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CHECK report for switchBox on malbec1

This page was generated on 2018-04-12 13:12:37 -0400 (Thu, 12 Apr 2018).

Package 1377/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
switchBox 1.14.0
Bahman Afsari , Luigi Marchionni
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/switchBox
Branch: RELEASE_3_6
Last Commit: 49e776a
Last Changed Date: 2017-10-30 12:40:34 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: switchBox
Version: 1.14.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings switchBox_1.14.0.tar.gz
StartedAt: 2018-04-12 03:15:34 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:16:12 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 37.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: switchBox.Rcheck
Warnings: 3

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings switchBox_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/switchBox.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘switchBox/DESCRIPTION’ ... OK
* this is package ‘switchBox’ version ‘1.14.0’
* 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 ‘switchBox’ 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
* 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
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘KTSP.CalculateSignedScore’ ‘KTSP.tiedRank’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotGenePairBoxplot: no visible global function definition for
  ‘boxplot’
plotGenePairBoxplot: no visible global function definition for
  ‘stripchart’
plotGenePairBoxplot: no visible global function definition for ‘legend’
plotGenePairBoxplot: no visible global function definition for ‘grid’
plotGenePairClassesBoxplot: no visible global function definition for
  ‘boxplot’
plotGenePairClassesBoxplot: no visible global function definition for
  ‘axis’
plotGenePairClassesBoxplot: no visible global function definition for
  ‘legend’
plotGenePairClassesBoxplot: no visible global function definition for
  ‘abline’
plotGenePairClassesBoxplot: no visible global function definition for
  ‘grid’
plotGenePairScatter: no visible global function definition for ‘plot’
plotGenePairScatter: no visible global function definition for ‘abline’
plotGenePairScatter: no visible global function definition for ‘grid’
plotGenePairScatter: no visible global function definition for ‘legend’
plotGenes: no visible global function definition for ‘plot’
plotGenes: no visible global function definition for ‘lines’
plotGenes: no visible global function definition for ‘grid’
plotGenes: no visible global function definition for ‘abline’
plotGenes: no visible global function definition for ‘legend’
plotkTSPTrainTestROC: no visible global function definition for ‘plot’
plotkTSPTrainTestROC: no visible global function definition for ‘lines’
plotkTSPTrainTestROC: no visible global function definition for
  ‘legend’
plotkTSPTrainTestROC: no visible global function definition for ‘grid’
plotkTSPVotes: no visible global function definition for ‘plot.new’
Undefined global functions or variables:
  abline axis boxplot grid legend lines plot plot.new stripchart
Consider adding
  importFrom("graphics", "abline", "axis", "boxplot", "grid", "legend",
             "lines", "plot", "plot.new", "stripchart")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: SWAP.Kby.Measurement.Rd:70-72: Dropping empty section \examples
prepare_Rd: SWAP.Kby.Ttest.Rd:64-66: Dropping empty section \examples
prepare_Rd: SWAP.PlotKTSP.Votes.Rd:54-56: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Package unavailable to check Rd xrefs: ‘mammaPrintData’
Missing link or links in documentation object 'SWAP.PlotKTSP.TrainTestROC.Rd':
  ‘SWAP.GetkTSPTrainTestResults’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘SWAP.GetKFoldIndices’ ‘SWAP.MakeTrainTestData’
  ‘SWAP.ScoreMatrixToVector’ ‘SWAP.ScoreVectorToMatrix’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'SWAP.Kby.Measurement':
  k_opts = list(disjoint = TRUE, measurement = "auc")

Undocumented arguments in documentation object 'SWAP.PlotKTSP.GenePairScatter'
  ‘...’

Undocumented arguments in documentation object 'SWAP.PlotKTSP.Genes'
  ‘colors’ ‘legends’ ‘...’

Undocumented arguments in documentation object 'SWAP.PlotKTSP.TrainTestROC'
  ‘...’

Undocumented arguments in documentation object 'SWAP.PlotKTSP.Votes'
  ‘...’

