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BioC 3.4: CHECK report for Rmagpie on malbec1

This page was generated on 2017-04-15 16:09:53 -0400 (Sat, 15 Apr 2017).

Package 1056/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Rmagpie 1.30.0
Camille Maumet
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/Rmagpie
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Rmagpie
Version: 1.30.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rmagpie_1.30.0.tar.gz
StartedAt: 2017-04-15 00:57:55 -0400 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:59:16 -0400 (Sat, 15 Apr 2017)
EllapsedTime: 80.5 seconds
RetCode: 0
Status:  OK 
CheckDir: Rmagpie.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings Rmagpie_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/Rmagpie.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rmagpie/DESCRIPTION’ ... OK
* this is package ‘Rmagpie’ version ‘1.30.0’
* 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 ‘Rmagpie’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
A package should be listed in only one of these fields.
* 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
twoLayerExtCV: warning in performAValidation(data = eset, trainIndices
  = extInds[[i]], noGenes = upToBestSelectedFeature, classes = classes,
  classifierName = classifierName, verbose = verbose, kernel = kernel,
  featureSelectionFun = featureSelectionFun, trainTestFun =
  trainTestFun): partial argument match of 'data' to 'dataset'
getFeatureSelectionOptions<-,assessment: no visible global function
  definition for ‘getNoOfOptions<-’
getFeatureSelectionOptions<-,assessment: no visible global function
  definition for ‘getNoModels<-’
Undefined global functions or variables:
  getNoModels<- getNoOfOptions<-
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
runTwoLayerExtCV-methods 6.504  0.008    6.52
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/Rmagpie.Rcheck/00check.log’
for details.


Rmagpie.Rcheck/00install.out:

* installing *source* package ‘Rmagpie’ ...
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rmagpie)

Rmagpie.Rcheck/Rmagpie-Ex.timings:

nameusersystemelapsed
classifyNewSamples-methods0.9160.0040.919
experiment-class0.0320.0000.032
finalClassifier-class0.0400.0040.046
findFinalClassifier-methods0.0880.0040.092
geneSubsets-class0.0000.0040.005
getDataset-methods0.0080.0000.008
getFeatureSelectionOptions-methods0.0080.0000.007
getFinalClassifier0.1360.0240.159
getResults-methods3.1960.0163.215
plotErrorsFoldTwoLayerCV-methods3.3920.0043.402
plotErrorsRepeatedOneLayerCV0.6560.0000.657
plotErrorsSummaryOneLayerCV-methods0.6320.0000.631
rankedGenesImg-methods0.0000.0000.001
runOneLayerExtCV-methods0.5880.0000.589
runTwoLayerExtCV-methods6.5040.0086.520
setDataset-methods0.0040.0000.000
setFeatureSelectionOptions-methods0.0040.0000.007
thresholds-class0.0000.0000.001
vV70genes0.0040.0000.003