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BioC 3.1: CHECK report for XDE on petty

This page was generated on 2015-10-09 09:33:29 -0700 (Fri, 09 Oct 2015).

Package 1019/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XDE 2.14.0
Robert Scharpf
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/XDE
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: XDE
Version: 2.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings XDE_2.14.0.tar.gz
StartedAt: 2015-10-09 02:37:16 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:40:28 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 192.2 seconds
RetCode: 0
Status:  OK 
CheckDir: XDE.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings XDE_2.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/XDE.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘XDE/DESCRIPTION’ ... OK
* this is package ‘XDE’ version ‘2.14.0’
* 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 ... [39s/44s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’ ‘graphics’ ‘methods’ ‘genefilter’
A package should be listed in only one of these fields.
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘genefilter’ ‘GeneMeta’ ‘RColorBrewer’ ‘siggenes’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
':::' call which should be '::': ‘graphics:::pairs’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘pairs’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.studySplit,ExpressionSet : .local: warning in matrix(1, nr =
  nrow(eset[[1]]), nc = nsplit): partial argument match of 'nr' to
  'nrow'
.studySplit,ExpressionSet : .local: warning in matrix(1, nr =
  nrow(eset[[1]]), nc = nsplit): partial argument match of 'nc' to
  'ncol'
$,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’
ssStatistic : sam.wrapper: no visible global function definition for
  ‘sam’
ssStatistic : z.wrapper: no visible global function definition for
  ‘zScores’
pairs,matrix : panel: no visible global function definition for
  ‘brewer.pal’
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [8s/8s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘doRUnit.R’ [5s/5s]
 [6s/6s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/XDE.Rcheck/00check.log’
for details.

XDE.Rcheck/00install.out:

* installing *source* package ‘XDE’ ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Cholesky.cpp -o Cholesky.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Matrix_v2.cpp -o Matrix_v2.o
Matrix_v2.cpp: In function ‘void matrixMult(const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&)’:
Matrix_v2.cpp:244: warning: unused variable ‘k’
Matrix_v2.cpp:246: warning: unused variable ‘j’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Potential_v2.cpp -o Potential_v2.o
Potential_v2.cpp: In function ‘double potentialDDeltaStar_HyperInverseWishart(int, const double*, const double*, const double*, const double*, const double*, int, int, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Potential_v2.cpp:308: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:310: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:316: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:321: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:322: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:328: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:329: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:330: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:335: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:336: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:345: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:347: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:356: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:364: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:366: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:369: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:371: warning: comparison between signed and unsigned integer expressions
Potential_v2.cpp:374: warning: statement has no effect
Potential_v2.cpp: In function ‘double potentialOmega0(double, double, double)’:
Potential_v2.cpp:876: warning: suggest parentheses around assignment used as truth value
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Random_v2.cpp -o Random_v2.o
Random_v2.cpp: In member function ‘int Random::Discrete(const std::vector<double, std::allocator<double> >&)’:
Random_v2.cpp:159: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > Random::CorrelationStandardInverseWishartAlternativeParam(int, double)’:
Random_v2.cpp:512: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:515: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > > Random::HyperInverseWishart(double, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Random_v2.cpp:548: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:551: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:557: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:558: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:571: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:585: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:586: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:587: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:588: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:590: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:591: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:594: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:595: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:598: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:599: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:608: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:610: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:625: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:627: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:675: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:677: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:693: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:695: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:705: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:706: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:726: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:728: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:740: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:741: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:746: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:747: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:749: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:750: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:752: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:753: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:760: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:761: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<double, std::allocator<double> > Random::GaussianGraphicalModel(const