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BioC 2.13: CHECK report for geNetClassifier on perceval

This page was generated on 2014-04-05 09:53:05 -0700 (Sat, 05 Apr 2014).

Package 292/750HostnameOS / ArchBUILDCHECKBUILD BIN
geNetClassifier 1.2.0
Sara Aibar
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/geNetClassifier
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: geNetClassifier
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch geNetClassifier_1.2.0.tar.gz
StartedAt: 2014-04-05 01:32:26 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 01:35:56 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 209.7 seconds
RetCode: 0
Status:  OK 
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.0’
* 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 ‘geNetClassifier’ can be installed ... [7s/7s] 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 ... NOTE
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘EBarrays’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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’
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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘geNetClassifier-manual.pdf’ from 287Kb to 179Kb
  consider running tools::compactPDF() on these files
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [113s/117s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plot.GeNetClassifierReturn 23.30 26.910  51.881
plotNetwork                15.61 16.724  32.899
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [3s/3s]
 [4s/4s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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-class2.0500.1232.281
GeneralizationError-class0.7080.0750.797
GenesNetwork-class1.8010.2572.157
GenesRanking-class1.2160.0981.384
calculateGenesRanking0.7960.0940.921
externalValidation.probMatrix1.7400.1081.929
externalValidation.stats1.7510.1181.881
gClasses-methods0.3130.0270.343
geNetClassifier0.3890.0590.460
genesDetails-methods0.5510.0570.654
getEdges-methods0.3160.0330.389
getNodes-methods0.3110.0350.377
getNumEdges-methods0.3220.0310.355
getNumNodes-methods0.3170.0250.349
getRanking-methods0.3860.0470.492
getSubNetwork-methods0.3560.0390.408
getTopRanking-methods0.3430.0300.390
leukemiasClassifier0.4420.0560.504
network2txt0.5070.0500.578
numGenes-methods0.3320.0350.370
numSignificantGenes-methods0.5240.0400.566
overview-methods0.4050.0420.452
plot.GeNetClassifierReturn23.30026.91051.881
plot.GenesRanking0.3910.0420.474
plotAssignments1.6060.1091.726
plotDiscriminantPower1.0550.1231.205
plotExpressionProfiles2.5300.2532.857
plotNetwork15.61016.72432.899
queryGeNetClassifier2.4630.1692.806
querySummary1.3920.1241.659