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CHECK report for GeneBreak on celaya2

This page was generated on 2019-10-16 12:56:37 -0400 (Wed, 16 Oct 2019).

Package 624/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.14.0
Evert van den Broek
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/GeneBreak
Branch: RELEASE_3_9
Last Commit: 116ace4
Last Changed Date: 2019-05-02 11:53:58 -0400 (Thu, 02 May 2019)
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

Summary

Package: GeneBreak
Version: 1.14.0
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_1.14.0.tar.gz
StartedAt: 2019-10-16 03:02:27 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:06:54 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 266.2 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_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneBreak.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.14.0’
* 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                     10.507  1.982  12.495
bpPlot-CopyNumberBreakPoints-method                  8.433  1.818  10.259
bpStats-CopyNumberBreakPoints-method                 7.894  1.713   9.619
recurrentGenes-CopyNumberBreakPointGenes-method      7.567  1.619   9.187
breakpointsPerGene-CopyNumberBreakPointGenes-method  3.694  1.324   5.019
* 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:
###
###   /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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeneBreak)

Tests output


Example timings

GeneBreak.Rcheck/GeneBreak-Ex.timings

nameusersystemelapsed
CopyNumberBreakPointGenes-class10.507 1.98212.495
CopyNumberBreakPoints-class2.3090.3432.652
accessOptions-CopyNumberBreakPoints-method1.3790.2171.596
addGeneAnnotation-CopyNumberBreakPoints-method2.8770.3943.273
bpFilter-CopyNumberBreakPoints-method1.7760.3432.119
bpGenes-CopyNumberBreakPointGenes-method3.0010.4363.437
bpPlot-CopyNumberBreakPoints-method 8.433 1.81810.259
bpStats-CopyNumberBreakPoints-method7.8941.7139.619
breakpointData-CopyNumberBreakPoints-method2.2361.0973.336
breakpointsPerGene-CopyNumberBreakPointGenes-method3.6941.3245.019
callData-CopyNumberBreakPoints-method2.2850.9643.251
featureChromosomes-CopyNumberBreakPoints-method1.4600.2561.715
featureInfo-CopyNumberBreakPoints-method3.4290.6904.123
featuresPerGene-CopyNumberBreakPointGenes-method3.0930.4103.508
geneChromosomes-CopyNumberBreakPointGenes-method2.7520.4983.252
geneInfo-CopyNumberBreakPointGenes-method2.6000.4713.072
getBreakpoints2.0820.3752.457
namesFeatures-CopyNumberBreakPoints-method1.1540.2751.428
recurrentGenes-CopyNumberBreakPointGenes-method7.5671.6199.187
sampleNames-CopyNumberBreakPoints-method1.6980.2661.965
segmentData-CopyNumberBreakPoints-method2.0770.9543.031