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BioC 2.13: CHECK report for GRENITS on moscato1

This page was generated on 2014-04-05 09:50:24 -0700 (Sat, 05 Apr 2014).

Package 329/750HostnameOS / ArchBUILDCHECKBUILD BIN
GRENITS 1.14.1
Edward Morrissey
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/GRENITS
Last Changed Rev: 86057 / Revision: 88450
Last Changed Date: 2014-02-04 10:03:14 -0800 (Tue, 04 Feb 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ OK ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GRENITS
Version: 1.14.1
Command: rm -rf GRENITS.buildbin-libdir && mkdir GRENITS.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GRENITS.buildbin-libdir GRENITS_1.14.1.tar.gz >GRENITS-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=GRENITS.buildbin-libdir --install="check:GRENITS-install.out" --force-multiarch --no-vignettes --timings GRENITS_1.14.1.tar.gz && mv GRENITS.buildbin-libdir/* GRENITS.Rcheck/ && rmdir GRENITS.buildbin-libdir
StartedAt: 2014-04-05 04:26:41 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 04:37:51 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 669.9 seconds
RetCode: 0
Status:  OK  
CheckDir: GRENITS.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/GRENITS.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-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 '1.14.1'
* 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 whether package 'GRENITS' 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
* 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  'Rcpp' 'RcppArmadillo' 'ggplot2'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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 compilation flags in Makevars ... 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 'D:/biocbld/bbs-2.13-bioc/meat/GRENITS.buildbin-libdir/GRENITS/libs/i386/GRENITS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'D:/biocbld/bbs-2.13-bioc/meat/GRENITS.buildbin-libdir/GRENITS/libs/x64/GRENITS.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'GRENITS_package.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [228s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
function_NonLinearNet          106.11   0.00  106.82
function_ReplicatesNet_student  46.00   0.09   47.20
function_ReplicatesNet_gauss    28.13   0.05   29.36
analyse.output                  16.38   0.06   17.33
function_LinearNet              15.62   0.06   16.15
readChains                       7.53   0.00    7.54
** running examples for arch 'x64' ... [198s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
function_NonLinearNet          88.48   0.03   89.74
function_ReplicatesNet_student 47.39   0.09   48.17
function_ReplicatesNet_gauss   25.89   0.02   26.00
analyse.output                 11.35   0.04   12.20
function_LinearNet             10.97   0.00   12.16
readChains                      6.60   0.02    6.65
* 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/GRENITS.Rcheck/00check.log'
for details.

GRENITS.Rcheck/00install.out:


