data/.commands.R
  data/.createLogFiles.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘XDE’ can be installed ... [59s/61s] OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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
$,XdeMcmc: warning in matrix(mcmc, nr = iterations(x), nc =
  length(studyNames(x)), byrow = byrow): partial argument match of 'nr'
  to 'nrow'
$,XdeMcmc: warning in matrix(mcmc, nr = iterations(x), nc =
  length(studyNames(x)), byrow = byrow): partial argument match of 'nc'
  to 'ncol'
$,XdeMcmc: warning in matrix(mcmc, nc = 1, byrow = TRUE): partial
  argument match of 'nc' to 'ncol'
$,XdeMcmc: warning in matrix(mcmc, nc = S * (S - 1)/2, byrow = TRUE):
  partial argument match of 'nc' to 'ncol'
$,XdeMcmc: warning in matrix(mcmc, nc = 18, nr = iterations(x), byrow =
  TRUE): partial argument match of 'nr' to 'nrow'
$,XdeMcmc: warning in matrix(mcmc, nc = 18, nr = iterations(x), byrow =
  TRUE): partial argument match of 'nc' to 'ncol'
computeGOF: no visible binding for global variable ‘psi’
modelA_B_MIupdates: no visible binding for global variable ‘x’
modelA_B_MIupdates: no visible binding for global variable ‘d’
rupdateBDDeltaStar_HyperInverseWishart: no visible binding for global
  variable ‘phenodata’
* 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 ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [14s/14s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’ [9s/9s]
 [9s/9s] 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/XDE.Rcheck/00check.log’
for details.

XDE.Rcheck/00install.out:

* installing *source* package ‘XDE’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Cholesky.cpp -o Cholesky.o
g++ -I/home/biocbuild/bbs-2.12-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’ [-Wunused-variable]
Matrix_v2.cpp:246:9: warning: unused variable ‘j’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.12-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 [-Wsign-compare]
Potential_v2.cpp:310:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:316:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:321:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:322:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:328:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:329:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:330:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:335:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:336:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:345:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:347:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:356:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:364:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:366:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:369:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:371:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Potential_v2.cpp:374:38: warning: statement has no effect [-Wunused-value]
Potential_v2.cpp: In function ‘double potentialOmega0(double, double, double)’:
Potential_v2.cpp:876:19: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
g++ -I/home/biocbuild/bbs-2.12-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:159:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp: In member function ‘std::vector<std::vector<double> > Random::CorrelationStandardInverseWishartAlternativeParam(int, double)’:
Random_v2.cpp:512:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:515:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:548:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:551:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:557:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:558:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:571:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:585:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:586:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:587:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:588:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:590:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:591:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:594:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:595:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:598:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:599:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:608:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:610:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:625:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:627:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:675:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:677:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:693:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:695:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:705:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:706:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:726:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:728:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:740:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:741:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:746:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:747:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:749:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:750:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:752:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:753:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:760:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:761:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:790:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:807:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:812:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:821:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:834:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:835:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:836:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:837:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:840:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:841:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:844:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:845:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:848:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:849:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