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BioC 3.1: CHECK report for geNetClassifier on morelia

This page was generated on 2015-10-09 09:40:53 -0700 (Fri, 09 Oct 2015).

Package 387/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geNetClassifier 1.8.2
Sara Aibar
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/geNetClassifier
Last Changed Rev: 107483 / Revision: 109384
Last Changed Date: 2015-08-16 04:37:40 -0700 (Sun, 16 Aug 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: geNetClassifier
Version: 1.8.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings geNetClassifier_1.8.2.tar.gz
StartedAt: 2015-10-09 02:14:23 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 02:15:53 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 90.1 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 geNetClassifier_1.8.2.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/geNetClassifier.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.8.2’
* 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 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 ... [30s/40s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
plot.GeNetClassifierReturn 5.825  0.600   6.602
GenesNetwork-class         1.252  0.158  10.010
* 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
  ‘/Users/biocbuild/bbs-3.1-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-class0.8050.0490.886
GeneralizationError-class0.3980.0190.417
GenesNetwork-class 1.252 0.15810.010
GenesRanking-class0.7250.0580.781
calculateGenesRanking0.5870.0530.640
externalValidation.probMatrix1.0120.0831.131
externalValidation.stats0.8520.0750.926
gClasses-methods0.2630.0130.277
geNetClassifier0.2070.0140.220
geneSymbols0.0660.0010.066
genesDetails-methods0.4820.0300.511
getEdges-methods0.2940.0430.337
getNodes-methods0.2670.0070.274
getNumEdges-methods0.3050.0310.336
getNumNodes-methods0.3210.0260.347
getRanking-methods0.3920.0080.399
getSubNetwork-methods0.3860.0110.396
getTopRanking-methods0.3170.0300.348
leukemiasClassifier0.3800.0160.395
network2txt0.4080.0280.437
numGenes-methods0.3190.0230.343
numSignificantGenes-methods0.3020.0150.317
overview-methods0.3450.0130.358
plot.GeNetClassifierReturn5.8250.6006.602
plot.GenesRanking0.3190.0120.331
plotAssignments1.0160.0621.076
plotDiscriminantPower0.7670.0930.864
plotExpressionProfiles1.3680.1332.567
plotNetwork4.0340.3834.406
queryGeNetClassifier1.3300.0841.412
querySummary0.9360.0861.021