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BioC 3.5: CHECK report for MIMOSA on tokay2

This page was generated on 2017-08-16 13:22:58 -0400 (Wed, 16 Aug 2017).

Package 819/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MIMOSA 1.14.0
Greg Finak
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/MIMOSA
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MIMOSA
Version: 1.14.0
Command: rm -rf MIMOSA.buildbin-libdir MIMOSA.Rcheck && mkdir MIMOSA.buildbin-libdir MIMOSA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MIMOSA.buildbin-libdir MIMOSA_1.14.0.tar.gz >MIMOSA.Rcheck\00install.out 2>&1 && cp MIMOSA.Rcheck\00install.out MIMOSA-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MIMOSA.buildbin-libdir --install="check:MIMOSA-install.out" --force-multiarch --no-vignettes --timings MIMOSA_1.14.0.tar.gz
StartedAt: 2017-08-16 01:15:38 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:19:37 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 238.7 seconds
RetCode: 0
Status:  OK  
CheckDir: MIMOSA.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf MIMOSA.buildbin-libdir MIMOSA.Rcheck && mkdir MIMOSA.buildbin-libdir MIMOSA.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MIMOSA.buildbin-libdir MIMOSA_1.14.0.tar.gz >MIMOSA.Rcheck\00install.out 2>&1 && cp MIMOSA.Rcheck\00install.out MIMOSA-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=MIMOSA.buildbin-libdir --install="check:MIMOSA-install.out" --force-multiarch --no-vignettes --timings MIMOSA_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MIMOSA.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MIMOSA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MIMOSA' version '1.14.0'
* 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:
  .travis.yml
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'MIMOSA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.fitMCMC : <anonymous>: no visible global function definition for
  'read.table'
BetaMix: no visible global function definition for 'optim'
BetaMix : <anonymous>: no visible binding for global variable 'par'
ConstructMIMOSAExpressionSet : MIMOSAReshape: no visible global
  function definition for 'as.formula'
MDMix : <anonymous> : <anonymous>: no visible global function
  definition for 'fisher.test'
MDMix: no visible global function definition for 'p.adjust'
MDMix : <anonymous>: no visible global function definition for
  'fisher.test'
MDMix : f: no visible global function definition for 'dbeta'
MDMix: no visible global function definition for 'optim'
MIMOSAExpressionSet: no visible global function definition for
  'ExpressionSet'
MIMOSAExpressionSet: no visible global function definition for
  'AnnotatedDataFrame'
alphaProp1: no visible global function definition for 'rnorm'
betaintegral_R : <anonymous>: no visible global function definition for
  'pbeta'
betaintegral_R : <anonymous>: no visible global function definition for
  'rbeta'
betaintegral_R2: no visible global function definition for 'dbeta'
betaintegral_R2: no visible global function definition for 'pbeta'
boxplotMIMOSAResultList: no visible global function definition for
  'ldply'
boxplotMIMOSAResultList: no visible global function definition for
  'aes'
boxplotMIMOSAResultList: no visible binding for global variable
  'Proportion'
boxplotMIMOSAResultList: no visible binding for global variable
  'Proportion_REF'
boxplotMIMOSAResultList: no visible global function definition for
  'geom_boxplot'
boxplotMIMOSAResultList: no visible global function definition for
  'coord_trans'
boxplotMIMOSAResultList: no visible global function definition for
  'facet_wrap'
boxplotMIMOSAResultList: no visible global function definition for
  'ggtitle'
boxplotMIMOSAResultList: no visible global function definition for
  'geom_jitter'
boxplotMIMOSAResultList: no visible global function definition for
  'position_jitter'
boxplotMIMOSAResultList: no visible global function definition for
  'scale_fill_brewer'
boxplotMIMOSAResultList: no visible global function definition for
  'scale_color_brewer'
boxplotMIMOSAResultList: no visible global function definition for
  'geom_line'
boxplotMIMOSAResultList: no visible binding for global variable 'PTID'
contourPlot : <anonymous>: no visible global function definition for
  'rbinom'
contourPlot: no visible global function definition for 'contour'
contourPlot: no visible global function definition for 'points'
estimate_logZus: no visible global function definition for 'rbeta'
estimate_logZus: no visible global function definition for 'pbeta'
f1: no visible global function definition for 'dbeta'
f1: no visible global function definition for 'pbeta'
f1.log: no visible global function definition for 'dbeta'
f1.log: no visible global function definition for 'pbeta'
f2: no visible global function definition for 'dbeta'
f2: no visible global function definition for 'pbeta'
f2.log: no visible global function definition for 'dbeta'
f2.log: no visible global function definition for 'pbeta'
gibbsPsPu: no visible global function definition for 'rbeta'
gibbsPsPu: no visible global function definition for 'qbeta'
gibbsPsPu: no visible global function definition for 'runif'
gibbsPsPu: no visible global function definition for 'pbeta'
gibbsPsPu: no visible global function definition for 'ecdf'
