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BioC 2.14: CHECK report for geNetClassifier on morelia

This page was generated on 2014-10-08 09:06:20 -0700 (Wed, 08 Oct 2014).

Package 328/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.4.0
Sara Aibar
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/geNetClassifier
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: geNetClassifier
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch geNetClassifier_1.4.0.tar.gz
StartedAt: 2014-10-07 23:02:17 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 23:04:49 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 151.2 seconds
RetCode: 0
Status:  OK 
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch geNetClassifier_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.4.0’
* 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 ... [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 ... NOTE
Package in Depends field not imported from: ‘minet’
  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’
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [81s/82s] OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
plot.GeNetClassifierReturn 17.284 18.460  33.295
plotNetwork                11.513 12.151  21.924
GenesNetwork-class          1.267  0.114   6.165
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runTests.R’ [2s/2s]
 [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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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-class1.2750.0561.359
GeneralizationError-class0.5430.0210.564
GenesNetwork-class1.2670.1146.165
GenesRanking-class0.8080.0340.842
calculateGenesRanking0.6370.0290.677
externalValidation.probMatrix1.1840.0391.240
externalValidation.stats1.0950.0421.136
gClasses-methods0.3440.0090.354
geNetClassifier0.2630.0170.280
genesDetails-methods0.5380.0230.560
getEdges-methods0.3480.0140.362
getNodes-methods0.3180.0090.327
getNumEdges-methods0.3440.0100.354
getNumNodes-methods0.3140.0100.324
getRanking-methods0.3750.0110.386
getSubNetwork-methods0.3730.0170.390
getTopRanking-methods0.3460.0130.358
leukemiasClassifier0.4370.0160.451
network2txt0.4650.0220.487
numGenes-methods0.3480.0100.357
numSignificantGenes-methods0.3570.0080.366
overview-methods0.3870.0130.401
plot.GeNetClassifierReturn17.28418.46033.295
plot.GenesRanking0.3600.0150.376
plotAssignments1.0460.0331.080
plotDiscriminantPower0.9220.0620.988
plotExpressionProfiles1.9260.1262.052
plotNetwork11.51312.15121.924
queryGeNetClassifier1.5320.0511.581
querySummary0.9420.0470.988