Dario Strbenac
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/ClassifyR |
| Branch: RELEASE_3_8 |
| Last Commit: f4f1b0a |
| Last Changed Date: 2019-02-14 20:45:02 -0400 (Thu, 14 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:57:51 -0400 (Tue, 16 Apr 2019).
| Package 266/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ClassifyR 2.2.6 Dario Strbenac
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ClassifyR |
| Version: 2.2.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClassifyR_2.2.6.tar.gz |
| StartedAt: 2019-04-15 23:01:19 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 23:06:59 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 339.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ClassifyR.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ClassifyR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ClassifyR_2.2.6.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/ClassifyR.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.2.6’
* 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’
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’
runTests,DataFrame: no visible binding for global variable ‘setsNodes’
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.. 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 or elapsed time > 5s
user system elapsed
ClassifyResult-class 125.399 6.026 34.700
elasticNetFeatures 46.346 3.809 19.116
elasticNetGLMinterface 45.682 3.694 19.061
runTests 20.574 8.129 9.732
distribution 20.664 6.075 9.709
likelihoodRatioSelection 9.013 0.288 9.414
DMDselection 7.160 0.199 7.435
samplesMetricMap 6.382 0.523 6.971
previousTrained 4.180 2.435 3.325
previousSelection 4.197 2.360 3.297
edgeRselection 5.950 0.329 6.346
* 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
‘/Users/biocbuild/bbs-3.8-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.
ClassifyR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ClassifyR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘ClassifyR’ ... ** 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 * DONE (ClassifyR)
ClassifyR.Rcheck/ClassifyR-Ex.timings
| name | user | system | elapsed | |
| ClassifyResult-class | 125.399 | 6.026 | 34.700 | |
| DLDAinterface | 0.624 | 0.108 | 0.734 | |
| DMDselection | 7.160 | 0.199 | 7.435 | |
| FeatureSetCollection-class | 0.006 | 0.000 | 0.007 | |
| FeatureSetCollectionOrNULL-class | 0.003 | 0.000 | 0.003 | |
| KolmogorovSmirnovSelection | 2.637 | 0.037 | 2.701 | |
| KullbackLeiblerSelection | 1.450 | 0.026 | 1.484 | |
| NSCpredictInterface | 0.146 | 0.011 | 0.158 | |
| NSCselectionInterface | 0.103 | 0.007 | 0.110 | |
| NSCtrainInterface | 0.090 | 0.004 | 0.094 | |
| PredictParams-class | 0.003 | 0.001 | 0.003 | |
| ROCplot | 0.949 | 0.008 | 0.968 | |
| ResubstituteParams-class | 0.002 | 0.000 | 0.003 | |
| SVMinterface | 0.078 | 0.004 | 0.083 | |
| SelectParams-class | 0.009 | 0.001 | 0.011 | |
| SelectResult-class | 0.001 | 0.001 | 0.002 | |
| TrainParams-class | 0.001 | 0.000 | 0.001 | |
| TransformParams-class | 0.002 | 0.000 | 0.003 | |
| bartlettSelection | 2.081 | 0.008 | 2.110 | |
| calcPerformance | 0.003 | 0.000 | 0.003 | |
| characterOrDataFrame-class | 0.010 | 0.000 | 0.011 | |
| classifyInterface | 0.663 | 0.099 | 0.771 | |
| differentMeansSelection | 1.789 | 0.036 | 1.848 | |
| distribution | 20.664 | 6.075 | 9.709 | |
| edgeRselection | 5.950 | 0.329 | 6.346 | |
| edgesToHubNetworks | 0.002 | 0.001 | 0.003 | |
| elasticNetFeatures | 46.346 | 3.809 | 19.116 | |
| elasticNetGLMinterface | 45.682 | 3.694 | 19.061 | |
| featureSetSummary | 0.008 | 0.006 | 0.014 | |
| fisherDiscriminant | 0.124 | 0.027 | 0.152 | |
| forestFeatures | 0.282 | 0.046 | 0.331 | |
| functionOrList-class | 0.011 | 0.002 | 0.013 | |
| functionOrNULL-class | 0.006 | 0.000 | 0.008 | |
| getLocationsAndScales | 0.049 | 0.005 | 0.055 | |
| integerOrNumeric-class | 0.020 | 0.003 | 0.024 | |
| interactorDifferences | 0.058 | 0.006 | 0.064 | |
| kTSPclassifier | 0.135 | 0.013 | 0.149 | |
| knnInterface | 0.043 | 0.004 | 0.050 | |
| leveneSelection | 2.145 | 0.164 | 2.340 | |
| likelihoodRatioSelection | 9.013 | 0.288 | 9.414 | |
| limmaSelection | 0.658 | 0.005 | 0.682 | |
| mixmodels | 0.765 | 0.020 | 0.806 | |
| naiveBayesKernel | 0.656 | 0.007 | 0.672 | |
| networkCorrelationsSelection | 0.297 | 0.001 | 0.303 | |
| pairsDifferencesSelection | 0.340 | 0.001 | 0.343 | |
| performancePlot | 0.368 | 0.005 | 0.381 | |
| plotFeatureClasses | 3.618 | 0.025 | 3.676 | |
| previousSelection | 4.197 | 2.360 | 3.297 | |
| previousTrained | 4.180 | 2.435 | 3.325 | |
| randomForestInterface | 0.278 | 0.059 | 0.341 | |
| rankingPlot | 2.837 | 0.413 | 3.196 | |
| runTest | 0.885 | 0.032 | 0.924 | |
| runTests | 20.574 | 8.129 | 9.732 | |
| samplesMetricMap | 6.382 | 0.523 | 6.971 | |
| selectionPlot | 3.333 | 0.371 | 3.663 | |
| subtractFromLocation | 0.002 | 0.001 | 0.004 | |