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CHECK report for GeneBreak on malbec2

This page was generated on 2020-10-17 11:54:49 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GeneBreak PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 676/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.18.0
Evert van den Broek
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GeneBreak
Branch: RELEASE_3_11
Last Commit: 622fa51
Last Changed Date: 2020-04-27 14:52:15 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneBreak
Version: 1.18.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GeneBreak_1.18.0.tar.gz
StartedAt: 2020-10-17 01:34:40 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:37:37 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 177.1 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneBreak.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings GeneBreak_1.18.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/GeneBreak.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.18.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                      user system elapsed
CopyNumberBreakPointGenes-class      7.460  0.108   7.568
bpStats-CopyNumberBreakPoints-method 5.598  0.016   5.613
* 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
  ‘/home/biocbuild/bbs-3.11-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.



Installation output

GeneBreak.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL GeneBreak
###
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/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-class7.4600.1087.568
CopyNumberBreakPoints-class1.5260.0721.599
accessOptions-CopyNumberBreakPoints-method1.0520.0081.059
addGeneAnnotation-CopyNumberBreakPoints-method1.6160.0121.628
bpFilter-CopyNumberBreakPoints-method1.1220.0121.134
bpGenes-CopyNumberBreakPointGenes-method1.7490.0241.772
bpPlot-CopyNumberBreakPoints-method4.6250.0444.669
bpStats-CopyNumberBreakPoints-method5.5980.0165.613
breakpointData-CopyNumberBreakPoints-method1.2820.1481.429
breakpointsPerGene-CopyNumberBreakPointGenes-method1.9000.1442.044
callData-CopyNumberBreakPoints-method1.5600.1681.728
featureChromosomes-CopyNumberBreakPoints-method0.8070.0160.824
featureInfo-CopyNumberBreakPoints-method1.7670.0561.823
featuresPerGene-CopyNumberBreakPointGenes-method1.8100.0161.826
geneChromosomes-CopyNumberBreakPointGenes-method1.5730.0241.597
geneInfo-CopyNumberBreakPointGenes-method1.4410.0361.476
getBreakpoints1.5790.0281.607
namesFeatures-CopyNumberBreakPoints-method1.0620.0321.094
recurrentGenes-CopyNumberBreakPointGenes-method4.8020.0524.854
sampleNames-CopyNumberBreakPoints-method0.6540.0280.682
segmentData-CopyNumberBreakPoints-method1.3150.1881.503