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BioC 3.2: CHECK report for geNetClassifier on zin1

This page was generated on 2016-04-23 10:13:00 -0700 (Sat, 23 Apr 2016).

Package 412/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.10.0
Sara Aibar
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/geNetClassifier
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: geNetClassifier
Version: 1.10.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.10.0.tar.gz
StartedAt: 2016-04-23 01:00:32 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 01:01:35 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 62.6 seconds
RetCode: 0
Status:  OK 
CheckDir: geNetClassifier.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings geNetClassifier_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-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 ‘1.10.0’
* 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 ... [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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plot.GeNetClassifierReturn 5.033  0.145   5.202
* 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

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-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-class0.8630.0600.931
GeneralizationError-class0.5010.0120.513
GenesNetwork-class1.0940.0721.169
GenesRanking-class0.6930.0040.696
calculateGenesRanking0.5090.0080.516
externalValidation.probMatrix0.7280.0080.735
externalValidation.stats0.6800.0040.682
gClasses-methods0.2550.0000.257
geNetClassifier0.2430.0090.250
geneSymbols0.0790.0000.078
genesDetails-methods0.4310.0000.431
getEdges-methods0.2640.0030.267
getNodes-methods0.2940.0000.294
getNumEdges-methods0.3010.0000.300
getNumNodes-methods0.2980.0000.298
getRanking-methods0.3370.0080.345
getSubNetwork-methods0.3960.0040.400
getTopRanking-methods0.2920.0000.292
leukemiasClassifier0.3230.0080.333
network2txt0.3370.0120.348
numGenes-methods0.2600.0000.259
numSignificantGenes-methods0.2970.0080.305
overview-methods0.3510.0040.355
plot.GeNetClassifierReturn5.0330.1455.202
plot.GenesRanking0.3150.0000.315
plotAssignments0.7320.0080.744
plotDiscriminantPower0.7150.0200.734
plotExpressionProfiles1.0980.0241.117
plotNetwork3.4530.0933.521
queryGeNetClassifier0.9940.0281.022
querySummary0.7440.0040.757