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This page was generated on 2021-10-14 12:06:06 -0400 (Thu, 14 Oct 2021).

CHECK results for GeneBreak on merida1

To the developers/maintainers of the GeneBreak package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneBreak.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 706/2056HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.23.0  (landing page)
Evert van den Broek
Snapshot Date: 2021-10-13 14:50:09 -0400 (Wed, 13 Oct 2021)
git_url: https://git.bioconductor.org/packages/GeneBreak
git_branch: master
git_last_commit: c48ff88
git_last_commit_date: 2021-05-19 12:16:21 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneBreak
Version: 1.23.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneBreak_1.23.0.tar.gz
StartedAt: 2021-10-14 03:28:56 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 03:32:45 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 228.5 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/Resources/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GeneBreak_1.23.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GeneBreak.Rcheck’
* using R version 4.1.1 Patched (2021-08-22 r80813)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.23.0’
* 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 (user + system) or elapsed time > 5s
                                                 user system elapsed
CopyNumberBreakPointGenes-class                 8.743  0.664   9.425
bpStats-CopyNumberBreakPoints-method            7.474  0.538   8.021
bpPlot-CopyNumberBreakPoints-method             7.197  0.476   7.684
recurrentGenes-CopyNumberBreakPointGenes-method 6.829  0.510   7.349
* 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-3.14-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.



Installation output

GeneBreak.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GeneBreak
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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-class8.7430.6649.425
CopyNumberBreakPoints-class2.1440.1242.275
accessOptions-CopyNumberBreakPoints-method1.2740.0671.343
addGeneAnnotation-CopyNumberBreakPoints-method2.3220.1082.432
bpFilter-CopyNumberBreakPoints-method2.0410.1082.153
bpGenes-CopyNumberBreakPointGenes-method2.9120.1603.077
bpPlot-CopyNumberBreakPoints-method7.1970.4767.684
bpStats-CopyNumberBreakPoints-method7.4740.5388.021
breakpointData-CopyNumberBreakPoints-method1.6200.7992.523
breakpointsPerGene-CopyNumberBreakPointGenes-method2.7290.8403.600
callData-CopyNumberBreakPoints-method1.6750.9092.680
featureChromosomes-CopyNumberBreakPoints-method0.9040.0850.990
featureInfo-CopyNumberBreakPoints-method2.5550.3482.907
featuresPerGene-CopyNumberBreakPointGenes-method2.3060.1402.450
geneChromosomes-CopyNumberBreakPointGenes-method2.7450.1662.916
geneInfo-CopyNumberBreakPointGenes-method2.1400.1742.358
getBreakpoints1.7270.0601.789
namesFeatures-CopyNumberBreakPoints-method1.0800.0791.160
recurrentGenes-CopyNumberBreakPointGenes-method6.8290.5107.349
sampleNames-CopyNumberBreakPoints-method1.2260.0621.291
segmentData-CopyNumberBreakPoints-method1.7190.8822.652