ClassifyR 1.5.3
Dario Strbenac
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ClassifyR | | Last Changed Rev: 109901 / Revision: 109948 | | Last Changed Date: 2015-10-25 02:00:12 -0400 (Sun, 25 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |  |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ClassifyR_1.5.3.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ClassifyR.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘1.5.3’
* 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 ... [3s/3s] 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
TrainParams,ANY: no visible binding for global variable ‘dlda’
distribution,ClassifyResult: no visible binding for global variable
‘..density..’
errorMap,list: no visible binding for global variable ‘Class’
errorMap,list: no visible binding for global variable ‘name’
errorMap,list: no visible binding for global variable ‘type’
errorMap,list: no visible binding for global variable ‘Error’
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous>: no
visible binding for global variable ‘classes’
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
<anonymous> : <anonymous>: no visible binding for global variable
‘largerClass’
mixModelsTest,list-ExpressionSet : <anonymous> : <anonymous> :
<anonymous> : <anonymous>: no visible binding for global variable
‘classes’
naiveBayesKernel,ExpressionSet: no visible binding for global variable
‘featureValues’
performancePlot,list: no visible binding for global variable ‘Freq’
plotFeatureClasses,ExpressionSet : <anonymous>: no visible binding for
global variable ‘expr’
plotFeatureClasses,ExpressionSet : <anonymous>: no visible binding for
global variable ‘..density..’
selectionPlot,list: no visible binding for global variable ‘Freq’
Undefined global functions or variables:
..density.. Class Error Freq classes dlda expr featureValues
largerClass name type
* 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 ... [105s/96s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
distribution 11.260 0.376 9.512
DMDselection 7.923 0.068 7.995
selectionPlot 6.814 1.168 2.141
ClassifyResult-class 7.700 0.177 8.353
runTest 7.670 0.128 7.807
likelihoodRatioSelection 7.403 0.000 7.409
KullbackLeiblerSelection 7.296 0.000 7.300
edgeRselection 7.134 0.068 7.218
runTests 6.671 0.100 9.166
KolmogorovSmirnovSelection 6.692 0.004 6.702
* 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-3.3-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)