std::vector<double, std::allocator<double> >&, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Random_v2.cpp:790: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:807: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:812: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:821: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:834: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:835: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:836: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:837: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:840: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:841: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:844: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:845: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:848: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:849: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:863: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:864: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:877: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:884: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:889: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:894: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:899: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:901: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:913: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:918: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:923: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:928: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > Random::MatrixVariateNormal(const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Random_v2.cpp:948: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:950: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:966: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:968: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:973: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:976: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:978: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:994: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1007: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1008: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1009: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1010: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1012: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1013: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1016: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1017: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1020: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1021: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1035: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1036: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1048: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1050: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1057: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1062: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1067: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1070: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1072: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1074: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1086: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1088: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1093: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1096: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1098: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1133: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1135: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1143: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1144: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialHyperInverseWishart(double, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&)’:
Random_v2.cpp:1183: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1188: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1196: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1197: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1199: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1200: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialGaussianGraphicalModel(const std::vector<double, std::allocator<double> >&, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<double, std::allocator<double> >&)’:
Random_v2.cpp:1225: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1232: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1236: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1240: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1241: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1244: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1251: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1258: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1265: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1267: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1271: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialMatrixVariateNormal(const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&)’:
Random_v2.cpp:1297: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1299: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1310: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::PotentialMatrixVariateNormal(const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >&)’:
Random_v2.cpp:1335: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1336: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1343: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1345: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1350: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1351: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1355: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1356: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1357: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1360: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1361: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1380: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1385: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1391: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1393: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1396: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp:1398: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘std::vector<int, std::allocator<int> > Random::Permutation(int)’:
