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Package 294/658HostnameOS / ArchBUILDCHECKBUILD BIN
GRENITS 1.11.0
Edward Morrissey
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GRENITS
Last Changed Rev: 74684 / Revision: 74774
Last Changed Date: 2013-03-22 10:04:58 -0700 (Fri, 22 Mar 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: GRENITS
Version: 1.11.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GRENITS_1.11.0.tar.gz
StartedAt: 2013-03-25 02:57:06 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 03:04:35 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 448.8 seconds
RetCode: 0
Status:  OK 
CheckDir: GRENITS.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GRENITS.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.11.0'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'GRENITS' can be installed ... [96s/97s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.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-2.12-bioc/meat/GRENITS.Rcheck/GRENITS/libs/i386/GRENITS.so':
  Found '__ZSt4cout', possibly from 'std::cout' (C++)
    Object: 'commonFunctions.o'

Compiled code should not call entry points 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 ... [297s/303s] OK
Examples with CPU or elapsed time > 5s
                                  user system elapsed
function_NonLinearNet          154.035  5.829 165.361
function_ReplicatesNet_student  53.524  0.277  54.336
function_ReplicatesNet_gauss    35.961  0.238  36.627
function_LinearNet              19.365  0.182  19.665
analyse.output                  16.996  0.202  17.286
readChains                       7.051  0.089   7.317
* 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-2.12-bioc/meat/GRENITS.Rcheck/00check.log'
for details.

GRENITS.Rcheck/00install.out:

* installing *source* package 'GRENITS' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/RcppArmadillo/include"   -fPIC  -g -O2 -Wall -fasm-blocks  -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include" -I"/Library/Frameworks/R.framework/Versions/3.0/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/3.0/Resources/library/Rcpp/lib/i386/libRcpp.a -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRlapack -L/Library/Frameworks/R.framework/Resources/lib/i386 -lRblas -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-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)

GRENITS.Rcheck/GRENITS-Ex.timings:

nameusersystemelapsed
analyse.output16.996 0.20217.286
defaultParams_gauss0.1020.0140.117
defaultParams_linear0.0600.0170.076
defaultParams_nonLinear0.3300.0220.360
defaultParams_student0.1020.0160.121
function_LinearNet19.365 0.18219.665
function_NonLinearNet154.035 5.829165.361
function_ReplicatesNet_gauss35.961 0.23836.627
function_ReplicatesNet_student53.524 0.27754.336
plotPriors0.1970.0130.210
readChains7.0510.0897.317