Dario Strbenac
| Snapshot Date: 2021-12-08 10:53:01 -0500 (Wed, 08 Dec 2021) |
| git_url: https://git.bioconductor.org/packages/ClassifyR |
| git_branch: master |
| git_last_commit: 9fa7bbd |
| git_last_commit_date: 2021-11-05 15:34:35 -0500 (Fri, 05 Nov 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2021-12-09 12:34:36 -0500 (Thu, 09 Dec 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 320/2069 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ClassifyR 2.15.1 (landing page) Dario Strbenac
| nebbiolo1 | Linux (Ubuntu 20.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | OK | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: ClassifyR |
| Version: 2.15.1 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClassifyR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ClassifyR_2.15.1.tar.gz |
| StartedAt: 2021-12-08 19:32:11 -0500 (Wed, 08 Dec 2021) |
| EndedAt: 2021-12-08 19:38:28 -0500 (Wed, 08 Dec 2021) |
| EllapsedTime: 377.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ClassifyR.Rcheck |
| Warnings: 0 |
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### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:ClassifyR.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings ClassifyR_2.15.1.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/ClassifyR.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'ClassifyR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ClassifyR' version '2.15.1'
* 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 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
.getFeaturesStrings : <anonymous>: no visible global function
definition for 'first'
.getFeaturesStrings : <anonymous>: no visible global function
definition for 'second'
.getFeaturesStrings : <anonymous> : <anonymous>: no visible global
function definition for 'first'
.getFeaturesStrings : <anonymous> : <anonymous>: no visible global
function definition for 'second'
.posterior_probs : <anonymous>: no visible global function definition
for 'dmvnorm'
ROCplot,list : <anonymous>: no visible binding for global variable
'FPR'
ROCplot,list : <anonymous>: no visible binding for global variable
'TPR'
easyHardClassifierPredict,EasyHardClassifier-MultiAssayExperiment: no
visible binding for global variable 'measurements'
easyHardClassifierTrain,MultiAssayExperiment: no visible binding for
global variable 'datasetName'
easyHardClassifierTrain,MultiAssayExperiment: no visible binding for
global variable 'classificationName'
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: no visible binding for global variable 'top'
rankingPlot,list: no visible binding for global variable 'overlap'
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: no visible binding for global variable 'overlap'
selectionPlot,list: no visible binding for global variable 'size'
selectionPlot,list: no visible binding for global variable 'Freq'
Undefined global functions or variables:
..density.. .iteration Class FPR Freq Group ID Metric Pairs TPR
classificationName dataset datasetName dmvnorm first key legends
grouping mcols mcols<- measurement measurements name overlap second
setsNodes size top 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
DMDselection 4.92 0.17 5.09
runTests 2.15 0.22 40.64
distribution 1.73 0.17 26.56
selectionPlot 1.82 0.03 7.75
ClassifyResult-class 1.53 0.20 43.23
previousSelection 1.61 0.03 22.07
previousTrained 1.54 0.05 20.15
rankingPlot 1.15 0.02 8.08
elasticNetGLMinterface 0.87 0.03 17.56
elasticNetFeatures 0.81 0.05 16.52
* 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
'D:/biocbuild/bbs-3.15-bioc/meat/ClassifyR.Rcheck/00check.log'
for details.
ClassifyR.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.15/bioc/src/contrib/ClassifyR_2.15.1.tar.gz && rm -rf ClassifyR.buildbin-libdir && mkdir ClassifyR.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=ClassifyR.buildbin-libdir ClassifyR_2.15.1.tar.gz && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL ClassifyR_2.15.1.zip && rm ClassifyR_2.15.1.tar.gz ClassifyR_2.15.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1009k 100 1009k 0 0 2427k 0 --:--:-- --:--:-- --:--:-- 2427k
* installing *source* package 'ClassifyR' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'ClassifyR'
finding HTML links ... done
ClassifyResult-class html
finding level-2 HTML links ... done
DLDAinterface html
DMDselection html
EasyHardClassifier-class html
FeatureSetCollection-class html
FeatureSetCollectionOrNULL-class html
KolmogorovSmirnovSelection html
KullbackLeiblerSelection html
MixModelsListsSet-class html
NSCpredictInterface html
