Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
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 |
Package 359/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ClassifyR 3.10.4 (landing page) Dario Strbenac
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the ClassifyR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ClassifyR.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. |
Package: ClassifyR |
Version: 3.10.4 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClassifyR_3.10.4.tar.gz |
StartedAt: 2024-12-20 01:11:11 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 01:22:17 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 665.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: ClassifyR.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings ClassifyR_3.10.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/ClassifyR.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 ‘ClassifyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ClassifyR’ version ‘3.10.4’ * package encoding: UTF-8 * 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 ‘ClassifyR’ can be installed ... WARNING Found the following significant warnings: coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:529:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:569:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:656:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ClassifyR.Rcheck/00install.out’ for details. * used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .addUserLevels: no visible binding for global variable ‘median’ .dmvnorm_diag: no visible global function definition for ‘dnorm’ .doSelection : <anonymous> : <anonymous>: no visible global function definition for ‘setNames’ .doSelection : <anonymous> : <anonymous>: no visible global function definition for ‘na.omit’ .doSelection : <anonymous> : <anonymous>: no visible global function definition for ‘median’ .doSelection : <anonymous>: no visible binding for global variable ‘trainParams’ .doSelection : <anonymous>: no visible binding for global variable ‘predictParams’ .doSelection : <anonymous>: no visible binding for global variable ‘measurementsSubset’ .doSelection : <anonymous>: no visible global function definition for ‘median’ .doSelection : <anonymous>: no visible binding for global variable ‘aResult’ .doSelection: no visible binding for global variable ‘featuresLists’ .doTrain : <anonymous>: no visible global function definition for ‘median’ .filterCharacteristics: no visible global function definition for ‘na.omit’ .getFeaturesStrings : <anonymous>: no visible global function definition for ‘first’ .getFeaturesStrings : <anonymous>: no visible global function definition for ‘second’ .posterior_probs : <anonymous>: no visible global function definition for ‘dmvnorm’ .precisionPathwaysTrain: no visible global function definition for ‘setNames’ DLDApredictInterface: no visible global function definition for ‘predict’ DMDranking : <anonymous>: no visible global function definition for ‘dist’ GLMpredictInterface: no visible global function definition for ‘predict’ GLMtrainInterface: no visible global function definition for ‘glm’ GLMtrainInterface: no visible binding for global variable ‘quasibinomial’ SVMpredictInterface: no visible global function definition for ‘predict’ bubblePlot.PrecisionPathways: no visible binding for global variable ‘accuracy’ bubblePlot.PrecisionPathways: no visible binding for global variable ‘cost’ bubblePlot.PrecisionPathways: no visible binding for global variable ‘Sequence’ calcCostsAndPerformance : <anonymous>: no visible global function definition for ‘na.omit’ classifyInterface: no visible binding for global variable ‘trainingMatrix’ classifyInterface: no visible binding for global variable ‘testingMatrix’ colCoxTests: no visible global function definition for ‘pnorm’ colCoxTests : <anonymous>: no visible global function definition for ‘coxph’ coxnetPredictInterface: no visible global function definition for ‘predict’ coxnetTrainInterface: no visible global function definition for ‘predict’ coxphPredictInterface: no visible global function definition for ‘predict’ crissCrossPlot: no visible binding for global variable ‘params’ crissCrossPlot: no visible binding for global variable ‘real’ crissCrossPlot: no visible binding for global variable ‘Var1’ crissCrossPlot: no visible binding for global variable ‘Var2’ crissCrossPlot: no visible binding for global variable ‘value’ crissCrossPlot: no visible binding for global variable ‘random’ crissCrossValidate : <anonymous> : <anonymous>: no visible global function definition for ‘predict’ crissCrossValidate : <anonymous> : <anonymous>: no visible global function definition for ‘na.omit’ differentMeansRanking : <anonymous>: no visible global function definition for ‘chisq.test’ edgeRranking: no visible global function definition for ‘model.matrix’ extremeGradientBoostingPredictInterface: no visible global function definition for ‘predict’ fastCox: no visible global function definition for ‘pnorm’ fisherDiscriminant: no visible binding for global variable ‘trainingMatrix’ fisherDiscriminant: no visible binding for global variable ‘var’ flowchart.PrecisionPathways: no visible binding for global variable ‘Predicted’ flowchart.PrecisionPathways: no visible binding for global variable ‘Tier’ getLocationsAndScales: no visible global function definition for ‘setNames’ getLocationsAndScales: no visible binding for global variable ‘median’ getLocationsAndScales: no visible binding for global variable ‘sd’ getLocationsAndScales: no visible binding for global variable ‘mad’ kNNinterface: no visible global function definition for ‘setNames’ kTSPclassifier : <anonymous>: no visible binding for global variable ‘trainingMatrix’ kTSPclassifier : <anonymous>: no visible global function definition for ‘Pairs’ kTSPclassifier: no visible binding for global variable ‘testingMatrix’ likelihoodRatioRanking : <anonymous>: no visible global function definition for ‘dnorm’ likelihoodRatioRanking : <anonymous> : <anonymous>: no visible global function definition for ‘dnorm’ limmaRanking: no visible global function definition for ‘model.matrix’ mixModelsPredict : <anonymous>: no visible global function definition for ‘setNames’ mixModelsPredict : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for ‘dnorm’ mixModelsPredict : <anonymous> : <anonymous>: no visible global function definition for ‘splinefun’ mixModelsTrain: no visible global function definition for ‘setNames’ naiveBayesKernel: no visible binding for global variable ‘density’ naiveBayesKernel : <anonymous> : <anonymous>: no visible global function definition for ‘splinefun’ naiveBayesKernel: no visible binding for global variable ‘test’ naiveBayesKernel : <anonymous>: no visible global function definition for ‘setNames’ pcaPredictInterface : <anonymous>: no visible global function definition for ‘predict’ pcaTrainInterface : <anonymous>: no visible global function definition for ‘prcomp’ penalisedGLMpredictInterface: no visible global function definition for ‘predict’ penalisedGLMtrainInterface : <anonymous>: no visible global function definition for ‘predict’ performanceTable : <anonymous> : <anonymous>: no visible global function definition for ‘median’ performanceTable : <anonymous>: no visible binding for global variable ‘characteristic’ performanceTable : <anonymous>: no visible binding for global variable ‘value’ randomForestPredictInterface: no visible global function definition for ‘predict’ rfsrcPredictInterface: no visible global function definition for ‘predict’ samplesSplits : <anonymous>: no visible binding for global variable ‘classes’ strataPlot.PrecisionPathways: no visible binding for global variable ‘Tier’ strataPlot.PrecisionPathways: no visible binding for global variable ‘trueClass’ strataPlot.PrecisionPathways: no visible binding for global variable ‘Accuracy’ strataPlot.PrecisionPathways: no visible binding for global variable ‘ID’ subtractFromLocation: no visible binding for global variable ‘median’ train.DataFrame: no visible binding for global variable ‘outcome’ train.DataFrame : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for ‘na.omit’ train.DataFrame: no visible binding for global variable ‘crossValParams’ ROCplot,list : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for ‘quantile’ ROCplot,list : <anonymous>: no visible binding for global variable ‘FPR’ ROCplot,list : <anonymous>: no visible binding for global variable ‘TPR’ ROCplot,list : <anonymous>: no visible binding for global variable ‘lower’ ROCplot,list : <anonymous>: no visible binding for global variable ‘upper’ crossValidate,DataFrame : <anonymous>: no visible global function definition for ‘combn’ distribution,ClassifyResult: no visible global function definition for ‘first’ distribution,ClassifyResult: no visible global function definition for ‘second’ distribution,ClassifyResult: no visible global function definition for ‘aggregate’ distribution,ClassifyResult: no visible global function definition for ‘mcols<-’ featureSetSummary,DataFrame: no visible binding for global variable ‘median’ featureSetSummary,MultiAssayExperiment: no visible binding for global variable ‘median’ featureSetSummary,matrix: no visible binding