:863:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:864:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:877:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:884:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:889:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:894:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:899:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:901:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:913:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:918:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:923:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:928:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:948:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:950:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:966:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:968:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:973:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:976:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:978:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:994:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1007:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1008:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1009:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1010:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1012:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1013:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1016:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1017:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1020:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1021:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1035:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1036:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1048:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1050:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1057:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1062:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1067:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1070:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1072:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1074:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1086:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1088:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1093:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1096:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1098:25: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1133:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1135:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1143:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1144:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:1183:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1188:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1196:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1197:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1199:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1200:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:1225:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1232:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1236:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1240:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1241:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1244:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1251:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1258:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1265:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1267:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1271:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:1297:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1299:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1310:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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:1335:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1336:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1343:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1345:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1350:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1351:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1355:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1356:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1357:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1360:61: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1361:38: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1380:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1385:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1391:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1393:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1396:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp:1398:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp: In member function ‘std::vector<int> Random::Permutation(int)’:
Random_v2.cpp:1822:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Random_v2.cpp: In member function ‘double Random::lnGamma(double)’:
Random_v2.cpp:1847:10: warning: unused variable ‘x’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.12-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:2:
Random.h:19:0: warning: "PI" redefined [enabled by default]
/home/biocbuild/bbs-2.12-bioc/R/include/R_ext/Constants.h:32:0: note: this is the location of the previous definition
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c Structure.cpp -o Structure.o
In file included from Structure.cpp:29:0:
ReportPotential.h: In constructor ‘ReportPotential::ReportPotential(const string&, const std::vector<Potential*>&)’:
ReportPotential.h:32:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
ReportPotential.h: In constructor ‘ReportPotential::ReportPotential(double*, const std::vector<Potential*>&)’:
ReportPotential.h:48:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
ReportPotential.h: In member function ‘virtual void ReportPotential::report(const Structure*)’:
ReportPotential.h:69:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
ReportPotential.h:78:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from Structure.cpp:30:0:
ReportAcceptance.h: In constructor ‘ReportAcceptance::ReportAcceptance(const string&, const std::vector<Update*>&)’:
