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CHECK report for GeneBreak on merida2

This page was generated on 2019-04-09 13:32:16 -0400 (Tue, 09 Apr 2019).

Package 615/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.13.0
Evert van den Broek
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/GeneBreak
Branch: master
Last Commit: 0213223
Last Changed Date: 2018-10-30 11:54:35 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK 

Summary

Package: GeneBreak
Version: 1.13.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneBreak_1.13.0.tar.gz
StartedAt: 2019-04-09 01:03:15 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 01:06:31 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 196.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneBreak.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneBreak_1.13.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneBreak.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.13.0’
* 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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                                 user system elapsed
CopyNumberBreakPointGenes-class                 7.911  0.796   8.749
bpPlot-CopyNumberBreakPoints-method             6.646  0.676   7.370
bpStats-CopyNumberBreakPoints-method            6.435  0.763   7.229
recurrentGenes-CopyNumberBreakPointGenes-method 5.774  0.654   6.465
* 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-3.9-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.



Installation output

GeneBreak.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneBreak
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘GeneBreak’ ...
** R
** data
** byte-compile and prepare 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)

Tests output


Example timings

GeneBreak.Rcheck/GeneBreak-Ex.timings

nameusersystemelapsed
CopyNumberBreakPointGenes-class7.9110.7968.749
CopyNumberBreakPoints-class1.9480.2232.185
accessOptions-CopyNumberBreakPoints-method1.4050.1321.542
addGeneAnnotation-CopyNumberBreakPoints-method2.8860.2353.134
bpFilter-CopyNumberBreakPoints-method1.6430.1941.841
bpGenes-CopyNumberBreakPointGenes-method2.3390.2202.580
bpPlot-CopyNumberBreakPoints-method6.6460.6767.370
bpStats-CopyNumberBreakPoints-method6.4350.7637.229
breakpointData-CopyNumberBreakPoints-method1.5540.5162.080
breakpointsPerGene-CopyNumberBreakPointGenes-method2.6860.6013.305
callData-CopyNumberBreakPoints-method1.7200.5472.276
featureChromosomes-CopyNumberBreakPoints-method0.7140.1430.860
featureInfo-CopyNumberBreakPoints-method3.0330.4093.466
featuresPerGene-CopyNumberBreakPointGenes-method2.4240.2972.728
geneChromosomes-CopyNumberBreakPointGenes-method2.3270.2582.597
geneInfo-CopyNumberBreakPointGenes-method2.1730.3142.494
getBreakpoints1.4830.1851.673
namesFeatures-CopyNumberBreakPoints-method1.0170.1491.171
recurrentGenes-CopyNumberBreakPointGenes-method5.7740.6546.465
sampleNames-CopyNumberBreakPoints-method1.0100.1141.130
segmentData-CopyNumberBreakPoints-method1.5620.5372.104