ClassifyR 1.4.5
Dario Strbenac
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/ClassifyR | | Last Changed Rev: 110123 / Revision: 110496 | | Last Changed Date: 2015-10-31 21:00:09 -0700 (Sat, 31 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ClassifyR_1.4.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/ClassifyR.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.4.5’
* 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 ... [5s/5s] 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 loading without being on the library search path ... 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
distribution,ClassifyResult : .local: no visible binding for global
variable ‘..density..’
errorMap,list : .local: no visible binding for global variable ‘Class’
errorMap,list : .local: no visible binding for global variable ‘name’
errorMap,list : .local: no visible binding for global variable ‘type’
errorMap,list : .local: no visible binding for global variable ‘Error’
mixModelsTest,list-ExpressionSet : .local : <anonymous> : <anonymous>:
no visible binding for global variable ‘classes’
mixModelsTest,list-ExpressionSet : .local : <anonymous> : <anonymous> :
<anonymous> : <anonymous>: no visible binding for global variable
‘largerClass’
mixModelsTest,list-ExpressionSet : .local : <anonymous> : <anonymous> :
<anonymous> : <anonymous>: no visible binding for global variable
‘classes’
naiveBayesKernel,ExpressionSet : .local: no visible binding for global
variable ‘featureValues’
performancePlot,list : .local: no visible binding for global variable
‘Freq’
plotFeatureClasses,ExpressionSet : .local : <anonymous>: no visible
binding for global variable ‘expr’
plotFeatureClasses,ExpressionSet : .local : <anonymous>: no visible
binding for global variable ‘..density..’
selectionPlot,list : .local: no visible binding for global variable
‘Freq’
TrainParams,ANY : .local: no visible binding for global variable ‘dlda’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [161s/144s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ClassifyResult-class 16.350 0.829 15.131
distribution 13.243 0.632 14.131
selectionPlot 8.552 3.960 3.466
runTest 11.839 0.330 12.171
edgeRselection 11.481 0.393 11.924
runTests 9.991 0.217 13.774
DMDselection 9.430 0.184 9.614
KolmogorovSmirnovSelection 9.528 0.055 9.583
likelihoodRatioSelection 9.442 0.021 9.464
KullbackLeiblerSelection 9.261 0.056 9.317
rankingPlot 5.216 2.929 3.815
mixmodels 8.042 0.066 8.191
previousSelection 2.724 1.076 5.843
* 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-3.2-bioc/meat/ClassifyR.Rcheck/00check.log’
for details.
* installing *source* package ‘ClassifyR’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘performance’ in package ‘ClassifyR’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ClassifyR)