NSCselectionInterface html
NSCtrainInterface html
PredictParams-class html
ROCplot html
ResubstituteParams-class html
SVMinterface html
SelectParams-class html
SelectResult-class html
TrainParams-class html
TransformParams-class html
asthmaDataset html
bartlettSelection html
calcPerformance html
characterOrDataFrame-class html
classifyInterface html
differentMeansSelection html
distribution html
dlda-class html
easyHardClassifier html
REDIRECT:topic Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/meat/ClassifyR.buildbin-libdir/00LOCK-ClassifyR/00new/ClassifyR/help/easyHardClassifier.html
easyHardFeatures html
edgeRselection html
edgesToHubNetworks html
elasticNetFeatures html
elasticNetGLMinterface html
featureSetSummary html
fisherDiscriminant html
forestFeatures html
functionOrList-class html
functionOrNULL-class html
getLocationsAndScales html
integerOrNumeric-class html
interactorDifferences html
kTSPclassifier html
knnInterface html
leveneSelection html
likelihoodRatioSelection html
limmaSelection html
listOrCharacterOrNULL-class html
listOrNULL-class html
mixmodels html
multnet-class html
naiveBayesKernel html
networkCorrelationsSelection html
pairsDifferencesSelection html
pamrtrained-class html
performancePlot html
plotFeatureClasses html
previousSelection html
previousTrained html
randomForest-class html
randomForestInterface html
rankingPlot html
runTest html
runTests html
samplesMetricMap html
selectionPlot html
subtractFromLocation html
svm-class html
** 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
* MD5 sums
packaged installation of 'ClassifyR' as ClassifyR_2.15.1.zip
* DONE (ClassifyR)
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
package 'ClassifyR' successfully unpacked and MD5 sums checked
ClassifyR.Rcheck/ClassifyR-Ex.timings
| name | user | system | elapsed | |
| ClassifyResult-class | 1.53 | 0.20 | 43.23 | |
| DLDAinterface | 0.05 | 0.00 | 0.05 | |
| DMDselection | 4.92 | 0.17 | 5.09 | |
| EasyHardClassifier-class | 0.01 | 0.00 | 0.02 | |
| FeatureSetCollection-class | 0 | 0 | 0 | |
| FeatureSetCollectionOrNULL-class | 0.04 | 0.00 | 0.03 | |
| KolmogorovSmirnovSelection | 1.42 | 0.02 | 1.43 | |
| KullbackLeiblerSelection | 0.61 | 0.00 | 0.61 | |
| MixModelsListsSet-class | 0.33 | 0.00 | 0.35 | |
| NSCpredictInterface | 0.09 | 0.01 | 0.11 | |
| NSCselectionInterface | 0.05 | 0.00 | 0.04 | |
| NSCtrainInterface | 0.04 | 0.00 | 0.05 | |
| PredictParams-class | 0.02 | 0.00 | 0.02 | |
| ROCplot | 0.42 | 0.00 | 0.42 | |
| ResubstituteParams-class | 0.02 | 0.00 | 0.01 | |
| SVMinterface | 0.03 | 0.02 | 0.05 | |
| SelectParams-class | 0.04 | 0.00 | 0.05 | |
| SelectResult-class | 0 | 0 | 0 | |
| TrainParams-class | 0 | 0 | 0 | |
| TransformParams-class | 0.02 | 0.00 | 0.01 | |
| bartlettSelection | 1.19 | 0.00 | 1.19 | |
| calcPerformance | 0 | 0 | 0 | |
| characterOrDataFrame-class | 0 | 0 | 0 | |
| classifyInterface | 0.65 | 0.08 | 0.74 | |
| differentMeansSelection | 1.10 | 0.03 | 1.12 | |
| distribution | 1.73 | 0.17 | 26.56 | |
| easyHardClassifier | 0.41 | 0.00 | 0.41 | |
| easyHardFeatures | 0.31 | 0.08 | 0.39 | |
| edgeRselection | 4.36 | 0.09 | 4.48 | |
| edgesToHubNetworks | 0.02 | 0.00 | 0.02 | |
| elasticNetFeatures | 0.81 | 0.05 | 16.52 | |
| elasticNetGLMinterface | 0.87 | 0.03 | 17.56 | |
| featureSetSummary | 0 | 0 | 0 | |
| fisherDiscriminant | 0.03 | 0.02 | 0.04 | |
| forestFeatures | 0.16 | 0.01 | 0.18 | |
| functionOrList-class | 0.03 | 0.00 | 0.03 | |
| functionOrNULL-class | 0.02 | 0.00 | 0.01 | |
| getLocationsAndScales | 0.01 | 0.00 | 0.02 | |
| integerOrNumeric-class | 0.02 | 0.00 | 0.01 | |
| interactorDifferences | 0.03 | 0.00 | 0.04 | |
| kTSPclassifier | 0.06 | 0.00 | 0.06 | |
| knnInterface | 0.03 | 0.00 | 0.03 | |
| leveneSelection | 0.68 | 0.13 | 0.80 | |
| likelihoodRatioSelection | 3.81 | 0.25 | 4.06 | |
| limmaSelection | 0.15 | 0.00 | 0.16 | |
| listOrCharacterOrNULL-class | 0 | 0 | 0 | |
| listOrNULL-class | 0 | 0 | 0 | |
| mixmodels | 0.11 | 0.00 | 0.11 | |
| naiveBayesKernel | 0.36 | 0.00 | 0.36 | |
| networkCorrelationsSelection | 0.14 | 0.00 | 0.14 | |
| pairsDifferencesSelection | 0.13 | 0.00 | 0.13 | |
| performancePlot | 0.26 | 0.00 | 0.26 | |
| plotFeatureClasses | 2.08 | 0.00 | 2.07 | |
| previousSelection | 1.61 | 0.03 | 22.07 | |
| previousTrained | 1.54 | 0.05 | 20.15 | |
| randomForestInterface | 0.33 | 0.00 | 0.33 | |
| rankingPlot | 1.15 | 0.02 | 8.08 | |
| runTest | 1.14 | 0.03 | 1.17 | |
| runTests | 2.15 | 0.22 | 40.64 | |
| samplesMetricMap | 2.68 | 0.00 | 2.69 | |
| selectionPlot | 1.82 | 0.03 | 7.75 | |
| subtractFromLocation | 0 | 0 | 0 | |