for global variable ‘median’ plotFeatureClasses,DataFrame : <anonymous>: no visible binding for global variable ‘measurement’ plotFeatureClasses,DataFrame : <anonymous>: no visible binding for global variable ‘density’ plotFeatureClasses,DataFrame : <anonymous>: no visible binding for global variable ‘legends grouping’ plotFeatureClasses,DataFrame : <anonymous>: no visible binding for global variable ‘key’ plotFeatureClasses,DataFrame : <anonymous>: no visible binding for global variable ‘value’ plotFeatureClasses,DataFrame : <anonymous>: no visible binding for global variable ‘ID’ precisionPathwaysTrain,MultiAssayExperimentOrList: no visible global function definition for ‘setNames’ prepareData,DataFrame: no visible global function definition for ‘unqiue’ prepareData,DataFrame : <anonymous>: no visible binding for global variable ‘var’ prepareData,MultiAssayExperiment: possible error in union(useFeatures[["clinical"]], group, outcomeColumns): unused argument (outcomeColumns) rankingPlot,list: no visible binding for global variable ‘top’ rankingPlot,list: no visible binding for global variable ‘overlap’ runTest,DataFrame: no visible global function definition for ‘na.omit’ runTest,DataFrame : <anonymous>: no visible global function definition for ‘na.omit’ runTest,MultiAssayExperiment: no visible binding for global variable ‘extrasInputs’ runTest,MultiAssayExperiment: no visible binding for global variable ‘prepArgs’ samplesMetricMap,list: no visible binding for global variable ‘Class’ samplesMetricMap,list: no visible binding for global variable ‘Group’ samplesMetricMap,list: no visible binding for global variable ‘measurements’ samplesMetricMap,list: no visible binding for global variable ‘name’ samplesMetricMap,list: no visible binding for global variable ‘type’ samplesMetricMap,list: no visible binding for global variable ‘Metric’ samplesMetricMap,matrix: no visible binding for global variable ‘Class’ samplesMetricMap,matrix: no visible binding for global variable ‘Group’ samplesMetricMap,matrix: no visible binding for global variable ‘measurements’ samplesMetricMap,matrix: no visible binding for global variable ‘name’ samplesMetricMap,matrix: no visible binding for global variable ‘type’ samplesMetricMap,matrix: no visible binding for global variable ‘Metric’ selectionPlot,list: no visible global function definition for ‘tail’ selectionPlot,list: no visible binding for global variable ‘overlap’ selectionPlot,list: no visible binding for global variable ‘median’ selectionPlot,list : <anonymous>: no visible binding for global variable ‘feature’ selectionPlot,list: no visible binding for global variable ‘feature’ selectionPlot,list: no visible binding for global variable ‘colourVariable’ selectionPlot,list: no visible binding for global variable ‘size’ selectionPlot,list: no visible binding for global variable ‘Freq’ show,PredictParams: no visible global function definition for ‘na.omit’ show,SelectParams: no visible global function definition for ‘na.omit’ show,TrainParams: no visible global function definition for ‘na.omit’ show,TransformParams: no visible global function definition for ‘na.omit’ Undefined global functions or variables: Accuracy Class FPR Freq Group ID Metric Pairs Predicted Sequence TPR Tier Var1 Var2 aResult accuracy aggregate characteristic chisq.test classes colourVariable combn cost coxph crossValParams density dist dmvnorm dnorm extrasInputs feature featuresLists first glm key legends grouping lower mad mcols<- measurement measurements measurementsSubset median model.matrix na.omit name outcome overlap params pnorm prcomp predict predictParams prepArgs quantile quasibinomial random real sd second setNames size splinefun tail test testingMatrix top trainParams trainingMatrix trueClass type unqiue upper value var Consider adding importFrom("base", "grouping") importFrom("stats", "aggregate", "chisq.test", "density", "dist", "dnorm", "glm", "mad", "median", "model.matrix", "na.omit", "pnorm", "prcomp", "predict", "quantile", "quasibinomial", "sd", "setNames", "splinefun", "var") importFrom("utils", "combn", "tail") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * 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 line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed crossValidate 135.003 2.324 127.002 ClassifyResult-class 34.396 0.756 31.860 runTests 22.882 6.227 13.432 distribution 28.380 0.399 25.729 samplesMetricMap 7.011 0.323 7.821 runTest 6.213 0.411 7.189 * 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: 1 WARNING, 3 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/ClassifyR.Rcheck/00check.log’ for details.
