Dario Strbenac
| Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022) |
| git_url: https://git.bioconductor.org/packages/ClassifyR |
| git_branch: RELEASE_3_15 |
| git_last_commit: 1d0f471 |
| git_last_commit_date: 2022-05-11 01:40:01 -0400 (Wed, 11 May 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-10-19 13:22:43 -0400 (Wed, 19 Oct 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4386 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" | 4138 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | 4.2.1 (2022-06-23) -- "Funny-Looking Kid" | 4205 |
| 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 | ||||
|
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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 332/2140 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ClassifyR 3.0.3 (landing page) Dario Strbenac
| nebbiolo1 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ClassifyR |
| Version: 3.0.3 |
| 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_3.0.3.tar.gz |
| StartedAt: 2022-10-19 00:35:03 -0400 (Wed, 19 Oct 2022) |
| EndedAt: 2022-10-19 00:58:16 -0400 (Wed, 19 Oct 2022) |
| EllapsedTime: 1393.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ClassifyR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /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_3.0.3.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/ClassifyR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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 ‘3.0.3’
* 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 ... NOTE
Found the following hidden files and directories:
dump/.-package.R
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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
.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
‘classesTrain’
.doSelection : <anonymous>: no visible binding for global variable
‘measurementsSubset’
.doSelection : <anonymous>: no visible binding for global variable
‘aResult’
.doTrain : <anonymous>: no visible binding for global variable
‘crossValParams’
.doTrain : <anonymous>: no visible binding for global variable
‘performanceName’
.doTrain: no visible binding for global variable ‘performanceType’
.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’
.samplesSplits : <anonymous>: no visible binding for global variable
‘classes’
.splitDataAndOutcomes: no visible binding for global variable
‘classColumn’
.splitDataAndOutcomes: no visible global function definition for
‘mcols<-’
elasticNetPreval: no visible binding for global variable
‘elasticNetGLMtrainInterfacePreval’
generateModellingParams: no visible global function definition for
‘kNNparams’
logisticParams: no visible binding for global variable
‘logisticTrainInterface’
logisticParams: no visible binding for global variable
‘logisticPredictInterface’
KolmogorovSmirnovRanking,MultiAssayExperiment: no visible binding for
global variable ‘dataTable’
KullbackLeiblerRanking,MultiAssayExperiment: no visible binding for
global variable ‘dataTable’
PredictParams,functionOrNULL: no visible global function definition for
‘DataFrame’
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’
SelectParams,functionOrList: no visible global function definition for
‘DataFrame’
TrainParams,function: no visible global function definition for
‘DataFrame’
crossValidate,data.frame: no visible global function definition for
‘mcols<-’
crossValidate,list : <anonymous>: no visible global function definition
for ‘mcols<-’
crossValidate,matrix: no visible global function definition for
‘mcols<-’
distribution,ClassifyResult: no visible binding for global variable
‘allPredictions’
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
‘mcols<-’
elasticNetGLMpredictInterface,multnet-matrix: no visible global
function definition for ‘DataFrame’
fisherDiscriminant,MultiAssayExperiment: no visible binding for global
variable ‘measurements’
fisherDiscriminant,matrix: no visible global function definition for
‘DataFrame’
kTSPclassifier,DataFrame : <anonymous>: no visible global function
definition for ‘Pairs’
kTSPclassifier,MultiAssayExperiment: no visible binding for global
variable ‘measurementsTest’
naiveBayesKernel,DataFrame: no visible binding for global variable
‘weight’
naiveBayesKernel,DataFrame: no visible binding for global variable
‘test’
naiveBayesKernel,MultiAssayExperiment: no visible binding for global
variable ‘measurements’
pcaPredictInterface,pcaModel-DFrame: no visible global function
definition for ‘mcols<-’
pcaTrainInterface,DFrame: no visible global function definition for