Random_v2.cpp:1822: warning: comparison between signed and unsigned integer expressions
Random_v2.cpp: In member function ‘double Random::lnGamma(double)’:
Random_v2.cpp:1847: warning: unused variable ‘x’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Rinterface_v2.cpp -o Rinterface_v2.o
In file included from Update_v2.h:8,
                 from Rinterface_v2.cpp:2:
Random.h:19:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:44,
                 from Rinterface_v2.cpp:1:
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:32:1: warning: this is the location of the previous definition
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Structure.cpp -o Structure.o
In file included from Structure.cpp:29:
ReportPotential.h: In constructor ‘ReportPotential::ReportPotential(const std::string&, const std::vector<Potential*, std::allocator<Potential*> >&)’:
ReportPotential.h:32: warning: comparison between signed and unsigned integer expressions
ReportPotential.h: In constructor ‘ReportPotential::ReportPotential(double*, const std::vector<Potential*, std::allocator<Potential*> >&)’:
ReportPotential.h:48: warning: comparison between signed and unsigned integer expressions
ReportPotential.h: In member function ‘virtual void ReportPotential::report(const Structure*)’:
ReportPotential.h:69: warning: comparison between signed and unsigned integer expressions
ReportPotential.h:78: warning: comparison between signed and unsigned integer expressions
In file included from Structure.cpp:30:
ReportAcceptance.h: In constructor ‘ReportAcceptance::ReportAcceptance(const std::string&, const std::vector<Update*, std::allocator<Update*> >&)’:
ReportAcceptance.h:32: warning: comparison between signed and unsigned integer expressions
ReportAcceptance.h: In constructor ‘ReportAcceptance::ReportAcceptance(double*, const std::vector<Update*, std::allocator<Update*> >&)’:
ReportAcceptance.h:48: warning: comparison between signed and unsigned integer expressions
ReportAcceptance.h: In member function ‘virtual void ReportAcceptance::report(const Structure*)’:
ReportAcceptance.h:67: warning: comparison between signed and unsigned integer expressions
ReportAcceptance.h:76: warning: comparison between signed and unsigned integer expressions
In file included from ReportProbDelta.h:9,
                 from Structure.cpp:31:
PotentialSum.h: In constructor ‘PotentialSum::PotentialSum(const std::vector<Potential*, std::allocator<Potential*> >&)’:
PotentialSum.h:30: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In destructor ‘virtual PotentialSum::˜PotentialSum()’:
PotentialSum.h:41: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In member function ‘virtual double PotentialSum::potential(Random&) const’:
PotentialSum.h:61: warning: comparison between signed and unsigned integer expressions
In file included from Structure.cpp:31:
ReportProbDelta.h: In constructor ‘ReportProbDelta::ReportProbDelta(const std::string&, Structure*, int)’:
ReportProbDelta.h:53: warning: comparison between signed and unsigned integer expressions
ReportProbDelta.h: In constructor ‘ReportProbDelta::ReportProbDelta(double*, Structure*, int)’:
ReportProbDelta.h:85: warning: comparison between signed and unsigned integer expressions
ReportProbDelta.h: In destructor ‘virtual ReportProbDelta::˜ReportProbDelta()’:
ReportProbDelta.h:96: warning: comparison between signed and unsigned integer expressions
Structure.cpp: In member function ‘void Structure::setParameterValues(std::string&)’:
Structure.cpp:528: warning: unused variable ‘c’
Structure.cpp: In member function ‘void Structure::setNumberOfUpdates(std::string&, std::vector<int, std::allocator<int> >&, std::vector<Update*, std::allocator<Update*> >&) const’:
Structure.cpp:1642: warning: unused variable ‘nRead’
Structure.cpp:1668: warning: unused variable ‘nRead’
Structure.cpp:1579: warning: unused variable ‘c’
Structure.cpp: In member function ‘ReportDiffexpressed* Structure::setReports(std::string&, int&, std::vector<Potential*, std::allocator<Potential*> >&, std::vector<Update*, std::allocator<Update*> >&, std::vector<Report*, std::allocator<Report*> >&, int)’:
Structure.cpp:1728: warning: unused variable ‘c’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Update_v2.cpp -o Update_v2.o
Update_v2.cpp: In function ‘void updateOmega_HyperInverseWishart(unsigned int*, int*, std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, int, int, const double*, const double*, const double*, const double*, const double*, double, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Update_v2.cpp:3919: warning: unused variable ‘pot’
Update_v2.cpp: In function ‘void updateDDeltaStar_HyperInverseWishart(unsigned int*, int*, double*, int, int, const int*, const double*, const int*, const double*, const int*, const double*, const double*, const double*, const double*, const double*, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&)’:
Update_v2.cpp:3973: warning: unused variable ‘pot’
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c Utility_v2.cpp -o Utility_v2.o
Utility_v2.cpp: In function ‘double nuGibbs(double*, int, int, const int*, double, const double*, const double*, const double*, const double*, const double*, const int*, const double*, const int*, const double*, Random&, int)’:
Utility_v2.cpp:221: warning: unused variable ‘detPrior’
Utility_v2.cpp:228: warning: unused variable ‘detPosterior’
Utility_v2.cpp: In function ‘double DeltaGibbs(int, double*, int, int, const int*, double, const double*, const double*, const double*, const double*, const double*, const int*, const double*, const int*, const double*, Random&, int)’:
Utility_v2.cpp:303: warning: unused variable ‘s’
Utility_v2.cpp:328: warning: unused variable ‘detPrior’
Utility_v2.cpp:334: warning: unused variable ‘detPosterior’
Utility_v2.cpp: In function ‘void updateMRF1perfect_onedelta(int, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, double, double, double, Random&)’:
Utility_v2.cpp:413: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:435: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:447: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘double perfectMRF1_onedelta(int*, int, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, double, double, double, unsigned int*, int)’:
