Package: switchBox

Version: 1.20.0

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_1.20.0.tar.gz

StartedAt: 2019-10-16 07:17:21 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 07:18:24 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 63.7 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_1.20.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/switchBox.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.20.0’
* 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 7.04  0.239   7.281
* 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-3.9-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/3.6/Resources/library’
* installing *source* package ‘switchBox’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c CalculateSignedScoreRestrictedPairsCoreTieHandler.cc -o CalculateSignedScoreRestrictedPairsCoreTieHandler.o
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:35:10: warning: unused variable 'score1' [-Wunused-variable]
                double score1, score2, type;
                       ^
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:25:11: warning: unused variable 'countplace' [-Wunused-variable]
                int i,l,countplace,pairsNo;
                        ^
2 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c rinit.c -o rinit.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c vect2compC.cc -o vect2compC.o
clang++ -std=gnu++11 -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/3.6/Resources/library/00LOCK-switchBox/00new/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 from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (switchBox)

name	user	system	elapsed
KTSP.Classify	0.046	0.010	0.058
KTSP.Train	0.014	0.005	0.020
SWAP.Calculate.BasicTSPScores	0.006	0.002	0.007
SWAP.Calculate.SignedTSPScores	0.010	0.003	0.013
SWAP.CalculateScores	0.057	0.006	0.063
SWAP.CalculateSignedScore	0.043	0.008	0.052
SWAP.Filter.Wilcoxon	0.028	0.005	0.033
SWAP.GetKTSP.PredictionStats	0.073	0.013	0.086
SWAP.GetKTSP.Result	0.075	0.008	0.084
SWAP.GetKTSP.TrainTestResults	0.109	0.009	0.119
SWAP.KTSP.CV	0.301	0.011	0.312
SWAP.KTSP.Classify	0.077	0.010	0.087
SWAP.KTSP.LOO	7.040	0.239	7.281
SWAP.KTSP.Statistic	0.200	0.023	0.222
SWAP.KTSP.Train	0.732	0.018	0.749
SWAP.MakeTSPTable	0.025	0.003	0.028
SWAP.PlotKTSP.GenePairBoxplot	0.072	0.006	0.078
SWAP.PlotKTSP.GenePairClassesBoxplot	0.067	0.006	0.072
SWAP.PlotKTSP.GenePairScatter	0.064	0.010	0.075
SWAP.PlotKTSP.Genes	0.055	0.003	0.059
SWAP.PlotKTSP.TrainTestROC	0.086	0.006	0.093
SWAP.Train.1TSP	0.032	0.002	0.034
SWAP.Train.KTSP	0.099	0.010	0.108
matTesting	0.004	0.003	0.007
matTraining	0.003	0.002	0.004
testingGroup	0.005	0.003	0.008
trainingGroup	0.003	0.003	0.005