‘mcols<-’
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’
prevalPredictInterface,prevalModel-DFrame: no visible global function
definition for ‘mcols<-’
prevalTrainInterface,DFrame: no visible global function definition for
‘mcols<-’
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
‘DataFrame’
runTest,MultiAssayExperiment: no visible binding for global variable
‘measurements’
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 binding for global variable ‘overlap’
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’
Undefined global functions or variables:
..density.. Class DataFrame FPR Freq Group ID Metric Pairs TPR
aResult allPredictions classColumn classes classesTrain
colourVariable crossValParams dataTable dmvnorm
elasticNetGLMtrainInterfacePreval feature first kNNparams key legends
grouping logisticPredictInterface logisticTrainInterface lower
mcols<- measurement measurements measurementsSubset measurementsTest
name overlap performanceName performanceType predictParams second
size test top trainParams type upper value weight
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
crossValidate 857.484 2.860 882.012
ClassifyResult-class 267.461 8.824 76.927
elasticNetGLM 47.408 3.972 20.647
elasticNetFeatures 47.060 3.866 20.482
distribution 36.054 3.832 14.319
runTests 29.541 4.710 12.579
previousTrained 5.899 3.361 3.121
previousSelection 5.207 3.600 3.033
edgeRranking 6.425 0.366 6.806
samplesMetricMap 5.648 0.281 5.938
runTest 4.786 0.213 5.011
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.15-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/4.2/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 | 267.461 | 8.824 | 76.927 | |
| CrossValParams-class | 0.087 | 0.009 | 0.096 | |
| DLDAinterface | 0.063 | 0.007 | 0.070 | |
| DMDranking | 0.135 | 0.017 | 0.151 | |
| FeatureSetCollection | 0.010 | 0.002 | 0.012 | |
| FeatureSetCollectionOrNULL-class | 0.036 | 0.003 | 0.039 | |
| KolmogorovSmirnovRanking | 0.235 | 0.028 | 0.264 | |
| KullbackLeiblerRanking | 0.103 | 0.011 | 0.115 | |
| ModellingParams-class | 0.149 | 0.014 | 0.163 | |
| NSCinterface | 0.323 | 0.029 | 0.354 | |
| PredictParams-class | 0.022 | 0.000 | 0.022 | |
| PredictParamsOrNULL | 0.06 | 0.00 | 0.06 | |
| ROCplot | 1.527 | 0.073 | 1.605 | |
| SVMinterface | 0.135 | 0.006 | 0.142 | |
| SelectParams-class | 0.130 | 0.001 | 0.131 | |
| SelectParamsOrNULL-class | 0.130 | 0.001 | 0.132 | |
| TrainParams-class | 0.017 | 0.000 | 0.017 | |
| TransformParams-class | 0.021 | 0.000 | 0.021 | |
| TransformParamsOrNULL-class | 0.166 | 0.001 | 0.168 | |
| bartlettRanking | 1.464 | 0.021 | 1.486 | |
| calcPerformance | 0.009 | 0.000 | 0.010 | |
| characterOrDataFrame-class | 0.026 | 0.000 | 0.026 | |
| classifyInterface | 0.878 | 0.074 | 0.955 | |
| coxnetInterface | 3.552 | 0.051 | 3.607 | |
| coxphInterface | 0 | 0 | 0 | |
| crossValidate | 857.484 | 2.860 | 882.012 | |
| differentMeansRanking | 0.037 | 0.001 | 0.038 | |
| distribution | 36.054 | 3.832 | 14.319 | |
| edgeRranking | 6.425 | 0.366 | 6.806 | |
| edgesToHubNetworks | 0.004 | 0.000 | 0.003 | |
| elasticNetFeatures | 47.060 | 3.866 | 20.482 | |
| elasticNetGLM | 47.408 | 3.972 | 20.647 | |
| featureSetSummary | 0.007 | 0.002 | 0.008 | |
| fisherDiscriminant | 0.061 | 0.009 | 0.070 | |
| forestFeatures | 0.295 | 0.031 | 0.328 | |
| functionOrList-class | 0.068 | 0.007 | 0.075 | |
| functionOrNULL-class | 0.033 | 0.004 | 0.037 | |
| generateCrossValParams | 0.002 | 0.000 | 0.002 | |
| generateModellingParams | 0.706 | 0.060 | 0.767 | |
| getLocationsAndScales | 0.047 | 0.006 | 0.052 | |
| interactorDifferences | 0.056 | 0.009 | 0.066 | |
| kNNinterface | 0.053 | 0.005 | 0.057 | |
| kTSPclassifier | 0.234 | 0.049 | 0.283 | |
| leveneRanking | 0.683 | 0.067 | 0.752 | |
| likelihoodRatioRanking | 0.646 | 0.060 | 0.707 | |
| limmaRanking | 0.040 | 0.005 | 0.044 | |
| listOrNULL-class | 0.006 | 0.001 | 0.006 | |
| mixModels | 0.944 | 0.056 | 1.008 | |
| naiveBayesKernel | 0.622 | 0.029 | 0.652 | |
| pairsDifferencesRanking | 0.096 | 0.002 | 0.098 | |
| performancePlot | 0.789 | 0.017 | 0.806 | |
| plotFeatureClasses | 3.750 | 0.033 | 3.822 | |
| previousSelection | 5.207 | 3.600 | 3.033 | |
| previousTrained | 5.899 | 3.361 | 3.121 | |
| randomForest | 0.561 | 0.048 | 0.611 | |
| rankingPlot | 1.351 | 0.572 | 1.511 | |
| runTest | 4.786 | 0.213 | 5.011 | |
| runTests | 29.541 | 4.710 | 12.579 | |
| samplesMetricMap | 5.648 | 0.281 | 5.938 | |
| selectionPlot | 2.932 | 0.871 | 3.289 | |
| subtractFromLocation | 0.002 | 0.001 | 0.003 | |