Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:05:37 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the ClassifyR package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 317/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
ClassifyR 2.12.0 (landing page) Dario Strbenac
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: ClassifyR |
Version: 2.12.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ClassifyR_2.12.0.tar.gz |
StartedAt: 2021-10-14 09:15:58 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 09:20:13 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 254.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ClassifyR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings ClassifyR_2.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ClassifyR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ClassifyR’ version ‘2.12.0’ * 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 ‘ClassifyR’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE .posterior_probs : <anonymous>: no visible global function definition for ‘dmvnorm’ easyHardClassifierPredict,EasyHardClassifier-MultiAssayExperiment: no visible binding for global variable ‘measurements’ kTSPclassifier,DataFrame : <anonymous>: no visible global function definition for ‘Pairs’ 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’ rankingPlot,list : <anonymous> : <anonymous>: no visible global function definition for ‘first’ rankingPlot,list : <anonymous> : <anonymous>: no visible global function definition for ‘second’ rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for ‘first’ rankingPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for ‘second’ runTest,DataFrame: no visible binding for global variable ‘setsNodes’ runTestEasyHard,MultiAssayExperiment: no visible binding for global variable ‘setsNodes’ runTests,DataFrame: no visible binding for global variable ‘setsNodes’ runTestsEasyHard,MultiAssayExperiment: no visible binding for global variable ‘setsNodes’ runTestsEasyHard,MultiAssayExperiment: no visible binding for global variable ‘.iteration’ 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 : <anonymous> : <anonymous>: no visible global function definition for ‘first’ selectionPlot,list : <anonymous> : <anonymous>: no visible global function definition for ‘second’ selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for ‘first’ selectionPlot,list : <anonymous> : <anonymous> : <anonymous>: no visible global function definition for ‘second’ selectionPlot,list: no visible binding for global variable ‘Freq’ Undefined global functions or variables: ..density.. .iteration Class Freq Group ID Metric Pairs dmvnorm first key legends grouping measurement measurements name second setsNodes type value Consider adding importFrom("base", "grouping") 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed ClassifyResult-class 75.098 4.337 27.858 runTests 22.790 7.941 10.854 elasticNetGLMinterface 26.663 3.373 11.027 elasticNetFeatures 16.291 2.487 11.846 distribution 10.501 3.128 5.408 samplesMetricMap 7.280 1.220 3.958 runTest 7.087 0.268 7.356 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.13-bioc/meat/ClassifyR.Rcheck/00check.log’ for details.
ClassifyR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL ClassifyR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘ClassifyR’ ... ** using staged installation ** 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 ** 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 | 75.098 | 4.337 | 27.858 | |
DLDAinterface | 0.060 | 0.004 | 0.063 | |
DMDselection | 4.731 | 0.104 | 4.835 | |
EasyHardClassifier-class | 0.014 | 0.000 | 0.014 | |
FeatureSetCollection-class | 0.007 | 0.000 | 0.007 | |
FeatureSetCollectionOrNULL-class | 0.001 | 0.003 | 0.003 | |
KolmogorovSmirnovSelection | 1.705 | 0.020 | 1.725 | |
KullbackLeiblerSelection | 0.799 | 0.004 | 0.804 | |
MixModelsListsSet-class | 0.295 | 0.008 | 0.308 | |
NSCpredictInterface | 0.108 | 0.004 | 0.111 | |
NSCselectionInterface | 0.08 | 0.00 | 0.08 | |
NSCtrainInterface | 0.067 | 0.000 | 0.066 | |
PredictParams-class | 0.002 | 0.000 | 0.002 | |
ROCplot | 0.571 | 0.000 | 0.571 | |
ResubstituteParams-class | 0.000 | 0.002 | 0.002 | |
SVMinterface | 0.054 | 0.005 | 0.059 | |
SelectParams-class | 0.01 | 0.00 | 0.01 | |
SelectResult-class | 0.000 | 0.000 | 0.001 | |
TrainParams-class | 0.000 | 0.001 | 0.000 | |
TransformParams-class | 0.001 | 0.001 | 0.001 | |
bartlettSelection | 1.726 | 0.004 | 1.730 | |
calcPerformance | 0.003 | 0.000 | 0.003 | |
characterOrDataFrame-class | 0.009 | 0.000 | 0.010 | |
classifyInterface | 0.419 | 0.044 | 0.463 | |
differentMeansSelection | 1.523 | 0.004 | 1.527 | |
distribution | 10.501 | 3.128 | 5.408 | |
easyHardClassifier | 0.400 | 0.054 | 0.454 | |
easyHardFeatures | 0.315 | 0.012 | 0.327 | |
edgeRselection | 3.378 | 0.123 | 3.505 | |
edgesToHubNetworks | 0.003 | 0.000 | 0.003 | |
elasticNetFeatures | 16.291 | 2.487 | 11.846 | |
elasticNetGLMinterface | 26.663 | 3.373 | 11.027 | |
featureSetSummary | 0.006 | 0.000 | 0.005 | |
fisherDiscriminant | 0.096 | 0.004 | 0.101 | |
forestFeatures | 0.096 | 0.004 | 0.101 | |
functionOrList-class | 0.004 | 0.004 | 0.007 | |
functionOrNULL-class | 0.004 | 0.000 | 0.003 | |
getLocationsAndScales | 0.017 | 0.008 | 0.025 | |
integerOrNumeric-class | 0.014 | 0.000 | 0.014 | |
interactorDifferences | 0.038 | 0.000 | 0.038 | |
kTSPclassifier | 0.083 | 0.008 | 0.091 | |
knnInterface | 0.030 | 0.004 | 0.035 | |
leveneSelection | 1.665 | 0.108 | 1.772 | |
likelihoodRatioSelection | 4.104 | 0.120 | 4.225 | |
limmaSelection | 0.416 | 0.008 | 0.423 | |
listOrCharacterOrNULL-class | 0.003 | 0.000 | 0.004 | |
listOrNULL-class | 0.003 | 0.000 | 0.003 | |
mixmodels | 0.164 | 0.000 | 0.164 | |
naiveBayesKernel | 0.387 | 0.016 | 0.403 | |
networkCorrelationsSelection | 0.180 | 0.004 | 0.184 | |
pairsDifferencesSelection | 0.273 | 0.000 | 0.273 | |
performancePlot | 0.441 | 0.020 | 0.460 | |
plotFeatureClasses | 2.005 | 0.024 | 2.030 | |
previousSelection | 2.216 | 1.226 | 2.033 | |
previousTrained | 2.094 | 1.298 | 1.616 | |
randomForestInterface | 0.413 | 0.140 | 0.280 | |
rankingPlot | 1.327 | 0.311 | 1.455 | |
runTest | 7.087 | 0.268 | 7.356 | |
runTests | 22.790 | 7.941 | 10.854 | |
samplesMetricMap | 7.280 | 1.220 | 3.958 | |
selectionPlot | 1.349 | 0.314 | 1.452 | |
subtractFromLocation | 0.000 | 0.002 | 0.002 | |