Package: GRENITS

Version: 1.9.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GRENITS_1.9.0.tar.gz

StartedAt: 2012-06-21 00:44:04 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 00:52:25 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 501.3 seconds

RetCode: 0

Status:  OK

CheckDir: GRENITS.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/GRENITS.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.9.0'
* 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 'Var2'
.heatMap.ggplot: no visible binding for global variable 'Var1'
.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-2.11-bioc/meat/GRENITS.Rcheck/GRENITS/libs/i386/GRENITS.so':
  Found '__ZSt4cout', possibly from 'std::cout' (C++)
    Object: 'commonFunctions.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/GRENITS.Rcheck/00check.log'
for details.

* installing *source* package 'GRENITS' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/include -I/Library/Frameworks/R.framework/Versions/2.15/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/Rcpp/lib/i386/libRcpp.a -L/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Versions/2.15/Resources/lib/i386 -lRblas -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/GRENITS.Rcheck/GRENITS/libs/i386
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'GRENITS_package.Rnw' 
** testing if installed package can be loaded

* DONE (GRENITS)

name	user	system	elapsed
analyse.output	19.792	0.224	20.166
defaultParams_gauss	0.020	0.002	0.022
defaultParams_linear	0.031	0.003	0.035
defaultParams_nonLinear	0.274	0.007	0.285
defaultParams_student	0.070	0.003	0.075
function_LinearNet	19.589	0.220	20.701
function_NonLinearNet	155.642	10.531	169.815
function_ReplicatesNet_gauss	43.317	0.386	45.428
function_ReplicatesNet_student	65.949	0.484	67.224
plotPriors	0.280	0.009	0.295
readChains	9.589	0.139	10.044