Multiple platform build/check report for BioC 3.20 - CHECK results for switchBox on merida1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 merida1

To the developers/maintainers of the switchBox package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: switchBox

Version: 1.42.0

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_1.42.0.tar.gz

StartedAt: 2024-12-20 10:32:12 -0500 (Fri, 20 Dec 2024)

EndedAt: 2024-12-20 10:33:32 -0500 (Fri, 20 Dec 2024)

EllapsedTime: 79.8 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_1.42.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/switchBox.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘switchBox/DESCRIPTION’ ... OK
* this is package ‘switchBox’ version ‘1.42.0’
* 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
* used C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 code 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
checkRd: (-1) matTesting.Rd:24: Lost braces
    24 |   Group information (emph{``bad'' versus ``good'' }prognosis)
       |                          ^
checkRd: (-1) matTraining.Rd:24: Lost braces
    24 |   Group information (emph{``bad'' versus ``good'' }prognosis)
       |                          ^
checkRd: (-1) switchBox-package.Rd:27-28: Lost braces
    27 |   {B)  Compute the scores for all available feature pairs
       |   ^
checkRd: (-1) switchBox-package.Rd:30-31: Lost braces
    30 |   {C)  Compute the scores for selected feature pairs
       |   ^
checkRd: (-1) switchBox-package.Rd:33: Lost braces; missing escapes or markup?
    33 |   {D)  Identify the number of $K$ TSP to be used in the final classifier using the analysis of variance;}
       |   ^
checkRd: (-1) switchBox-package.Rd:35-36: Lost braces
    35 |   {E)  Compute individual TSP votes for one class or the other 
       |   ^
checkRd: (-1) switchBox-package.Rd:38-39: Lost braces
    38 |   {F)  Classify new samples based on the top KTSP 
       |   ^
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Package unavailable to check Rd xrefs: ‘mammaPrintData’
Missing link or links in Rd file '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 Rd file 'SWAP.Kby.Measurement.Rd':
  k_opts = list(disjoint = TRUE, measurement = "auc")

Undocumented arguments in Rd file 'SWAP.PlotKTSP.GenePairScatter.Rd'
  ‘...’

Undocumented arguments in Rd file 'SWAP.PlotKTSP.Genes.Rd'
  ‘colors’ ‘legends’ ‘...’

Undocumented arguments in Rd file 'SWAP.PlotKTSP.TrainTestROC.Rd'
  ‘...’

Undocumented arguments in Rd file 'SWAP.PlotKTSP.Votes.Rd'
  ‘...’

Bad \usage lines found in Rd file 'SWAP.Kby.Measurement.Rd':
  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 9.858  0.137  11.762
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.20-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/4.4-x86_64/Resources/library’
* installing *source* package ‘switchBox’ ...
** using staged installation
** libs
using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CalculateSignedScoreCore.cc -o CalculateSignedScoreCore.o
CalculateSignedScoreCore.cc:36:26: warning: variable 'pairsNo' set but not used [-Wunused-but-set-variable]
    int i,j,l,countplace,pairsNo;
                         ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -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++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c CalculateSignedScoreRestrictedPairsCore.cc -o CalculateSignedScoreRestrictedPairsCore.o
CalculateSignedScoreRestrictedPairsCore.cc:22:11: warning: variable 'countplace' set but not used [-Wunused-but-set-variable]
                int i,l,countplace,pairsNo;
                        ^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -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 -arch x86_64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rinit.c -o rinit.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c vect2compC.cc -o vect2compC.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.4-x86_64/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

name	user	system	elapsed
KTSP.Classify	0.094	0.018	0.114
KTSP.Train	0.015	0.005	0.021
SWAP.Calculate.BasicTSPScores	0.008	0.003	0.011
SWAP.Calculate.SignedTSPScores	0.012	0.004	0.017
SWAP.CalculateScores	0.064	0.005	0.070
SWAP.CalculateSignedScore	0.056	0.007	0.064
SWAP.Filter.Wilcoxon	0.035	0.006	0.041
SWAP.GetKTSP.PredictionStats	0.088	0.008	0.098
SWAP.GetKTSP.Result	0.097	0.007	0.106
SWAP.GetKTSP.TrainTestResults	0.145	0.011	0.157
SWAP.KTSP.CV	0.488	0.014	0.508
SWAP.KTSP.Classify	0.081	0.009	0.092
SWAP.KTSP.LOO	9.858	0.137	11.762
SWAP.KTSP.Statistic	0.273	0.027	0.368
SWAP.KTSP.Train	0.574	0.013	0.654
SWAP.MakeTSPTable	0.034	0.004	0.045
SWAP.PlotKTSP.GenePairBoxplot	0.097	0.005	0.123
SWAP.PlotKTSP.GenePairClassesBoxplot	0.095	0.005	0.114
SWAP.PlotKTSP.GenePairScatter	0.083	0.004	0.097
SWAP.PlotKTSP.Genes	0.092	0.006	0.111
SWAP.PlotKTSP.TrainTestROC	0.143	0.008	0.170
SWAP.Train.1TSP	0.083	0.004	0.100
SWAP.Train.KTSP	0.158	0.007	0.193
matTesting	0.004	0.004	0.008
matTraining	0.003	0.004	0.017
testingGroup	0.004	0.003	0.012
trainingGroup	0.003	0.003	0.006