Bad \usage lines found in documentation object 'SWAP.Kby.Measurement':
  SWAP.Kby.Measurement(inputMat, phenoGroup, 
    scoreTable, classes, krange, 

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/switchBox.Rcheck/00check.log’
for details.



Installation output

switchBox.Rcheck/00install.out

* installing *source* package ‘switchBox’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o
CalculateSignedScoreCore.cc: In function ‘void CalculateSignedScoreCore(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*, double*, double*, double*)’:
CalculateSignedScoreCore.cc:36:26: warning: variable ‘pairsNo’ set but not used [-Wunused-but-set-variable]
     int i,j,l,countplace,pairsNo;
                          ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c CalculateSignedScoreCoreTieHandler.cc -o CalculateSignedScoreCoreTieHandler.o
CalculateSignedScoreCoreTieHandler.cc: In function ‘void CalculateSignedScoreCoreTieHandler(int*, int*, double*, int*, double*, int*, double*, double*, double*, double*)’:
CalculateSignedScoreCoreTieHandler.cc:49:12: warning: unused variable ‘score1’ [-Wunused-variable]
     double score1, score2, type;
            ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o
CalculateSignedScoreRestrictedPairsCore.cc: In function ‘void CalculateSignedScoreRestrictedPairsCore(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*)’:
CalculateSignedScoreRestrictedPairsCore.cc:22:11: warning: variable ‘countplace’ set but not used [-Wunused-but-set-variable]
   int i,l,countplace,pairsNo;
           ^
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c CalculateSignedScoreRestrictedPairsCoreTieHandler.cc -o CalculateSignedScoreRestrictedPairsCoreTieHandler.o
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc: In function ‘void CalculateSignedScoreRestrictedPairsCoreTieHandler(int*, int*, double*, int*, double*, int*, int*, int*, int*, double*, double*, double*, double*)’:
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:25:11: warning: unused variable ‘countplace’ [-Wunused-variable]
   int i,l,countplace,pairsNo;
           ^
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:35:10: warning: unused variable ‘score1’ [-Wunused-variable]
   double score1, score2, type;
          ^
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rinit.c -o rinit.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c vect2compC.cc -o vect2compC.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o switchBox.so CalculateSignedScoreCore.o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCoreTieHandler.o rinit.o vect2compC.o -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/switchBox.Rcheck/switchBox/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 (switchBox)

Tests output


Example timings

switchBox.Rcheck/switchBox-Ex.timings

nameusersystemelapsed
KTSP.Classify0.0320.0040.037
KTSP.Train0.1080.0000.106
SWAP.Calculate.BasicTSPScores0.0160.0000.015
SWAP.Calculate.SignedTSPScores0.0040.0000.004
SWAP.CalculateScores0.1080.0000.110
SWAP.CalculateSignedScore0.0400.0040.044
SWAP.Filter.Wilcoxon0.0360.0000.036
SWAP.GetKTSP.PredictionStats0.0840.0000.085
SWAP.GetKTSP.Result0.3880.0000.388
SWAP.GetKTSP.TrainTestResults0.0640.0000.065
SWAP.KTSP.CV0.2520.0000.250
SWAP.KTSP.Classify0.0400.0000.039
SWAP.KTSP.LOO3.4160.0003.420
SWAP.KTSP.Statistic0.1640.0000.165
SWAP.KTSP.Train0.3120.0000.313
SWAP.MakeTSPTable0.0200.0000.017
SWAP.PlotKTSP.GenePairBoxplot0.0280.0000.031
SWAP.PlotKTSP.GenePairClassesBoxplot0.0320.0000.035
SWAP.PlotKTSP.GenePairScatter0.0280.0040.031
SWAP.PlotKTSP.Genes0.0320.0000.031
SWAP.PlotKTSP.TrainTestROC0.1120.0000.112
SWAP.Train.1TSP0.0240.0000.025
SWAP.Train.KTSP0.060.000.06
matTesting0.0040.0000.004
matTraining0.0040.0000.002
testingGroup0.0040.0000.003
trainingGroup0.0040.0000.002