Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 13:30:16 -0400 (Tue, 09 Apr 2019).
Package 1586/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
switchBox 1.19.0 Bahman Afsari
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: switchBox |
Version: 1.19.0 |
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_1.19.0.tar.gz |
StartedAt: 2019-04-09 04:02:59 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 04:03:46 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 46.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: switchBox.Rcheck |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running 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_1.19.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/switchBox.Rcheck’ * using R Under development (unstable) (2018-11-27 r75683) * 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 ‘1.19.0’ * 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 5.913 0.088 6.06 * 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.
switchBox.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL switchBox ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘switchBox’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 -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 -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 -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 -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 -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/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 * DONE (switchBox)
switchBox.Rcheck/switchBox-Ex.timings
name | user | system | elapsed | |
KTSP.Classify | 0.040 | 0.005 | 0.047 | |
KTSP.Train | 0.011 | 0.002 | 0.013 | |
SWAP.Calculate.BasicTSPScores | 0.007 | 0.001 | 0.009 | |
SWAP.Calculate.SignedTSPScores | 0.007 | 0.001 | 0.009 | |
SWAP.CalculateScores | 0.038 | 0.003 | 0.041 | |
SWAP.CalculateSignedScore | 0.031 | 0.003 | 0.105 | |
SWAP.Filter.Wilcoxon | 0.017 | 0.003 | 0.021 | |
SWAP.GetKTSP.PredictionStats | 0.069 | 0.005 | 0.075 | |
SWAP.GetKTSP.Result | 0.045 | 0.003 | 0.049 | |
SWAP.GetKTSP.TrainTestResults | 0.107 | 0.005 | 0.113 | |
SWAP.KTSP.CV | 0.284 | 0.009 | 0.297 | |
SWAP.KTSP.Classify | 0.063 | 0.006 | 0.070 | |
SWAP.KTSP.LOO | 5.913 | 0.088 | 6.060 | |
SWAP.KTSP.Statistic | 0.159 | 0.006 | 0.168 | |
SWAP.KTSP.Train | 0.499 | 0.006 | 0.514 | |
SWAP.MakeTSPTable | 0.016 | 0.001 | 0.017 | |
SWAP.PlotKTSP.GenePairBoxplot | 0.053 | 0.004 | 0.058 | |
SWAP.PlotKTSP.GenePairClassesBoxplot | 0.053 | 0.002 | 0.057 | |
SWAP.PlotKTSP.GenePairScatter | 0.048 | 0.004 | 0.052 | |
SWAP.PlotKTSP.Genes | 0.045 | 0.003 | 0.049 | |
SWAP.PlotKTSP.TrainTestROC | 0.078 | 0.003 | 0.082 | |
SWAP.Train.1TSP | 0.050 | 0.002 | 0.052 | |
SWAP.Train.KTSP | 0.114 | 0.002 | 0.117 | |
matTesting | 0.003 | 0.001 | 0.004 | |
matTraining | 0.002 | 0.001 | 0.004 | |
testingGroup | 0.004 | 0.001 | 0.005 | |
trainingGroup | 0.003 | 0.002 | 0.004 | |