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BioC 3.0: CHECK report for GRENITS on zin1

This page was generated on 2015-04-10 09:39:28 -0700 (Fri, 10 Apr 2015).

Package 404/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRENITS 1.18.0
Edward Morrissey
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/GRENITS
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: GRENITS
Version: 1.18.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GRENITS_1.18.0.tar.gz
StartedAt: 2015-04-10 00:49:19 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:53:40 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 260.9 seconds
RetCode: 0
Status:  OK 
CheckDir: GRENITS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings GRENITS_1.18.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/GRENITS.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.18.0’
* 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 ... [76s/80s] OK
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
* 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
* 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 loading without being on the library search path ... 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.
* 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 global function definition for ‘ggplot’
.heatMap.ggplot: no visible global function definition for ‘aes’
.heatMap.ggplot: no visible binding for global variable ‘Var2’
.heatMap.ggplot: no visible binding for global variable ‘Var1’
.heatMap.ggplot: no visible global function definition for ‘geom_tile’
.heatMap.ggplot: no visible binding for global variable ‘value’
.heatMap.ggplot: no visible global function definition for
  ‘scale_fill_gradient’
.heatMap.ggplot: no visible global function definition for ‘theme’
.heatMap.ggplot: no visible global function definition for
  ‘element_blank’
.heatMap.ggplot: no visible global function definition for
  ‘element_text’
.heatMap.ggplot: no visible global function definition for ‘ggtitle’
.heatMap.ggplot: no visible global function definition for ‘labs’
.heatMap.ggplot: no visible global function definition for
  ‘scale_x_discrete’
.heatMap.ggplot: no visible global function definition for
  ‘scale_y_discrete’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘ggplot’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘aes’
.plotDistribParents.LargeMat: no visible binding for global variable
  ‘variable’
.plotDistribParents.LargeMat: no visible binding for global variable
  ‘GeneNames’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘geom_tile’
.plotDistribParents.LargeMat: no visible binding for global variable
  ‘value’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘scale_fill_gradient’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘theme’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘element_blank’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘element_text’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘ggtitle’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘labs’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘scale_x_discrete’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘scale_y_discrete’
.plotDistribParents.LargeMat: no visible global function definition for
  ‘facet_wrap’
* 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [149s/155s] OK
Examples with CPU or elapsed time > 5s
                                 user system elapsed
function_NonLinearNet          74.744  0.100  76.963
function_ReplicatesNet_student 30.801  0.092  31.672
function_ReplicatesNet_gauss   19.042  0.080  20.484
analyse.output                  9.084  0.052  10.278
function_LinearNet              9.009  0.028   9.190
* 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
* DONE

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/GRENITS.Rcheck/00check.log’
for details.

GRENITS.Rcheck/00install.out:

* installing *source* package ‘GRENITS’ ...
** libs
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c R_C_interface.cpp -o R_C_interface.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c commonFunctions.cc -o commonFunctions.o
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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c functionsErrorModel.cc -o functionsErrorModel.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-bioc/R/library/RcppArmadillo/include"   -fpic  -g -O2  -Wall -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
g++ -I/home/biocbuild/bbs-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-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-3.0-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.0-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.0-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/home/biocbuild/bbs-3.0-bioc/R/lib -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-3.0-bioc/R/lib -lRlapack -L/home/biocbuild/bbs-3.0-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -L/home/biocbuild/bbs-3.0-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.0-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.output 9.084 0.05210.278
defaultParams_gauss0.0160.0000.018
defaultParams_linear0.0240.0000.022
defaultParams_nonLinear0.1360.0000.135
defaultParams_student0.0480.0000.047
function_LinearNet9.0090.0289.190
function_NonLinearNet74.744 0.10076.963
function_ReplicatesNet_gauss19.042 0.08020.484
function_ReplicatesNet_student30.801 0.09231.672
plotPriors0.1160.0080.124
readChains4.3130.0204.449