Dario Strbenac
| Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022) |
| git_url: https://git.bioconductor.org/packages/ClassifyR |
| git_branch: RELEASE_3_14 |
| git_last_commit: 133d20a |
| git_last_commit_date: 2021-10-26 12:15:09 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:47 -0400 (Wed, 13 Apr 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
| tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
| machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
| 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 324/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ClassifyR 2.14.0 (landing page) Dario Strbenac
| nebbiolo2 | Linux (Ubuntu 20.04.4 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: 2.14.0 |
| 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_2.14.0.tar.gz |
| StartedAt: 2022-04-12 11:35:13 -0400 (Tue, 12 Apr 2022) |
| EndedAt: 2022-04-12 11:42:31 -0400 (Tue, 12 Apr 2022) |
| EllapsedTime: 438.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ClassifyR.Rcheck |
| Warnings: 0 |
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### 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_2.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/ClassifyR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘2.14.0’
* 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 ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘MultiAssayExperiment’
A package should be listed in only one of these fields.
* 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 global function definition for ‘mcols’
runTests,DataFrame: no visible binding for global variable ‘setsNodes’
runTests,DataFrame: no visible binding for global variable ‘dataset’
runTests,DataFrame : <anonymous>: no visible global function definition
for ‘mcols’
runTests,DataFrame : <anonymous>: no visible global function definition
for ‘mcols<-’
runTests,DataFrame: no visible global function definition for ‘mcols<-’
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 dataset
dmvnorm first key legends grouping mcols mcols<- 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 119.392 5.146 43.323
elasticNetGLMinterface 45.007 3.864 18.473
elasticNetFeatures 44.172 4.015 17.890
runTests 34.915 9.023 14.612
DLDAinterface 40.036 1.727 0.204
distribution 24.116 3.797 11.298
previousTrained 8.902 6.472 7.596
DMDselection 10.016 0.373 10.397
previousSelection 5.568 3.267 7.485
likelihoodRatioSelection 8.116 0.127 8.278
randomForestInterface 3.492 3.255 0.418
ROCplot 5.331 0.045 5.380
edgeRselection 5.145 0.179 5.329
runTest 4.829 0.264 5.101
* 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-3.14-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/4.1/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 | 119.392 | 5.146 | 43.323 | |
| DLDAinterface | 40.036 | 1.727 | 0.204 | |
| DMDselection | 10.016 | 0.373 | 10.397 | |
| EasyHardClassifier-class | 0.025 | 0.001 | 0.025 | |
| FeatureSetCollection-class | 0.007 | 0.001 | 0.008 | |
| FeatureSetCollectionOrNULL-class | 0.004 | 0.001 | 0.005 | |
| KolmogorovSmirnovSelection | 3.285 | 0.109 | 3.398 | |
| KullbackLeiblerSelection | 2.032 | 0.030 | 2.062 | |
| MixModelsListsSet-class | 0.592 | 0.013 | 0.613 | |
| NSCpredictInterface | 0.179 | 0.014 | 0.195 | |
| NSCselectionInterface | 0.112 | 0.005 | 0.116 | |
| NSCtrainInterface | 0.12 | 0.01 | 0.13 | |
| PredictParams-class | 0.002 | 0.000 | 0.002 | |
| ROCplot | 5.331 | 0.045 | 5.380 | |
| ResubstituteParams-class | 0.003 | 0.000 | 0.003 | |
| SVMinterface | 0.250 | 0.013 | 0.263 | |
| SelectParams-class | 0.016 | 0.005 | 0.020 | |
| SelectResult-class | 0.001 | 0.001 | 0.002 | |
| TrainParams-class | 0.001 | 0.000 | 0.001 | |
| TransformParams-class | 0.002 | 0.001 | 0.002 | |
| bartlettSelection | 3.311 | 0.053 | 3.367 | |
| calcPerformance | 0.005 | 0.000 | 0.006 | |
| characterOrDataFrame-class | 0.016 | 0.000 | 0.017 | |
| classifyInterface | 1.090 | 0.114 | 1.205 | |
| differentMeansSelection | 2.450 | 0.034 | 2.485 | |
| distribution | 24.116 | 3.797 | 11.298 | |
| easyHardClassifier | 0.527 | 0.057 | 0.585 | |
| easyHardFeatures | 0.602 | 0.049 | 0.651 | |
| edgeRselection | 5.145 | 0.179 | 5.329 | |
| edgesToHubNetworks | 0.003 | 0.000 | 0.004 | |
| elasticNetFeatures | 44.172 | 4.015 | 17.890 | |
| elasticNetGLMinterface | 45.007 | 3.864 | 18.473 | |
| featureSetSummary | 0.004 | 0.002 | 0.007 | |
| fisherDiscriminant | 0.124 | 0.028 | 0.152 | |
| forestFeatures | 0.186 | 0.028 | 0.213 | |
| functionOrList-class | 0.009 | 0.004 | 0.014 | |
| functionOrNULL-class | 0.004 | 0.001 | 0.005 | |
| getLocationsAndScales | 0.055 | 0.007 | 0.062 | |
| integerOrNumeric-class | 0.021 | 0.004 | 0.025 | |
| interactorDifferences | 0.053 | 0.007 | 0.060 | |
| kTSPclassifier | 0.151 | 0.019 | 0.171 | |
| knnInterface | 0.056 | 0.006 | 0.062 | |
| leveneSelection | 1.745 | 0.074 | 1.822 | |
| likelihoodRatioSelection | 8.116 | 0.127 | 8.278 | |
| limmaSelection | 0.618 | 0.009 | 0.630 | |
| listOrCharacterOrNULL-class | 0.005 | 0.000 | 0.005 | |
| listOrNULL-class | 0.004 | 0.000 | 0.005 | |
| mixmodels | 0.346 | 0.008 | 0.355 | |
| naiveBayesKernel | 0.678 | 0.019 | 0.697 | |
| networkCorrelationsSelection | 0.311 | 0.004 | 0.315 | |
| pairsDifferencesSelection | 0.488 | 0.010 | 0.499 | |
| performancePlot | 0.576 | 0.014 | 0.594 | |
| plotFeatureClasses | 3.580 | 0.033 | 3.618 | |
| previousSelection | 5.568 | 3.267 | 7.485 | |
| previousTrained | 8.902 | 6.472 | 7.596 | |
| randomForestInterface | 3.492 | 3.255 | 0.418 | |
| rankingPlot | 3.360 | 0.834 | 4.021 | |
| runTest | 4.829 | 0.264 | 5.101 | |
| runTests | 34.915 | 9.023 | 14.612 | |
| samplesMetricMap | 4.593 | 0.198 | 4.792 | |
| selectionPlot | 2.866 | 1.224 | 3.549 | |
| subtractFromLocation | 0.003 | 0.002 | 0.005 | |