huberFilter: no visible global function definition for 'huber'
initBetaMix: no visible global function definition for 'var'
initBetaMix: no visible global function definition for 'optim'
initBetaMix : <anonymous>: no visible global function definition for
  'fisher.test'
initBetaMix: no visible global function definition for 'p.adjust'
initBetaMix : <anonymous>: no visible binding for global variable 'par'
integrand : <anonymous>: no visible global function definition for
  'dbeta'
integrand : <anonymous>: no visible global function definition for
  'pbeta'
match.elispot.antigens: no visible global function definition for
  'na.omit'
plot.BetaMixResult: no visible global function definition for 'plot'
plotPriors: no visible global function definition for 'qbeta'
plotPriors: no visible global function definition for 'dbeta'
plotPriors: no visible global function definition for 'pbeta'
plotPriors: no visible global function definition for 'plot'
plotPriors: no visible global function definition for 'lines'
plotPriors: no visible global function definition for 'legend'
plotPriors: no visible global function definition for 'title'
posteriorSample : <anonymous>: no visible global function definition
  for 'rbinom'
refactorPData: no visible global function definition for 'pData<-'
setpData.icsdata: no visible global function definition for 'pData<-'
simAlpha.s: no visible global function definition for 'dexp'
simAlpha.s: no visible global function definition for 'runif'
simAlpha.u: no visible global function definition for 'dexp'
simAlpha.u: no visible global function definition for 'runif'
simMD: no visible global function definition for 'runif'
simMD : <anonymous>: no visible global function definition for
  'rmultinom'
simQ: no visible global function definition for 'rbeta'
simulate2: no visible global function definition for 'rbeta'
simulate2: no visible global function definition for 'rnorm'
simulate2: no visible global function definition for 'rbinom'
test: no visible global function definition for 'optim'
volcanoPlot.MIMOSAResultList: no visible global function definition for
  'is.formula'
volcanoPlot.MIMOSAResultList: no visible global function definition for
  'facet_grid'
MIMOSA,formula-ExpressionSet: no visible binding for global variable
  'RefTreat'
MIMOSA,formula-ExpressionSet: no visible global function definition for
  'terms'
MIMOSA,formula-ExpressionSet: no visible global function definition for
  'model.frame'
MIMOSA,formula-ExpressionSet : <anonymous>: no visible global function
  definition for 'quantile'
MIMOSA,formula-ExpressionSet : <anonymous> : <anonymous>: no visible
  global function definition for 'quantile'
MIMOSA,formula-ExpressionSet: no visible global function definition for
  'mclapply'
MIMOSA,formula-ExpressionSet : <anonymous> : <anonymous> : <anonymous>:
  no visible global function definition for 'quantile'
initialize,MIMOSAResult: no visible global function definition for
  'callNextMethod'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric:
  no visible global function definition for 'image'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric:
  no visible global function definition for 'gray.colors'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric:
  no visible global function definition for 'contour'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric:
  no visible global function definition for 'points'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric
  : <anonymous>: no visible global function definition for 'p.adjust'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric
  : <anonymous>: no visible global function definition for
  'fisher.test'
likelihoodSurfacePlot,BetaMixResult-integer-integer-integer-integer-numeric:
  no visible global function definition for 'lines'
pData<-,BetaMixResult-data.frame: no visible global function definition
  for 'pData<-'
summary,BetaMixResult: no visible global function definition for 'show'
Undefined global functions or variables:
  AnnotatedDataFrame ExpressionSet PTID Proportion Proportion_REF
  RefTreat aes as.formula callNextMethod contour coord_trans dbeta dexp
  ecdf facet_grid facet_wrap fisher.test geom_boxplot geom_jitter
  geom_line ggtitle gray.colors huber image is.formula ldply legend
  lines mclapply model.frame na.omit optim p.adjust pData<- par pbeta
  plot points position_jitter qbeta quantile rbeta rbinom read.table
  rmultinom rnorm runif scale_color_brewer scale_fill_brewer show terms
  title var
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "contour", "image", "legend", "lines", "par",
             "plot", "points", "title")
  importFrom("methods", "callNextMethod", "show")
  importFrom("stats", "as.formula", "dbeta", "dexp", "ecdf",
             "fisher.test", "model.frame", "na.omit", "optim",
             "p.adjust", "pbeta", "qbeta", "quantile", "rbeta", "rbinom",
             "rmultinom", "rnorm", "runif", "terms", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.5-bioc/meat/MIMOSA.buildbin-libdir/MIMOSA/libs/i386/MIMOSA.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
MIMOSA-accessors 7.88   0.05    7.92
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 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: 3 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/MIMOSA.Rcheck/00check.log'
for details.


