Dario Strbenac
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/ClassifyR |
| Branch: RELEASE_3_9 |
| Last Commit: a2993e1 |
| Last Changed Date: 2019-06-14 02:44:32 -0400 (Fri, 14 Jun 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:53:41 -0400 (Wed, 16 Oct 2019).
| Package 280/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ClassifyR 2.4.4 Dario Strbenac
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ClassifyR |
| Version: 2.4.4 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClassifyR_2.4.4.tar.gz |
| StartedAt: 2019-10-16 01:29:37 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 01:37:14 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 456.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ClassifyR.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClassifyR_2.4.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/ClassifyR.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (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 ‘2.4.4’ * 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 :: no visible global function definition for ‘dmvnorm’ kTSPclassifier,DataFrame : : no visible global function definition for ‘Pairs’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘measurement’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘..density..’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘legends grouping’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘key’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘value’ plotFeatureClasses,DataFrame : : no visible binding for global variable ‘ID’ rankingPlot,list : : : no visible global function definition for ‘first’ rankingPlot,list : : : no visible global function definition for ‘second’ rankingPlot,list : : : : no visible global function definition for ‘first’ rankingPlot,list : : : : no visible global function definition for ‘second’ runTest,DataFrame: no visible binding for global variable ‘setsNodes’ runTests,DataFrame: no visible binding for global variable ‘setsNodes’ 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 ‘first’ selectionPlot,list : : : no visible global function definition for ‘second’ selectionPlot,list : : : : no visible global function definition for ‘first’ selectionPlot,list : : : : no visible global function definition for ‘second’ selectionPlot,list: no visible binding for global variable ‘Freq’ Undefined global functions or variables: ..density.. 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 or elapsed time > 5s user system elapsed ClassifyResult-class 156.887 13.982 45.831 elasticNetGLMinterface 51.836 7.517 23.214 elasticNetFeatures 51.406 7.303 22.865 distribution 24.599 8.120 14.056 runTests 21.507 6.762 11.884 DMDselection 10.026 0.991 11.016 previousSelection 7.100 3.843 7.003 previousTrained 6.911 4.026 7.139 likelihoodRatioSelection 8.944 0.352 9.297 samplesMetricMap 7.132 0.395 7.554 edgeRselection 6.229 0.515 6.748 selectionPlot 5.712 1.012 6.571 rankingPlot 4.938 1.108 5.905 * 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 ‘/Users/biocbuild/bbs-3.9-bioc/meat/ClassifyR.Rcheck/00check.log’ for details.
ClassifyR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ClassifyR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/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 | 156.887 | 13.982 | 45.831 | |
| DLDAinterface | 0.160 | 0.033 | 0.194 | |
| DMDselection | 10.026 | 0.991 | 11.016 | |
| FeatureSetCollection-class | 0.011 | 0.002 | 0.013 | |
| FeatureSetCollectionOrNULL-class | 0.005 | 0.001 | 0.006 | |
| KolmogorovSmirnovSelection | 3.076 | 0.119 | 3.196 | |
| KullbackLeiblerSelection | 1.685 | 0.035 | 1.721 | |
| MixModelsListsSet-class | 0.535 | 0.029 | 0.570 | |
| NSCpredictInterface | 0.189 | 0.015 | 0.208 | |
| NSCselectionInterface | 0.143 | 0.011 | 0.155 | |
| NSCtrainInterface | 0.124 | 0.008 | 0.132 | |
| PredictParams-class | 0.003 | 0.000 | 0.004 | |
| ROCplot | 1.210 | 0.010 | 1.221 | |
| ResubstituteParams-class | 0.003 | 0.001 | 0.003 | |
| SVMinterface | 0.067 | 0.004 | 0.071 | |
| SelectParams-class | 0.014 | 0.003 | 0.016 | |
| SelectResult-class | 0.002 | 0.001 | 0.002 | |
| TrainParams-class | 0.001 | 0.001 | 0.002 | |
| TransformParams-class | 0.002 | 0.000 | 0.002 | |
| bartlettSelection | 2.315 | 0.030 | 2.346 | |
| calcPerformance | 0.006 | 0.000 | 0.007 | |
| characterOrDataFrame-class | 0.012 | 0.000 | 0.013 | |
| classifyInterface | 1.104 | 0.268 | 1.372 | |
| differentMeansSelection | 1.961 | 0.076 | 2.036 | |
| distribution | 24.599 | 8.120 | 14.056 | |
| edgeRselection | 6.229 | 0.515 | 6.748 | |
| edgesToHubNetworks | 0.006 | 0.000 | 0.006 | |
| elasticNetFeatures | 51.406 | 7.303 | 22.865 | |
| elasticNetGLMinterface | 51.836 | 7.517 | 23.214 | |
| featureSetSummary | 0.010 | 0.008 | 0.018 | |
| fisherDiscriminant | 0.179 | 0.054 | 0.233 | |
| forestFeatures | 0.285 | 0.062 | 0.348 | |
| functionOrList-class | 0.012 | 0.003 | 0.015 | |
| functionOrNULL-class | 0.009 | 0.001 | 0.010 | |
| getLocationsAndScales | 0.055 | 0.010 | 0.065 | |
| integerOrNumeric-class | 0.020 | 0.005 | 0.024 | |
| interactorDifferences | 0.058 | 0.012 | 0.070 | |
| kTSPclassifier | 0.205 | 0.033 | 0.240 | |
| knnInterface | 0.065 | 0.011 | 0.076 | |
| leveneSelection | 2.299 | 0.206 | 2.505 | |
| likelihoodRatioSelection | 8.944 | 0.352 | 9.297 | |
| limmaSelection | 0.419 | 0.010 | 0.429 | |
| mixmodels | 0.560 | 0.038 | 0.598 | |
| naiveBayesKernel | 0.660 | 0.028 | 0.688 | |
| networkCorrelationsSelection | 0.304 | 0.004 | 0.308 | |
| pairsDifferencesSelection | 0.309 | 0.017 | 0.326 | |
| performancePlot | 0.407 | 0.004 | 0.413 | |
| plotFeatureClasses | 4.831 | 0.051 | 4.921 | |
| previousSelection | 7.100 | 3.843 | 7.003 | |
| previousTrained | 6.911 | 4.026 | 7.139 | |
| randomForestInterface | 0.431 | 0.085 | 0.516 | |
| rankingPlot | 4.938 | 1.108 | 5.905 | |
| runTest | 1.000 | 0.071 | 1.072 | |
| runTests | 21.507 | 6.762 | 11.884 | |
| samplesMetricMap | 7.132 | 0.395 | 7.554 | |
| selectionPlot | 5.712 | 1.012 | 6.571 | |
| subtractFromLocation | 0.003 | 0.002 | 0.004 | |