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BioC 2.12: CHECK report for GRENITS on george2

This page was generated on 2013-10-09 09:37:46 -0700 (Wed, 09 Oct 2013).

Package 299/671HostnameOS / ArchBUILDCHECKBUILD BIN
GRENITS 1.12.0
Edward Morrissey
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/GRENITS
Last Changed Rev: 75263 / Revision: 81334
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: GRENITS
Version: 1.12.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings GRENITS_1.12.0.tar.gz
StartedAt: 2013-10-09 02:25:45 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 02:31:46 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 360.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GRENITS.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/GRENITS.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GRENITS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GRENITS’ version ‘1.12.0’
* 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 ... [113s/114s] OK
* checking installed package size ... NOTE
  installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
* 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 ‘/home/biocbuild/bbs-2.12-bioc/meat/GRENITS.Rcheck/GRENITS/libs/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 installed files from ‘inst/doc’ ... OK
* checking examples ... [201s/203s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
function_NonLinearNet          96.102  0.156  97.158
function_ReplicatesNet_student 42.771  0.268  43.851
function_ReplicatesNet_gauss   25.638  0.192  26.572
analyse.output                 12.812  0.124  13.220
function_LinearNet             12.549  0.068  12.629
readChains                      6.532  0.040   6.575
* 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 3 notes.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/GRENITS.Rcheck/00check.log’
for details.

GRENITS.Rcheck/00install.out:

* installing *source* package ‘GRENITS’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c R_C_interface.cpp -o R_C_interface.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -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]
/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include/armadillo_bits/lapack_bones.hpp:324:1: 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++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -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++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-2.12-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -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++ -shared -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 -L/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-2.12-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/GRENITS.Rcheck/GRENITS/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GRENITS)

GRENITS.Rcheck/GRENITS-Ex.timings:

nameusersystemelapsed
analyse.output12.812 0.12413.220
defaultParams_gauss0.0640.0000.066
defaultParams_linear0.0720.0120.083
defaultParams_nonLinear0.2640.0080.274
defaultParams_student0.1080.0080.118
function_LinearNet12.549 0.06812.629
function_NonLinearNet96.102 0.15697.158
function_ReplicatesNet_gauss25.638 0.19226.572
function_ReplicatesNet_student42.771 0.26843.851
plotPriors0.440.000.44
readChains6.5320.0406.575