ReportAcceptance.h:32:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
ReportAcceptance.h: In constructor ‘ReportAcceptance::ReportAcceptance(double*, const std::vector<Update*>&)’:
ReportAcceptance.h:48:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
ReportAcceptance.h: In member function ‘virtual void ReportAcceptance::report(const Structure*)’:
ReportAcceptance.h:67:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
ReportAcceptance.h:76:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wsign-compare]
PotentialSum.h: In destructor ‘virtual PotentialSum::˜PotentialSum()’:
PotentialSum.h:41:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
PotentialSum.h: In member function ‘virtual double PotentialSum::potential(Random&) const’:
PotentialSum.h:61:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from Structure.cpp:31:0:
ReportProbDelta.h: In constructor ‘ReportProbDelta::ReportProbDelta(const string&, Structure*, int)’:
ReportProbDelta.h:53:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
ReportProbDelta.h: In constructor ‘ReportProbDelta::ReportProbDelta(double*, Structure*, int)’:
ReportProbDelta.h:85:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
ReportProbDelta.h: In destructor ‘virtual ReportProbDelta::˜ReportProbDelta()’:
ReportProbDelta.h:96:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Structure.cpp: In member function ‘void Structure::setParameterValues(std::string&)’:
Structure.cpp:528:8: warning: unused variable ‘c’ [-Wunused-variable]
Structure.cpp: In member function ‘void Structure::setNumberOfUpdates(std::string&, std::vector<int>&, std::vector<Update*>&) const’:
Structure.cpp:1642:8: warning: unused variable ‘nRead’ [-Wunused-variable]
Structure.cpp:1668:12: warning: unused variable ‘nRead’ [-Wunused-variable]
Structure.cpp:1579:12: warning: unused variable ‘c’ [-Wunused-variable]
Structure.cpp: In member function ‘ReportDiffexpressed* Structure::setReports(std::string&, int&, std::vector<Potential*>&, std::vector<Update*>&, std::vector<Report*>&, int)’:
Structure.cpp:1728:12: warning: unused variable ‘c’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.12-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:3919:10: warning: unused variable ‘pot’ [-Wunused-variable]
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:3973:10: warning: unused variable ‘pot’ [-Wunused-variable]
g++ -I/home/biocbuild/bbs-2.12-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’ [-Wunused-variable]
Utility_v2.cpp:228:12: warning: unused variable ‘detPosterior’ [-Wunused-variable]
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’ [-Wunused-variable]
Utility_v2.cpp:328:12: warning: unused variable ‘detPrior’ [-Wunused-variable]
Utility_v2.cpp:334:12: warning: unused variable ‘detPosterior’ [-Wunused-variable]
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 [-Wsign-compare]
Utility_v2.cpp:435:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:447:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wsign-compare]
Utility_v2.cpp:600:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wsign-compare]
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 [-Wsign-compare]
Utility_v2.cpp:760:39: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:764:6: warning: unused variable ‘ngg’ [-Wunused-variable]
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 [-Wsign-compare]
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 [-Wsign-compare]
Utility_v2.cpp:949:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:954:8: warning: unused variable ‘ngg’ [-Wunused-variable]
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 [-Wsign-compare]
Utility_v2.cpp:1028:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1036:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1041:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1047:56: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1059:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1060:42: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wsign-compare]
Utility_v2.cpp:1101:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1104:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1107:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1115:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1129:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1133:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1135:59: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1238:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1240:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1242:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1258:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1260:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1262:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1409:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1458:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1460:43: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1463:33: warning: variable ‘itextra’ set but not used [-Wunused-but-set-variable]
Utility_v2.cpp:1501:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1563:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1565:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1600:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1602:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1653:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1693:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1713:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
Utility_v2.cpp:1779:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wsign-compare]
Utility_v2.cpp:1877:46: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -I/home/biocbuild/bbs-2.12-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:16:0:
Random.h:19:0: warning: "PI" redefined [enabled by default]
/home/biocbuild/bbs-2.12-bioc/R/include/R_ext/Constants.h:32:0: note: this is the location of the previous definition
In file included from diffExpressed_main.cpp:22:0:
PotentialX.h: In destructor ‘virtual PotentialX::˜PotentialX()’:
PotentialX.h:44:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
PotentialX.h: In member function ‘virtual double PotentialX::potential(Random&) const’:
PotentialX.h:64:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:31:0:
PotentialSigma2.h: In destructor ‘virtual PotentialSigma2::˜PotentialSigma2()’:
PotentialSigma2.h:44:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
