Dario Strbenac
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/ClassifyR |
| git_branch: RELEASE_3_13 |
| git_last_commit: ede130d |
| git_last_commit_date: 2021-05-19 12:06:37 -0400 (Wed, 19 May 2021) |
| 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 |
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### 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
###
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* 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 | |