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 13:20:06 -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: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ClassifyR_3.0.3.tar.gz |
| StartedAt: 2022-10-18 19:03:20 -0400 (Tue, 18 Oct 2022) |
| EndedAt: 2022-10-18 19:13:52 -0400 (Tue, 18 Oct 2022) |
| EllapsedTime: 632.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ClassifyR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings ClassifyR_3.0.3.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/ClassifyR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘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 372.865 2.226 375.102
ClassifyResult-class 107.189 5.579 32.306
elasticNetFeatures 24.244 2.371 11.103
elasticNetGLM 22.485 2.296 9.625
distribution 13.588 1.576 5.707
runTests 10.696 1.560 4.771
* 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
‘/home/biocbuild/bbs-3.15-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.
ClassifyR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL ClassifyR ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.15-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 | 107.189 | 5.579 | 32.306 | |
| CrossValParams-class | 0.042 | 0.012 | 0.053 | |
| DLDAinterface | 0.034 | 0.004 | 0.039 | |
| DMDranking | 0.069 | 0.000 | 0.069 | |
| FeatureSetCollection | 0.008 | 0.000 | 0.008 | |
| FeatureSetCollectionOrNULL-class | 0.018 | 0.000 | 0.018 | |
| KolmogorovSmirnovRanking | 0.111 | 0.012 | 0.123 | |
| KullbackLeiblerRanking | 0.043 | 0.007 | 0.050 | |
| ModellingParams-class | 0.066 | 0.024 | 0.090 | |
| NSCinterface | 0.166 | 0.020 | 0.186 | |
| PredictParams-class | 0.010 | 0.001 | 0.010 | |
| PredictParamsOrNULL | 0.026 | 0.000 | 0.026 | |
| ROCplot | 0.707 | 0.075 | 0.782 | |
| SVMinterface | 0.114 | 0.019 | 0.134 | |
| SelectParams-class | 0.067 | 0.003 | 0.070 | |
| SelectParamsOrNULL-class | 0.050 | 0.009 | 0.058 | |
| TrainParams-class | 0.009 | 0.000 | 0.009 | |
| TransformParams-class | 0.01 | 0.00 | 0.01 | |
| TransformParamsOrNULL-class | 0.079 | 0.003 | 0.083 | |
| bartlettRanking | 0.796 | 0.052 | 0.848 | |
| calcPerformance | 0.006 | 0.000 | 0.006 | |
| characterOrDataFrame-class | 0.015 | 0.000 | 0.014 | |
| classifyInterface | 0.494 | 0.036 | 0.529 | |
| coxnetInterface | 1.688 | 0.031 | 1.720 | |
| coxphInterface | 0.000 | 0.001 | 0.000 | |
| crossValidate | 372.865 | 2.226 | 375.102 | |
| differentMeansRanking | 0.017 | 0.000 | 0.017 | |
| distribution | 13.588 | 1.576 | 5.707 | |
| edgeRranking | 3.114 | 0.120 | 3.236 | |
| edgesToHubNetworks | 0.003 | 0.000 | 0.003 | |
| elasticNetFeatures | 24.244 | 2.371 | 11.103 | |
| elasticNetGLM | 22.485 | 2.296 | 9.625 | |
| featureSetSummary | 0.001 | 0.002 | 0.004 | |
| fisherDiscriminant | 0.028 | 0.009 | 0.037 | |
| forestFeatures | 1.076 | 0.212 | 1.288 | |
| functionOrList-class | 0.029 | 0.004 | 0.032 | |
| functionOrNULL-class | 0.014 | 0.000 | 0.015 | |
| generateCrossValParams | 0.749 | 0.120 | 0.890 | |
| generateModellingParams | 0.286 | 0.004 | 0.291 | |
| getLocationsAndScales | 0.011 | 0.004 | 0.015 | |
| interactorDifferences | 0.025 | 0.008 | 0.032 | |
| kNNinterface | 0.033 | 0.000 | 0.034 | |
| kTSPclassifier | 0.049 | 0.000 | 0.049 | |
| leveneRanking | 0.267 | 0.012 | 0.278 | |
| likelihoodRatioRanking | 0.334 | 0.028 | 0.363 | |
| limmaRanking | 0.022 | 0.000 | 0.021 | |
| listOrNULL-class | 0.001 | 0.003 | 0.003 | |
| mixModels | 0.357 | 0.028 | 0.389 | |
| naiveBayesKernel | 0.331 | 0.008 | 0.339 | |
| pairsDifferencesRanking | 0.052 | 0.004 | 0.057 | |
| performancePlot | 0.316 | 0.008 | 0.324 | |
| plotFeatureClasses | 1.739 | 0.084 | 1.823 | |
| previousSelection | 1.997 | 1.112 | 1.134 | |
| previousTrained | 1.808 | 1.033 | 1.021 | |
| randomForest | 0.333 | 0.024 | 0.356 | |
| rankingPlot | 0.515 | 0.196 | 0.577 | |
| runTest | 2.122 | 0.112 | 2.234 | |
| runTests | 10.696 | 1.560 | 4.771 | |
| samplesMetricMap | 2.501 | 0.160 | 2.660 | |
| selectionPlot | 1.181 | 0.208 | 1.258 | |
| subtractFromLocation | 0.000 | 0.002 | 0.003 | |