install for i386

* installing *source* package 'GRENITS' ...
** libs
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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' [-Wunused-variable]
AR1_Gauss_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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' [-Wunused-variable]
AR1_Student_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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' [-Wunused-variable]
AR1_biocond.cc:48:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_C_interface.cpp -o R_C_interface.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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 [enabled by default]
D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include/armadillo_bits/lapack_bones.hpp:344:1: 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*)' [enabled by default]
commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)':
commonFunctions.cc:270:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
commonFunctions.cc: In function 'void estimateRemainingTime(double&, double&, int, int, clock_t&)':
commonFunctions.cc:317:36: warning: variable 'so_far_clock' set but not used [-Wunused-but-set-variable]
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 [-Wsign-compare]
commonFunctions.cc:380:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
commonFunctions.cc: In function 'void updateCoefficients_reg(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&, const ucolvec&)':
commonFunctions.cc:440:59: warning: unused variable 'num_on' [-Wunused-variable]
commonFunctions.cc: In function 'void updateCoefficients(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&)':
commonFunctions.cc:482:59: warning: unused variable 'num_on' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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 colvec&, const mat&, const mat&, const mat&, const double&, const unsigned int&)':
updateFunctions_AR1.cc:128:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
updateFunctions_AR1.cc:134:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const colvec&, const mat&, const 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 [-Wsign-compare]
updateFunctions_AR1.cc: In function 'void calc_logMVPDF_withLinks(double&, const mat&, const rowvec&, arma::urowvec&)':
updateFunctions_AR1.cc:264:59: warning: unused variable 'num_on' [-Wunused-variable]
g++ -m32 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
updateFunctions_Splines.cc: In function 'void initBasesOn_rowvec(arma::urowvec&, const urowvec&, int, int)':
updateFunctions_Splines.cc:158:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable]
updateFunctions_Splines.cc:158:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable]
updateFunctions_Splines.cc: In function 'void initBasesOn(arma::urowvec&, const umat&, int, int)':
updateFunctions_Splines.cc:182:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable]
updateFunctions_Splines.cc:182:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable]
updateFunctions_Splines.cc: In function 'void updateTaus_reg(arma::mat&, arma::colvec&, const mat&, arma::urowvec&, const 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 [-Wsign-compare]
updateFunctions_Splines.cc: In function 'void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const mat&, const rowvec&, const colvec&, int, int, int, arma::urowvec&, const ucolvec&, const urowvec&, const ucolvec&, const uvec&)':
updateFunctions_Splines.cc:478:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wsign-compare]
g++ -m32 -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 -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lRlapack -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/GRENITS.buildbin-libdir/GRENITS/libs/i386
** R
** data
** 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 'GRENITS' ...
** libs
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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' [-Wunused-variable]
AR1_Gauss_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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' [-Wunused-variable]
AR1_Student_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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' [-Wunused-variable]
AR1_biocond.cc:48:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c R_C_interface.cpp -o R_C_interface.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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 [enabled by default]
D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include/armadillo_bits/lapack_bones.hpp:344:1: 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*)' [enabled by default]
commonFunctions.cc: In function 'void random_intSequence(arma::ucolvec&)':
commonFunctions.cc:270:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
commonFunctions.cc: In function 'void estimateRemainingTime(double&, double&, int, int, clock_t&)':
commonFunctions.cc:317:36: warning: variable 'so_far_clock' set but not used [-Wunused-but-set-variable]
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 [-Wsign-compare]
commonFunctions.cc:380:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
commonFunctions.cc: In function 'void updateCoefficients_reg(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&, const ucolvec&)':
commonFunctions.cc:440:59: warning: unused variable 'num_on' [-Wunused-variable]
commonFunctions.cc: In function 'void updateCoefficients(arma::mat&, const int&, const urowvec&, const mat&, const rowvec&)':
commonFunctions.cc:482:59: warning: unused variable 'num_on' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/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 colvec&, const mat&, const mat&, const mat&, const double&, const unsigned int&)':
updateFunctions_AR1.cc:128:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
updateFunctions_AR1.cc:134:11: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
updateFunctions_AR1.cc: In function 'void updateCoeffAndGibbsVars_reg(arma::mat&, arma::umat&, const colvec&, const mat&, const 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 [-Wsign-compare]
updateFunctions_AR1.cc: In function 'void calc_logMVPDF_withLinks(double&, const mat&, const rowvec&, arma::urowvec&)':
updateFunctions_AR1.cc:264:59: warning: unused variable 'num_on' [-Wunused-variable]
g++ -m64 -I"D:/biocbld/BBS-2˜1.13-/R/include" -DNDEBUG    -I"D:/biocbld/bbs-2.13-bioc/R/library/Rcpp/include" -I"D:/biocbld/bbs-2.13-bioc/R/library/RcppArmadillo/include" -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
updateFunctions_Splines.cc: In function 'void initBasesOn_rowvec(arma::urowvec&, const urowvec&, int, int)':
updateFunctions_Splines.cc:158:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable]
updateFunctions_Splines.cc:158:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable]
updateFunctions_Splines.cc: In function 'void initBasesOn(arma::urowvec&, const umat&, int, int)':
updateFunctions_Splines.cc:182:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable]
updateFunctions_Splines.cc:182:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable]
updateFunctions_Splines.cc: In function 'void updateTaus_reg(arma::mat&, arma::colvec&, const mat&, arma::urowvec&, const 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 [-Wsign-compare]
updateFunctions_Splines.cc: In function 'void updateGammaAndB_row_i_reg(arma::mat&, arma::umat&, const mat&, const rowvec&, const colvec&, int, int, int, arma::urowvec&, const ucolvec&, const urowvec&, const ucolvec&, const uvec&)':
updateFunctions_Splines.cc:478:40: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
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 [-Wsign-compare]
g++ -m64 -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 -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lRlapack -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.13-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.13-bioc/meat/GRENITS.buildbin-libdir/GRENITS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'GRENITS' as GRENITS_1.14.1.zip
* DONE (GRENITS)

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

nameusersystemelapsed
analyse.output16.38 0.0617.33
defaultParams_gauss0.030.000.03
defaultParams_linear0.050.000.05
defaultParams_nonLinear0.250.000.25
defaultParams_student0.080.000.08
function_LinearNet15.62 0.0616.15
function_NonLinearNet106.11 0.00106.82
function_ReplicatesNet_gauss28.13 0.0529.36
function_ReplicatesNet_student46.00 0.0947.20
plotPriors0.270.000.26
readChains7.530.007.54

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

nameusersystemelapsed
analyse.output11.35 0.0412.20
defaultParams_gauss0.080.000.07
defaultParams_linear0.020.020.03
defaultParams_nonLinear0.130.010.14
defaultParams_student0.050.000.04
function_LinearNet10.97 0.0012.16
function_NonLinearNet88.48 0.0389.74
function_ReplicatesNet_gauss25.89 0.0226.00
function_ReplicatesNet_student47.39 0.0948.17
plotPriors0.190.000.19
readChains6.600.026.65