ClassifyR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL ClassifyR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’ * installing *source* package ‘ClassifyR’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c coxformatrices.cpp -o coxformatrices.o coxformatrices.cpp:24:16: warning: unused variable 'sclback3' [-Wunused-variable] double sclback3=*sctest3; ^ coxformatrices.cpp:23:16: warning: unused variable 'sclback2' [-Wunused-variable] double sclback2=*sctest2; ^ coxformatrices.cpp:81:9: warning: suggest braces around initialization of subobject [-Wmissing-braces] NULL ^~~~ { } /Library/Developer/CommandLineTools/usr/lib/clang/14.0.0/include/stddef.h:84:18: note: expanded from macro 'NULL' # define NULL __null ^~~~~~ coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,j; ^~~~~~~~~ coxformatrices.cpp:528:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,j; ^~~~~~~~~ coxformatrices.cpp:529:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register double temp; ^~~~~~~~~ coxformatrices.cpp:569:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register double temp; ^~~~~~~~~ coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,j,k; ^~~~~~~~~ coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,j,k; ^~~~~~~~~ coxformatrices.cpp:570:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,j,k; ^~~~~~~~~ coxformatrices.cpp:656:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ coxformatrices.cpp:657:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register double **pointer; ^~~~~~~~~ 12 warnings generated. clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o ClassifyR.so coxformatrices.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-ClassifyR/00new/ClassifyR/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading in method for ‘ROCplot’ with signature ‘"ClassifyResult"’: no definition for class “ClassifyResult” ** help *** installing help indices *** copying figures ** 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 (ClassifyR)
ClassifyR.Rcheck/ClassifyR-Ex.timings
name | user | system | elapsed | |
ClassifyResult-class | 34.396 | 0.756 | 31.860 | |
CrossValParams-class | 4.569 | 0.048 | 4.832 | |
FeatureSetCollection | 0.012 | 0.002 | 0.016 | |
ModellingParams-class | 0.382 | 0.003 | 0.398 | |
PredictParams-class | 0.027 | 0.000 | 0.029 | |
ROCplot | 1.632 | 0.025 | 1.728 | |
SelectParams-class | 0.082 | 0.001 | 0.084 | |
TrainParams-class | 0.045 | 0.001 | 0.048 | |
TransformParams-class | 0.021 | 0.000 | 0.022 | |
available | 0.004 | 0.001 | 0.005 | |
calcPerformance | 0.045 | 0.002 | 0.050 | |
colCoxTests | 0.526 | 0.009 | 0.562 | |
crossValidate | 135.003 | 2.324 | 127.002 | |
distribution | 28.380 | 0.399 | 25.729 | |
edgesToHubNetworks | 0.004 | 0.001 | 0.005 | |
featureSetSummary | 0.008 | 0.002 | 0.011 | |
interactorDifferences | 0.056 | 0.003 | 0.058 | |
performancePlot | 0.822 | 0.006 | 0.906 | |
plotFeatureClasses | 3.921 | 0.104 | 4.273 | |
precisionPathways | 0.000 | 0.000 | 0.001 | |
rankingPlot | 0.723 | 0.335 | 0.981 | |
runTest | 6.213 | 0.411 | 7.189 | |
runTests | 22.882 | 6.227 | 13.432 | |
samplesMetricMap | 7.011 | 0.323 | 7.821 | |
samplesSplitting | 0.002 | 0.003 | 0.005 | |
selectionPlot | 2.164 | 0.490 | 2.649 | |