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CHECK report for GeneBreak on merida2

This page was generated on 2018-10-17 08:55:31 -0400 (Wed, 17 Oct 2018).

Package 561/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.10.0
Evert van den Broek
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/GeneBreak
Branch: RELEASE_3_7
Last Commit: 1a55884
Last Changed Date: 2018-04-30 10:35:38 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneBreak
Version: 1.10.0
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_1.10.0.tar.gz
StartedAt: 2018-10-16 21:33:38 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:36:44 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 186.2 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_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/GeneBreak.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.10.0’
* 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 ‘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                 7.733  0.733   8.501
bpStats-CopyNumberBreakPoints-method            6.101  0.697   6.820
bpPlot-CopyNumberBreakPoints-method             6.049  0.582   6.664
recurrentGenes-CopyNumberBreakPointGenes-method 5.929  0.695   6.652
* 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-3.7-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/3.5/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-class7.7330.7338.501
CopyNumberBreakPoints-class1.6240.1791.806
accessOptions-CopyNumberBreakPoints-method0.9300.1401.074
addGeneAnnotation-CopyNumberBreakPoints-method1.9530.2512.212
bpFilter-CopyNumberBreakPoints-method1.3970.2301.636
bpGenes-CopyNumberBreakPointGenes-method2.3710.2472.627
bpPlot-CopyNumberBreakPoints-method6.0490.5826.664
bpStats-CopyNumberBreakPoints-method6.1010.6976.820
breakpointData-CopyNumberBreakPoints-method1.5810.5312.122
breakpointsPerGene-CopyNumberBreakPointGenes-method2.5680.6413.216
callData-CopyNumberBreakPoints-method1.6030.4912.103
featureChromosomes-CopyNumberBreakPoints-method0.9720.1571.137
featureInfo-CopyNumberBreakPoints-method2.4180.3082.734
featuresPerGene-CopyNumberBreakPointGenes-method2.4730.2392.725
geneChromosomes-CopyNumberBreakPointGenes-method2.0790.2542.343
geneInfo-CopyNumberBreakPointGenes-method2.0720.2632.342
getBreakpoints1.6730.1981.877
namesFeatures-CopyNumberBreakPoints-method0.9540.1171.081
recurrentGenes-CopyNumberBreakPointGenes-method5.9290.6956.652
sampleNames-CopyNumberBreakPoints-method0.6860.1380.827
segmentData-CopyNumberBreakPoints-method1.7900.4472.245