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BioC 3.5: CHECK report for GeneBreak on oaxaca

This page was generated on 2017-03-04 16:50:51 -0500 (Sat, 04 Mar 2017).

Package 490/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.5.0
Evert van den Broek
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GeneBreak
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: GeneBreak
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GeneBreak_1.5.0.tar.gz
StartedAt: 2017-03-04 03:16:29 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 03:20:05 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 215.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneBreak.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 GeneBreak_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GeneBreak.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneBreak/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneBreak’ version ‘1.5.0’
* 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 ‘GeneBreak’ can be installed ... 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.glmbreak: no visible global function definition for ‘glm’
.glmbreak: no visible global function definition for ‘predict’
addGeneAnnotation,CopyNumberBreakPoints: no visible global function
  definition for ‘head’
bpStats,CopyNumberBreakPoints: no visible global function definition
  for ‘sd’
bpStats,CopyNumberBreakPoints: no visible global function definition
  for ‘p.adjust’
Undefined global functions or variables:
  glm head p.adjust predict sd
Consider adding
  importFrom("stats", "glm", "p.adjust", "predict", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
* 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 ... OK
Examples with CPU or elapsed time > 5s
                                                 user system elapsed
CopyNumberBreakPointGenes-class                 9.252  1.034  10.303
bpPlot-CopyNumberBreakPoints-method             7.876  1.018   8.945
bpStats-CopyNumberBreakPoints-method            6.587  0.915   7.512
recurrentGenes-CopyNumberBreakPointGenes-method 5.168  0.775   5.968
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.


GeneBreak.Rcheck/00install.out:

* installing *source* package ‘GeneBreak’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘segmentData’ in package ‘GeneBreak’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GeneBreak)

GeneBreak.Rcheck/GeneBreak-Ex.timings:

nameusersystemelapsed
CopyNumberBreakPointGenes-class 9.252 1.03410.303
CopyNumberBreakPoints-class2.3850.2252.633
accessOptions-CopyNumberBreakPoints-method1.4740.1491.625
addGeneAnnotation-CopyNumberBreakPoints-method2.8870.2583.145
bpFilter-CopyNumberBreakPoints-method1.7320.1902.230
bpGenes-CopyNumberBreakPointGenes-method3.3770.2683.646
bpPlot-CopyNumberBreakPoints-method7.8761.0188.945
bpStats-CopyNumberBreakPoints-method6.5870.9157.512
breakpointData-CopyNumberBreakPoints-method1.5910.3952.897
breakpointsPerGene-CopyNumberBreakPointGenes-method2.6770.4054.402
callData-CopyNumberBreakPoints-method1.2970.2992.016
featureChromosomes-CopyNumberBreakPoints-method0.9240.1051.380
featureInfo-CopyNumberBreakPoints-method2.9050.2883.912
featuresPerGene-CopyNumberBreakPointGenes-method2.5860.2373.279
geneChromosomes-CopyNumberBreakPointGenes-method2.8910.2423.138
geneInfo-CopyNumberBreakPointGenes-method2.8240.2493.131
getBreakpoints2.0860.1812.268
namesFeatures-CopyNumberBreakPoints-method0.9610.0951.141
recurrentGenes-CopyNumberBreakPointGenes-method5.1680.7755.968
sampleNames-CopyNumberBreakPoints-method0.9180.1051.147
segmentData-CopyNumberBreakPoints-method1.4760.3072.500