Utility_v2.cpp:556: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:600: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘void updateMRF2perfect_onedelta(int, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, double, double, Random&)’:
Utility_v2.cpp:635: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘double perfectMRF2_onedelta(int*, int, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, double, double, unsigned int*, int)’:
Utility_v2.cpp:723: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:760: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:764: warning: unused variable ‘ngg’
Utility_v2.cpp: In function ‘void updateMRF2perfect(int, int, int, int, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, double, double, double, Random&)’:
Utility_v2.cpp:793: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘double perfectMRF2(int*, int, int, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, const std::vector<double, std::allocator<double> >&, const std::vector<double, std::allocator<double> >&, double, double, double, unsigned int*, int)’:
Utility_v2.cpp:904: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:949: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:954: warning: unused variable ‘ngg’
Utility_v2.cpp: In function ‘double OmegaGibbs(double, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, int, int, const double*, const double*, const double*, const double*, const double*, std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, Random&, int)’:
Utility_v2.cpp:1027: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1028: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1036: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1041: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1047: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1059: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1060: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘double DeltaStarGibbs(const std::vector<int, std::allocator<int> >&, const std::vector<std::vector<int, std::allocator<int> >, std::allocator<std::vector<int, std::allocator<int> > > >&, int, int, const int*, double*, const double*, const double*, const double*, const double*, const double*, const double*, const int*, const int*, const double*, const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, Random&, int)’:
Utility_v2.cpp:1096: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1101: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1104: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1107: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1115: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1129: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1133: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1135: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1238: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1240: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1242: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1258: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1260: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1262: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1409: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1458: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1460: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1501: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1563: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1565: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1600: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1602: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1653: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1693: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1713: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1779: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp: In function ‘void inverseTransformOmega(const std::vector<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > >, std::allocator<std::vector<std::vector<double, std::allocator<double> >, std::allocator<std::vector<double, std::allocator<double> > > > > >&, double*)’:
Utility_v2.cpp:1875: warning: comparison between signed and unsigned integer expressions
Utility_v2.cpp:1877: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c diffExpressed_main.cpp -o diffExpressed_main.o
In file included from diffExpressed_main.cpp:16:
Random.h:19:1: warning: "PI" redefined
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:44,
                 from diffExpressed_main.cpp:4:
/Library/Frameworks/R.framework/Resources/include/R_ext/Constants.h:32:1: warning: this is the location of the previous definition
In file included from diffExpressed_main.cpp:22:
PotentialX.h: In destructor ‘virtual PotentialX::˜PotentialX()’:
PotentialX.h:44: warning: comparison between signed and unsigned integer expressions
PotentialX.h: In member function ‘virtual double PotentialX::potential(Random&) const’:
PotentialX.h:64: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:31:
PotentialSigma2.h: In destructor ‘virtual PotentialSigma2::˜PotentialSigma2()’:
PotentialSigma2.h:44: warning: comparison between signed and unsigned integer expressions
PotentialSigma2.h: In member function ‘virtual double PotentialSigma2::potential(Random&) const’:
PotentialSigma2.h:64: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:32:
PotentialPhi.h: In destructor ‘virtual PotentialPhi::˜PotentialPhi()’:
PotentialPhi.h:44: warning: comparison between signed and unsigned integer expressions
PotentialPhi.h: In member function ‘virtual double PotentialPhi::potential(Random&) const’:
PotentialPhi.h:64: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:33:
PotentialSum.h: In constructor ‘PotentialSum::PotentialSum(const std::vector<Potential*, std::allocator<Potential*> >&)’:
PotentialSum.h:30: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In destructor ‘virtual PotentialSum::˜PotentialSum()’:
PotentialSum.h:41: warning: comparison between signed and unsigned integer expressions
PotentialSum.h: In member function ‘virtual double PotentialSum::potential(Random&) const’:
PotentialSum.h:61: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:41:
UpdateDeltaMH.h: In constructor ‘UpdateDeltaMH::UpdateDeltaMH(Structure*, int)’:
UpdateDeltaMH.h:47: warning: comparison between signed and unsigned integer expressions
UpdateDeltaMH.h: In destructor ‘virtual UpdateDeltaMH::˜UpdateDeltaMH()’:
