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This page was generated on 2024-11-20 12:03 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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

Package 2101/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
switchBox 1.42.0  (landing page)
Bahman Afsari , Luigi Marchionni
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/switchBox
git_branch: RELEASE_3_20
git_last_commit: 174dd0f
git_last_commit_date: 2024-10-29 09:54:27 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    WARNINGS  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  


CHECK results for switchBox on teran2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:switchBox.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings switchBox_1.42.0.tar.gz
StartedAt: 2024-11-20 10:30:48 -0500 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 10:31:14 -0500 (Wed, 20 Nov 2024)
EllapsedTime: 26.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: switchBox.Rcheck
Warnings: 3

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:switchBox.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings switchBox_1.42.0.tar.gz
###
##############################################################################
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* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/switchBox.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* used C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
* 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 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 ‘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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/switchBox.Rcheck/00check.log’
for details.


Installation output

switchBox.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL switchBox
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘switchBox’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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]
   36 |     int i,j,l,countplace,pairsNo;
      |                          ^~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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]
   49 |     double score1, score2, type;
      |            ^~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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:22:25: warning: variable ‘countplace’ set but not used [-Wunused-but-set-variable]
   22 |                 int i,l,countplace,pairsNo;
      |                         ^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-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:25:25: warning: unused variable ‘countplace’ [-Wunused-variable]
   25 |                 int i,l,countplace,pairsNo;
      |                         ^~~~~~~~~~
CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:35:24: warning: unused variable ‘score1’ [-Wunused-variable]
   35 |                 double score1, score2, type;
      |                        ^~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall -c rinit.c -o rinit.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -Wall  -c vect2compC.cc -o vect2compC.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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.Classify0.0290.0040.033
KTSP.Train0.0040.0010.005
SWAP.Calculate.BasicTSPScores0.0020.0000.002
SWAP.Calculate.SignedTSPScores0.0030.0000.003
SWAP.CalculateScores0.0170.0000.017
SWAP.CalculateSignedScore0.0140.0000.014
SWAP.Filter.Wilcoxon0.0090.0000.009
SWAP.GetKTSP.PredictionStats0.0220.0030.025
SWAP.GetKTSP.Result0.0250.0000.025
SWAP.GetKTSP.TrainTestResults0.0340.0000.034
SWAP.KTSP.CV0.1150.0000.115
SWAP.KTSP.Classify0.0220.0020.023
SWAP.KTSP.LOO2.3460.0222.371
SWAP.KTSP.Statistic0.0640.0050.069
SWAP.KTSP.Train0.1430.0010.144
SWAP.MakeTSPTable0.0080.0010.009
SWAP.PlotKTSP.GenePairBoxplot0.0240.0010.025
SWAP.PlotKTSP.GenePairClassesBoxplot0.0280.0050.033
SWAP.PlotKTSP.GenePairScatter0.0240.0000.023
SWAP.PlotKTSP.Genes0.0220.0010.023
SWAP.PlotKTSP.TrainTestROC0.0390.0020.041
SWAP.Train.1TSP0.020.000.02
SWAP.Train.KTSP0.0400.0010.041
matTesting0.0020.0000.002
matTraining0.0000.0010.001
testingGroup0.0020.0000.002
trainingGroup0.0010.0010.001