Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:46 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
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 2072/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
switchBox 1.41.0 (landing page) Bahman Afsari
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: switchBox |
Version: 1.41.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:switchBox.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings switchBox_1.41.0.tar.gz |
StartedAt: 2024-08-21 09:47:41 -0000 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 09:48:17 -0000 (Wed, 21 Aug 2024) |
EllapsedTime: 36.1 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: switchBox.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:switchBox.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings switchBox_1.41.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/switchBox.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘switchBox/DESCRIPTION’ ... OK * this is package ‘switchBox’ version ‘1.41.0’ * 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 (GCC) 10.3.1’ * used C++ compiler: ‘g++ (GCC) 10.3.1’ * 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed SWAP.KTSP.LOO 5.6 0.003 5.616 * 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 ‘/home/biocbuild/bbs-3.20-bioc/meat/switchBox.Rcheck/00check.log’ for details.
switchBox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL switchBox ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’ * installing *source* package ‘switchBox’ ... ** using staged installation ** libs using C compiler: ‘gcc (GCC) 10.3.1’ using C++ compiler: ‘g++ (GCC) 10.3.1’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/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/R/R-4.4.1/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:22:11: warning: variable ‘countplace’ set but not used [-Wunused-but-set-variable] 22 | int i,l,countplace,pairsNo; | ^~~~~~~~~~ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/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:25:11: warning: unused variable ‘countplace’ [-Wunused-variable] 25 | int i,l,countplace,pairsNo; | ^~~~~~~~~~ CalculateSignedScoreRestrictedPairsCoreTieHandler.cc:35:10: warning: unused variable ‘score1’ [-Wunused-variable] 35 | double score1, score2, type; | ^~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c rinit.c -o rinit.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fPIC -g -O2 -Wall -c vect2compC.cc -o vect2compC.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o switchBox.so CalculateSignedScoreCore.o CalculateSignedScoreCoreTieHandler.o CalculateSignedScoreRestrictedPairsCore.o CalculateSignedScoreRestrictedPairsCoreTieHandler.o rinit.o vect2compC.o -L/home/biocbuild/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/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)
switchBox.Rcheck/switchBox-Ex.timings
name | user | system | elapsed | |
KTSP.Classify | 0.063 | 0.001 | 0.063 | |
KTSP.Train | 0.009 | 0.000 | 0.009 | |
SWAP.Calculate.BasicTSPScores | 0.004 | 0.000 | 0.005 | |
SWAP.Calculate.SignedTSPScores | 0.006 | 0.000 | 0.006 | |
SWAP.CalculateScores | 0.038 | 0.000 | 0.038 | |
SWAP.CalculateSignedScore | 0.032 | 0.000 | 0.032 | |
SWAP.Filter.Wilcoxon | 0.018 | 0.000 | 0.018 | |
SWAP.GetKTSP.PredictionStats | 0.054 | 0.000 | 0.054 | |
SWAP.GetKTSP.Result | 0.061 | 0.000 | 0.061 | |
SWAP.GetKTSP.TrainTestResults | 0.083 | 0.000 | 0.083 | |
SWAP.KTSP.CV | 0.287 | 0.000 | 0.287 | |
SWAP.KTSP.Classify | 0.050 | 0.000 | 0.049 | |
SWAP.KTSP.LOO | 5.600 | 0.003 | 5.616 | |
SWAP.KTSP.Statistic | 0.136 | 0.004 | 0.140 | |
SWAP.KTSP.Train | 0.313 | 0.004 | 0.319 | |
SWAP.MakeTSPTable | 0.016 | 0.000 | 0.016 | |
SWAP.PlotKTSP.GenePairBoxplot | 0.050 | 0.000 | 0.049 | |
SWAP.PlotKTSP.GenePairClassesBoxplot | 0.062 | 0.000 | 0.063 | |
SWAP.PlotKTSP.GenePairScatter | 0.046 | 0.000 | 0.046 | |
SWAP.PlotKTSP.Genes | 0.047 | 0.000 | 0.047 | |
SWAP.PlotKTSP.TrainTestROC | 0.084 | 0.000 | 0.084 | |
SWAP.Train.1TSP | 0.041 | 0.000 | 0.041 | |
SWAP.Train.KTSP | 0.088 | 0.000 | 0.088 | |
matTesting | 0.002 | 0.000 | 0.003 | |
matTraining | 0.002 | 0.000 | 0.002 | |
testingGroup | 0.003 | 0.000 | 0.003 | |
trainingGroup | 0.002 | 0.000 | 0.001 | |