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BioC 3.0: CHECK report for geNetClassifier on zin1

This page was generated on 2015-04-10 09:40:46 -0700 (Fri, 10 Apr 2015).

Package 358/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.6.3
Sara Aibar
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/geNetClassifier
Last Changed Rev: 96057 / Revision: 102249
Last Changed Date: 2014-10-27 06:54:40 -0700 (Mon, 27 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  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 

Summary

Package: geNetClassifier
Version: 1.6.3
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.6.3.tar.gz
StartedAt: 2015-04-10 00:18:49 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:20:12 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 82.3 seconds
RetCode: 0
Status:  OK 
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.6.3.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘geNetClassifier/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘geNetClassifier’ version ‘1.6.3’
* 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 ‘geNetClassifier’ can be installed ... [4s/4s] 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 ... NOTE
'library' or 'require' calls in package code:
  ‘RColorBrewer’ ‘igraph’ ‘infotheo’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calculateGenesRanking: no visible global function definition for
  ‘brewer.pal’
plotAssignments: no visible binding for global variable ‘coordinates’
plotErrorNumGenes: no visible global function definition for
  ‘brewer.pal’
plotNetwork: no visible global function definition for
  ‘graph.data.frame’
plotNetwork: no visible global function definition for ‘vcount’
plotNetwork: no visible global function definition for
  ‘layout.fruchterman.reingold’
plotNetwork: no visible global function definition for
  ‘get.vertex.attribute’
plotNetwork: no visible global function definition for
  ‘get.edge.attribute’
plotNetwork: no visible global function definition for ‘ecount’
plotNetwork: no visible global function definition for ‘tkplot’
* 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 ... [30s/31s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plot.GeNetClassifierReturn 7.573  0.172   8.117
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [1s/1s]
 [2s/2s] OK
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/geNetClassifier.Rcheck/00check.log’
for details.

geNetClassifier.Rcheck/00install.out:

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

geNetClassifier.Rcheck/geNetClassifier-Ex.timings:

nameusersystemelapsed
GeNetClassifierReturn-class1.0400.0281.101
GeneralizationError-class0.500.020.53
GenesNetwork-class1.1480.0521.473
GenesRanking-class0.7120.0080.729
calculateGenesRanking0.5440.0160.571
externalValidation.probMatrix1.0840.0121.110
externalValidation.stats0.9400.0200.986
gClasses-methods0.3000.0040.351
geNetClassifier0.2400.0000.253
geneSymbols0.0760.0040.081
genesDetails-methods0.4640.0000.467
getEdges-methods0.2960.0080.345
getNodes-methods0.2920.0040.300
getNumEdges-methods0.3000.0000.297
getNumNodes-methods0.3000.0040.307
getRanking-methods0.3560.0000.360
getSubNetwork-methods0.2960.0000.295
getTopRanking-methods0.2680.0000.275
leukemiasClassifier0.3320.0120.343
network2txt0.3840.0080.392
numGenes-methods0.2600.0080.267
numSignificantGenes-methods0.2680.0080.275
overview-methods0.3280.0000.326
plot.GeNetClassifierReturn7.5730.1728.117
plot.GenesRanking0.2760.0080.285
plotAssignments0.8160.0160.833
plotDiscriminantPower0.7800.0200.801
plotExpressionProfiles1.4160.0361.485
plotNetwork4.3440.1284.699
queryGeNetClassifier1.3400.0121.393
querySummary0.8400.0120.854