PotentialSigma2.h: In member function ‘virtual double PotentialSigma2::potential(Random&) const’:
PotentialSigma2.h:64:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:32:0:
PotentialPhi.h: In destructor ‘virtual PotentialPhi::˜PotentialPhi()’:
PotentialPhi.h:44:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
PotentialPhi.h: In member function ‘virtual double PotentialPhi::potential(Random&) const’:
PotentialPhi.h:64:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:33:0:
PotentialSum.h: In constructor ‘PotentialSum::PotentialSum(const std::vector<Potential*>&)’:
PotentialSum.h:30:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
PotentialSum.h: In destructor ‘virtual PotentialSum::˜PotentialSum()’:
PotentialSum.h:41:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
PotentialSum.h: In member function ‘virtual double PotentialSum::potential(Random&) const’:
PotentialSum.h:61:29: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:41:0:
UpdateDeltaMH.h: In constructor ‘UpdateDeltaMH::UpdateDeltaMH(Structure*, int)’:
UpdateDeltaMH.h:47:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateDeltaMH.h: In destructor ‘virtual UpdateDeltaMH::˜UpdateDeltaMH()’:
UpdateDeltaMH.h:59:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from UpdateSigma2MH.h:4:0,
                 from diffExpressed_main.cpp:43:
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 [-Wsign-compare]
UpdateMultiplicativePositive.h:53:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wsign-compare]
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 [-Wsign-compare]
UpdateMultiplicativePositive.h:127:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateMultiplicativePositive.h:130:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wsign-compare]
UpdateMultiplicativePositive.h:162:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateMultiplicativePositive.h: In member function ‘virtual int UpdateMultiplicativePositive::update(Random&)’:
UpdateMultiplicativePositive.h:213:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:43:0:
UpdateSigma2MH.h: In constructor ‘UpdateSigma2MH::UpdateSigma2MH(Structure*, double)’:
UpdateSigma2MH.h:49:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateSigma2MH.h: In destructor ‘virtual UpdateSigma2MH::˜UpdateSigma2MH()’:
UpdateSigma2MH.h:61:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateSigma2MH.h: In member function ‘virtual void UpdateSigma2MH::setEpsilon(double)’:
UpdateSigma2MH.h:71:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateSigma2MH.h: In member function ‘virtual int UpdateSigma2MH::update(Random&)’:
UpdateSigma2MH.h:96:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:44:0:
UpdateTMH.h: In constructor ‘UpdateTMH::UpdateTMH(Structure*, const Potential*, double)’:
UpdateTMH.h:48:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateTMH.h: In destructor ‘virtual UpdateTMH::˜UpdateTMH()’:
UpdateTMH.h:60:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateTMH.h: In member function ‘virtual int UpdateTMH::update(Random&)’:
UpdateTMH.h:84:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:45:0:
UpdateLMH.h: In constructor ‘UpdateLMH::UpdateLMH(Structure*, const Potential*, double)’:
UpdateLMH.h:49:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateLMH.h: In destructor ‘virtual UpdateLMH::˜UpdateLMH()’:
UpdateLMH.h:61:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateLMH.h: In member function ‘virtual void UpdateLMH::setEpsilon(double)’:
UpdateLMH.h:73:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateLMH.h: In member function ‘virtual int UpdateLMH::update(Random&)’:
UpdateLMH.h:99:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:46:0:
UpdatePhiMH.h: In constructor ‘UpdatePhiMH::UpdatePhiMH(Structure*, double)’:
UpdatePhiMH.h:45:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdatePhiMH.h: In destructor ‘virtual UpdatePhiMH::˜UpdatePhiMH()’:
UpdatePhiMH.h:57:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdatePhiMH.h: In member function ‘virtual void UpdatePhiMH::setEpsilon(double)’:
UpdatePhiMH.h:69:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdatePhiMH.h: In member function ‘virtual int UpdatePhiMH::update(Random&)’:
UpdatePhiMH.h:96:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:47:0:
UpdateThetaMH.h: In constructor ‘UpdateThetaMH::UpdateThetaMH(Structure*, const Potential*, double)’:
UpdateThetaMH.h:49:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateThetaMH.h: In destructor ‘virtual UpdateThetaMH::˜UpdateThetaMH()’:
UpdateThetaMH.h:61:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateThetaMH.h: In member function ‘virtual int UpdateThetaMH::update(Random&)’:
UpdateThetaMH.h:85:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:48:0:
UpdateLambdaMH.h: In constructor ‘UpdateLambdaMH::UpdateLambdaMH(Structure*, const Potential*, double)’:
UpdateLambdaMH.h:47:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateLambdaMH.h: In destructor ‘virtual UpdateLambdaMH::˜UpdateLambdaMH()’:
UpdateLambdaMH.h:59:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
UpdateLambdaMH.h: In member function ‘virtual int UpdateLambdaMH::update(Random&)’:
UpdateLambdaMH.h:83:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
In file included from diffExpressed_main.cpp:143:0:
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 [-Wsign-compare]
diffExpressed_main.cpp:202:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
diffExpressed_main.cpp:217:34: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
diffExpressed_main.cpp:224:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
diffExpressed_main.cpp:227:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
g++ -shared -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 -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-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
** testing if installed package can be loaded
* DONE (XDE)

XDE.Rcheck/XDE-Ex.timings:

nameusersystemelapsed
ExpressionSetList-class0.0560.0080.064
Parameters-class0.0200.0000.018
XdeMcmc-class0.0160.0040.018
XdeParameter-class0.0360.0000.033
burnin0.020.000.02
empiricalStart0.3400.0040.346
expressionSetList0.0320.0000.031
firstMcmc0.2520.0000.254
geneCenter0.1120.0000.115
hyperparameters0.2360.0000.236
lastMcmc0.0120.0040.015
output0.1040.0040.111
ssStatistic1.2880.0241.315
studyCenter0.1400.0040.144
symbolsInteresting0.2000.0160.217
xde0.4320.0000.434
xmcmc0.1400.0040.145
xsScores0.060.000.06