MIMOSA.Rcheck/00install.out:


install for i386

* installing *source* package 'MIMOSA' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c BetaMix.cpp -o BetaMix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c MCMC.cpp -o MCMC.o
MCMC.cpp: In function 'SEXPREC* fitMCMC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MCMC.cpp:73:9: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  if(file==NULL|fileP==NULL){
         ^
MCMC.cpp:88:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if(alphas.size()!=stim.ncol()){
                  ^
MCMC.cpp:188:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<alphas.size();i++){
               ^
MCMC.cpp:191:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<alphau.size();i++){
               ^
MCMC.cpp:523:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int j=0;j<p.size();j++){
                 ^
MCMC.cpp:542:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int obs=0;obs<alphas.size();obs++){
                     ^
MCMC.cpp:545:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int obs=0;obs<alphau.size();obs++){
                     ^
MCMC.cpp: In function 'double lkbeta(const std::vector<double, std::allocator<double> >&)':
MCMC.cpp:627:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<alpha.size();i++){
               ^
MCMC.cpp: In function 'void simZ(double&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<bool>&, int, int)':
MCMC.cpp:677:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(i=0;i < lnull.size(); i++){
            ^
MCMC.cpp: In function 'double normconstIBeta(double, double, double, double)':
MCMC.cpp:811:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<upper.size();i++){
               ^
MCMC.cpp: In function 'double nc(double, double, double, double, double)':
MCMC.cpp:884:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<(s.size()-1);i++){
               ^
MCMC.cpp:889:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<s.size();i++){
               ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c MIMOSA_init.c -o MIMOSA_init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c betaintegral.c -o betaintegral.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c betaintegralRcpp.cpp -o betaintegralRcpp.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o MIMOSA.dll tmp.def BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -lm -lstdc++ -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -IC:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/MIMOSA.buildbin-libdir/MIMOSA/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'MIMOSA' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c BetaMix.cpp -o BetaMix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c MCMC.cpp -o MCMC.o
MCMC.cpp: In function 'SEXPREC* fitMCMC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MCMC.cpp:73:9: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
  if(file==NULL|fileP==NULL){
         ^
MCMC.cpp:88:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  if(alphas.size()!=stim.ncol()){
                  ^
MCMC.cpp:188:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<alphas.size();i++){
               ^
MCMC.cpp:191:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<alphau.size();i++){
               ^
MCMC.cpp:523:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int j=0;j<p.size();j++){
                 ^
MCMC.cpp:542:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int obs=0;obs<alphas.size();obs++){
                     ^
MCMC.cpp:545:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for(int obs=0;obs<alphau.size();obs++){
                     ^
MCMC.cpp: In function 'double lkbeta(const std::vector<double, std::allocator<double> >&)':
MCMC.cpp:627:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<alpha.size();i++){
               ^
MCMC.cpp: In function 'void simZ(double&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<bool>&, int, int)':
MCMC.cpp:677:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(i=0;i < lnull.size(); i++){
            ^
MCMC.cpp: In function 'double normconstIBeta(double, double, double, double)':
MCMC.cpp:811:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<upper.size();i++){
               ^
MCMC.cpp: In function 'double nc(double, double, double, double, double)':
MCMC.cpp:884:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<(s.size()-1);i++){
               ^
MCMC.cpp:889:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for(int i=0;i<s.size();i++){
               ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c MIMOSA_init.c -o MIMOSA_init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c betaintegral.c -o betaintegral.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=core2 -c betaintegralRcpp.cpp -o betaintegralRcpp.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o MIMOSA.dll tmp.def BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -lm -lstdc++ -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -IC:/Users/biocbuild/bbs-3.5-bioc/R/library/RcppArmadillo/include -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/MIMOSA.buildbin-libdir/MIMOSA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MIMOSA' as MIMOSA_1.14.0.zip
* DONE (MIMOSA)

MIMOSA.Rcheck/examples_i386/MIMOSA-Ex.timings:

nameusersystemelapsed
ConstructMIMOSAExpressionSet0.580.030.61
MIMOSA-accessors4.610.014.62
MIMOSA1.610.031.64
MIMOSAExpressionSet0.200.000.21
countsTable2.690.002.69
fdr2.160.002.15
volcanoPlot2.690.002.68

MIMOSA.Rcheck/examples_x64/MIMOSA-Ex.timings:

nameusersystemelapsed
ConstructMIMOSAExpressionSet1.50.01.5
MIMOSA-accessors7.880.057.92
MIMOSA2.170.002.17
MIMOSAExpressionSet0.290.000.29
countsTable2.120.002.12
fdr2.190.002.19
volcanoPlot3.340.003.34