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Package 233/516HostnameOS / ArchBUILDCHECKBUILD BIN
GRENITS 1.6.0
Edward Morrissey
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/GRENITS
Last Changed Rev: 59920 / Revision: 61898
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: GRENITS
Version: 1.6.0
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch GRENITS_1.6.0.tar.gz
StartedAt: 2012-01-09 03:33:31 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 03:39:05 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 334.0 seconds
RetCode: 0
Status:  OK  
CheckDir: GRENITS.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/GRENITS.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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 ... 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

GRENITS.Rcheck/00install.out:

* installing *source* package 'GRENITS' ...
** libs
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -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:49:30: warning: unused variable 'numDiag'
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -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:49:30: warning: unused variable 'numDiag'
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -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:48:30: warning: unused variable 'numDiag'
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -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:45:63: warning: unused variable 'numDiag'
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -c R_C_interface.cpp -o R_C_interface.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc:22:66: warning: declaration of 'void dtrtrs_(char*, char*, char*, arma::blas_int*, arma::blas_int*, double*, arma::blas_int*, double*, arma::blas_int*, arma::blas_int*)' with C language linkage
D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include/armadillo_bits/lapack_bones.hpp:290:1: warning: conflicts with previous declaration 'void arma::dtrtrs_(char*, char*, char*, arma::blas_int*, arma::blas_int*, const double*, arma::blas_int*, double*, arma::blas_int*, arma::blas_int*)'
commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)':
commonFunctions.cc:270:27: 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:377:33: warning: comparison between signed and unsigned integer expressions
commonFunctions.cc:380:35: 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:440:59: 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:482:59: warning: unused variable 'num_on'
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -c functionsErrorModel.cc -o functionsErrorModel.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -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:128:36: warning: comparison between signed and unsigned integer expressions
updateFunctions_AR1.cc:134:11: 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:186:44: 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:264:59: warning: unused variable 'num_on'
x86_64-w64-mingw32-g++  -I"D:/biocbld/BBS-2˜1.9-B/R/include"    -I"D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.9-bioc/R/library/RcppArmadillo/include"      -O2 -Wall  -mtune=core2 -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:296:13: 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:478:40: 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:714:33: warning: comparison between signed and unsigned integer expressions
x86_64-w64-mingw32-g++ -shared -s -static-libgcc -o GRENITS.dll tmp.def 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 D:/biocbld/bbs-2.9-bioc/R/library/Rcpp/lib/x64/libRcpp.a -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lRlapack -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lRblas -lgfortran -LD:/biocbld/BBS-2˜1.9-B/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.9-bioc/meat/GRENITS.Rcheck/GRENITS/libs/x64
** 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)

GRENITS.Rcheck/GRENITS-Ex.timings:

nameusersystemelapsed
analyse.output16.80 0.0716.89
defaultParams_gauss0.010.000.01
defaultParams_linear0.020.000.02
defaultParams_nonLinear0.190.000.19
defaultParams_student0.050.000.05
function_LinearNet16.01 0.0216.17
function_NonLinearNet105.33 0.05105.84
function_ReplicatesNet_gauss36.33 0.0836.43
function_ReplicatesNet_student50.78 0.1051.20
plotPriors0.240.000.23
readChains7.570.007.67