Package: GRENITS

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GRENITS_1.6.0.tar.gz

StartedAt: 2012-01-26 04:45:05 -0800 (Thu, 26 Jan 2012)

EndedAt: 2012-01-26 04:53:38 -0800 (Thu, 26 Jan 2012)

EllapsedTime: 513.1 seconds

RetCode: 0

Status:  OK

CheckDir: GRENITS.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/GRENITS.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GRENITS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GRENITS' version '1.6.0'
* 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 whether package 'GRENITS' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.heatMap.ggplot: no visible binding for global variable 'X2'
.heatMap.ggplot: no visible binding for global variable 'X1'
.heatMap.ggplot: no visible binding for global variable 'value'
.plotDistribParents.LargeMat: no visible binding for global variable
  'variable'
.plotDistribParents.LargeMat: no visible binding for global variable
  'GeneNames'
.plotDistribParents.LargeMat: no visible binding for global variable
  'value'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File '/Users/biocbuild/bbs-2.9-bioc/meat/GRENITS.Rcheck/GRENITS/libs/i386/GRENITS.so':
  Found '__ZSt4cout', possibly from 'std::cout' (C++)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  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 sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package 'GRENITS' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
AR1_Gauss_biocond.cc: In function 'void Error_Gauss_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
AR1_Gauss_biocond.cc:49: warning: unused variable 'numDiag'
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
AR1_Student_biocond.cc: In function 'void Error_Student_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
AR1_Student_biocond.cc:49: warning: unused variable 'numDiag'
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c AR1_biocond.cc -o AR1_biocond.o
AR1_biocond.cc: In function 'void AR1_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
AR1_biocond.cc:48: warning: unused variable 'numDiag'
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c PSplines_biocond.cc -o PSplines_biocond.o
PSplines_biocond.cc: In function 'void PSplines_c(std::string&, arma::mat&, arma::colvec&, arma::mat&)':
PSplines_biocond.cc:45: warning: unused variable 'numDiag'
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c R_C_interface.cpp -o R_C_interface.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)':
commonFunctions.cc:270: warning: comparison between signed and unsigned integer expressions
commonFunctions.cc: In function 'void processFixedGammas(arma::mat&, int&, int&, arma::umat&, arma::umat&, arma::ucolvec&, arma::umat&, arma::uvec&, arma::uvec&)':
commonFunctions.cc:377: warning: comparison between signed and unsigned integer expressions
commonFunctions.cc:380: warning: comparison between signed and unsigned integer expressions
commonFunctions.cc: In function 'void updateCoefficients_reg(arma::mat&, const int&, const arma::urowvec&, const arma::mat&, const arma::rowvec&, const arma::ucolvec&)':
commonFunctions.cc:440: warning: unused variable 'num_on'
commonFunctions.cc: In function 'void updateCoefficients(arma::mat&, const int&, const arma::urowvec&, const arma::mat&, const arma::rowvec&)':
commonFunctions.cc:482: warning: unused variable 'num_on'
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, const arma::mat&, const double&, const unsigned int&)':
updateFunctions_AR1.cc:128: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc:134: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const arma::colvec&, const arma::mat&, const arma::mat&, double, const double&, const unsigned int&, arma::umat&, arma::ucolvec&, arma::umat&)':
updateFunctions_AR1.cc:186: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc: In function 'void calc_logMVPDF_withLinks(double&, const arma::mat&, const arma::rowvec&, arma::urowvec&)':
updateFunctions_AR1.cc:264: warning: unused variable 'num_on'
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
updateFunctions_Splines.cc: In function 'void updateTaus_reg(arma::mat&, arma::colvec&, const arma::mat&, arma::urowvec&, const arma::mat&, double, double, int, double, double, double, double, int, double, arma::uvec)':
updateFunctions_Splines.cc:296: warning: comparison between signed and unsigned integer expressions
updateFunctions_Splines.cc: In function 'void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const arma::mat&, const arma::rowvec&, const arma::colvec&, int, int, int, arma::urowvec&, const arma::ucolvec&, const arma::urowvec&, const arma::ucolvec&, const arma::uvec&)':
updateFunctions_Splines.cc:478: warning: comparison between signed and unsigned integer expressions
updateFunctions_Splines.cc: In function 'void fixedBasesFromFixedRegs(arma::umat&, arma::umat&, arma::ucolvec&, int)':
updateFunctions_Splines.cc:714: warning: comparison between signed and unsigned integer expressions
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GRENITS.so AR1_Gauss_biocond.o AR1_Student_biocond.o AR1_biocond.o PSplines_biocond.o R_C_interface.o ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.o /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/lib/i386/libRcpp.a -L/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Versions/2.14/Resources/lib/i386 -lRblas -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/GRENITS.Rcheck/GRENITS/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'GRENITS_package.Rnw' 
** testing if installed package can be loaded

* DONE (GRENITS)

name	user	system	elapsed
analyse.output	22.227	0.245	23.738
defaultParams_gauss	0.020	0.003	0.026
defaultParams_linear	0.030	0.003	0.035
defaultParams_nonLinear	0.269	0.007	0.279
defaultParams_student	0.072	0.004	0.076
function_LinearNet	21.862	0.182	22.609
function_NonLinearNet	157.918	9.829	172.278
function_ReplicatesNet_gauss	47.642	0.433	49.725
function_ReplicatesNet_student	69.757	0.516	76.526
plotPriors	0.265	0.009	0.276
readChains	9.976	0.130	10.244