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This page was generated on 2022-04-13 12:08:53 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for switchBox on machv2


To the developers/maintainers of the switchBox package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/switchBox.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1916/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
switchBox 1.30.0  (landing page)
Bahman Afsari , Luigi Marchionni
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/switchBox
git_branch: RELEASE_3_14
git_last_commit: 1b69b16
git_last_commit_date: 2021-10-26 12:15:40 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: switchBox
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:switchBox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings switchBox_1.30.0.tar.gz
StartedAt: 2022-04-12 19:12:08 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:13:08 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 60.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: switchBox.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:switchBox.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings switchBox_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/switchBox.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘switchBox/DESCRIPTION’ ... OK
* this is package ‘switchBox’ version ‘1.30.0’
* 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 ‘abline’
plotGenePairScatter: no visible global function definition for ‘grid’
plotGenePairScatter: no visible global function definition for ‘legend’
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 ‘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.new stripchart
Consider adding
  importFrom("graphics", "abline", "axis", "boxplot", "grid", "legend",
             "lines", "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 (user + system) or elapsed time > 5s
               user system elapsed
SWAP.KTSP.LOO 7.627  0.087   7.718
* 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-3.14-bioc/meat/switchBox.Rcheck/00check.log’
for details.



Installation output

switchBox.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL switchBox
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘switchBox’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -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 -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rinit.c -o rinit.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c vect2compC.cc -o vect2compC.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -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/4.1/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)

Tests output


Example timings

switchBox.Rcheck/switchBox-Ex.timings

nameusersystemelapsed
KTSP.Classify0.0520.0120.064
KTSP.Train0.0140.0050.018
SWAP.Calculate.BasicTSPScores0.0070.0030.011
SWAP.Calculate.SignedTSPScores0.0100.0030.013
SWAP.CalculateScores0.0560.0050.061
SWAP.CalculateSignedScore0.0310.0060.037
SWAP.Filter.Wilcoxon0.0220.0040.027
SWAP.GetKTSP.PredictionStats0.0580.0070.065
SWAP.GetKTSP.Result0.0850.0060.092
SWAP.GetKTSP.TrainTestResults0.1260.0090.134
SWAP.KTSP.CV0.3880.0080.396
SWAP.KTSP.Classify0.0750.0080.084
SWAP.KTSP.LOO7.6270.0877.718
SWAP.KTSP.Statistic0.2280.0170.245
SWAP.KTSP.Train0.5700.0090.579
SWAP.MakeTSPTable0.0240.0020.027
SWAP.PlotKTSP.GenePairBoxplot0.0460.0020.049
SWAP.PlotKTSP.GenePairClassesBoxplot0.0630.0040.068
SWAP.PlotKTSP.GenePairScatter0.0600.0030.063
SWAP.PlotKTSP.Genes0.0650.0020.067
SWAP.PlotKTSP.TrainTestROC0.0810.0060.089
SWAP.Train.1TSP0.0600.0020.062
SWAP.Train.KTSP0.1280.0050.132
matTesting0.0040.0030.007
matTraining0.0020.0020.004
testingGroup0.0030.0020.004
trainingGroup0.0020.0010.003