Package: switchBox

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:switchBox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings switchBox_1.16.0.tar.gz

StartedAt: 2018-10-17 00:21:21 -0400 (Wed, 17 Oct 2018)

EndedAt: 2018-10-17 00:22:14 -0400 (Wed, 17 Oct 2018)

EllapsedTime: 53.3 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: switchBox.Rcheck

Warnings: 3

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:switchBox.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings switchBox_1.16.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/switchBox.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘switchBox/DESCRIPTION’ ... OK
* this is package ‘switchBox’ version ‘1.16.0’
* 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 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 ... NOTE
Note: information on .o files is not available
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
SWAP.KTSP.LOO 5.573  0.113   5.734
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/switchBox.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL switchBox
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘switchBox’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c CalculateSignedScoreCoreTieHandler.cc -o CalculateSignedScoreCoreTieHandler.o
CalculateSignedScoreCoreTieHandler.cc:49:12: warning: unused variable 'score1' [-Wunused-variable]
    double score1, score2, type;
           ^
1 warning generated.
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c CalculateSignedScoreRestrictedPairsCoreTieHandler.cc -o CalculateSignedScoreRestrictedPairsCoreTieHandler.o
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;
                       ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rinit.c -o rinit.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c vect2compC.cc -o vect2compC.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o switchBox.so CalculateSignedScoreCore.o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCoreTieHandler.o rinit.o vect2compC.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/switchBox/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (switchBox)

name	user	system	elapsed
KTSP.Classify	0.045	0.005	0.052
KTSP.Train	0.016	0.002	0.018
SWAP.Calculate.BasicTSPScores	0.009	0.002	0.011
SWAP.Calculate.SignedTSPScores	0.008	0.002	0.009
SWAP.CalculateScores	0.040	0.008	0.047
SWAP.CalculateSignedScore	0.043	0.008	0.051
SWAP.Filter.Wilcoxon	0.026	0.005	0.031
SWAP.GetKTSP.PredictionStats	0.043	0.008	0.052
SWAP.GetKTSP.Result	0.046	0.003	0.049
SWAP.GetKTSP.TrainTestResults	0.075	0.004	0.082
SWAP.KTSP.CV	0.255	0.010	0.267
SWAP.KTSP.Classify	0.043	0.005	0.048
SWAP.KTSP.LOO	5.573	0.113	5.734
SWAP.KTSP.Statistic	0.190	0.007	0.197
SWAP.KTSP.Train	0.595	0.005	0.602
SWAP.MakeTSPTable	0.017	0.001	0.018
SWAP.PlotKTSP.GenePairBoxplot	0.055	0.003	0.060
SWAP.PlotKTSP.GenePairClassesBoxplot	0.057	0.003	0.062
SWAP.PlotKTSP.GenePairScatter	0.052	0.002	0.060
SWAP.PlotKTSP.Genes	0.051	0.003	0.053
SWAP.PlotKTSP.TrainTestROC	0.073	0.003	0.076
SWAP.Train.1TSP	0.032	0.002	0.033
SWAP.Train.KTSP	0.120	0.003	0.124
matTesting	0.005	0.001	0.006
matTraining	0.004	0.001	0.005
testingGroup	0.005	0.001	0.006
trainingGroup	0.003	0.001	0.004