UpdateDeltaMH.h:59: warning: comparison between signed and unsigned integer expressions
In file included from UpdateSigma2MH.h:4,
                 from diffExpressed_main.cpp:43:
UpdateMultiplicativePositive.h: In constructor ‘UpdateMultiplicativePositive::UpdateMultiplicativePositive(const std::vector<Potential*, std::allocator<Potential*> >&, const std::vector<double*, std::allocator<double*> >&, double)’:
UpdateMultiplicativePositive.h:50: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:53: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor ‘UpdateMultiplicativePositive::UpdateMultiplicativePositive(const Potential*, const std::vector<double*, std::allocator<double*> >&, double)’:
UpdateMultiplicativePositive.h:76: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor ‘UpdateMultiplicativePositive::UpdateMultiplicativePositive(const std::vector<Potential*, std::allocator<Potential*> >&, const std::vector<double*, std::allocator<double*> >&, const std::vector<double*, std::allocator<double*> >&, double)’:
UpdateMultiplicativePositive.h:124: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:127: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:130: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In constructor ‘UpdateMultiplicativePositive::UpdateMultiplicativePositive(const Potential*, const std::vector<double*, std::allocator<double*> >&, const std::vector<double*, std::allocator<double*> >&, double)’:
UpdateMultiplicativePositive.h:159: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h:162: warning: comparison between signed and unsigned integer expressions
UpdateMultiplicativePositive.h: In member function ‘virtual int UpdateMultiplicativePositive::update(Random&)’:
UpdateMultiplicativePositive.h:213: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:43:
UpdateSigma2MH.h: In constructor ‘UpdateSigma2MH::UpdateSigma2MH(Structure*, double)’:
UpdateSigma2MH.h:49: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In destructor ‘virtual UpdateSigma2MH::˜UpdateSigma2MH()’:
UpdateSigma2MH.h:61: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In member function ‘virtual void UpdateSigma2MH::setEpsilon(double)’:
UpdateSigma2MH.h:71: warning: comparison between signed and unsigned integer expressions
UpdateSigma2MH.h: In member function ‘virtual int UpdateSigma2MH::update(Random&)’:
UpdateSigma2MH.h:96: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:44:
UpdateTMH.h: In constructor ‘UpdateTMH::UpdateTMH(Structure*, const Potential*, double)’:
UpdateTMH.h:48: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In destructor ‘virtual UpdateTMH::˜UpdateTMH()’:
UpdateTMH.h:60: warning: comparison between signed and unsigned integer expressions
UpdateTMH.h: In member function ‘virtual int UpdateTMH::update(Random&)’:
UpdateTMH.h:84: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:45:
UpdateLMH.h: In constructor ‘UpdateLMH::UpdateLMH(Structure*, const Potential*, double)’:
UpdateLMH.h:49: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In destructor ‘virtual UpdateLMH::˜UpdateLMH()’:
UpdateLMH.h:61: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In member function ‘virtual void UpdateLMH::setEpsilon(double)’:
UpdateLMH.h:73: warning: comparison between signed and unsigned integer expressions
UpdateLMH.h: In member function ‘virtual int UpdateLMH::update(Random&)’:
UpdateLMH.h:99: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:46:
UpdatePhiMH.h: In constructor ‘UpdatePhiMH::UpdatePhiMH(Structure*, double)’:
UpdatePhiMH.h:45: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In destructor ‘virtual UpdatePhiMH::˜UpdatePhiMH()’:
UpdatePhiMH.h:57: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In member function ‘virtual void UpdatePhiMH::setEpsilon(double)’:
UpdatePhiMH.h:69: warning: comparison between signed and unsigned integer expressions
UpdatePhiMH.h: In member function ‘virtual int UpdatePhiMH::update(Random&)’:
UpdatePhiMH.h:96: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:47:
UpdateThetaMH.h: In constructor ‘UpdateThetaMH::UpdateThetaMH(Structure*, const Potential*, double)’:
UpdateThetaMH.h:49: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In destructor ‘virtual UpdateThetaMH::˜UpdateThetaMH()’:
UpdateThetaMH.h:61: warning: comparison between signed and unsigned integer expressions
UpdateThetaMH.h: In member function ‘virtual int UpdateThetaMH::update(Random&)’:
UpdateThetaMH.h:85: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:48:
UpdateLambdaMH.h: In constructor ‘UpdateLambdaMH::UpdateLambdaMH(Structure*, const Potential*, double)’:
UpdateLambdaMH.h:47: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In destructor ‘virtual UpdateLambdaMH::˜UpdateLambdaMH()’:
UpdateLambdaMH.h:59: warning: comparison between signed and unsigned integer expressions
UpdateLambdaMH.h: In member function ‘virtual int UpdateLambdaMH::update(Random&)’:
UpdateLambdaMH.h:83: warning: comparison between signed and unsigned integer expressions
In file included from diffExpressed_main.cpp:143:
PotentialFunction.h: In function ‘void xdeLIN_main(int*, int*, int*, int*, int*, int*, int*, double*, int*, int*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, int*, int*, char**, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, double*, int*)’:
PotentialFunction.h:55: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:202: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:217: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:224: warning: comparison between signed and unsigned integer expressions
diffExpressed_main.cpp:227: warning: comparison between signed and unsigned integer expressions
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -L/usr/local/lib -o XDE.so Cholesky.o Matrix_v2.o Potential_v2.o Random_v2.o Rinterface_v2.o Structure.o Update_v2.o Utility_v2.o diffExpressed_main.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.1-bioc/meat/XDE.Rcheck/XDE/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (XDE)

XDE.Rcheck/XDE-Ex.timings:

nameusersystemelapsed
ExpressionSetList-class0.0460.0060.051
Parameters-class0.0020.0010.003
XdeMcmc-class0.0010.0000.001
XdeParameter-class0.0030.0010.003
burnin0.0010.0000.001
empiricalStart0.3050.0220.326
expressionSetList0.0210.0030.025
firstMcmc0.2300.0040.234
geneCenter0.0740.0030.076
hyperparameters0.2120.0040.215
lastMcmc0.0010.0000.001
output0.0980.0080.106
ssStatistic0.8950.0090.943
studyCenter0.0700.0040.074
symbolsInteresting0.440.010.45
xde0.0010.0000.001
xmcmc0.1100.0070.118
xsScores0.0380.0060.044