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This page was generated on 2021-12-06 13:05:57 -0500 (Mon, 06 Dec 2021).

CHECK results for GeneBreak on machv2

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 719/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.24.0  (landing page)
Evert van den Broek
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/GeneBreak
git_branch: RELEASE_3_14
git_last_commit: 99d931d
git_last_commit_date: 2021-10-26 12:23:22 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: GeneBreak
Version: 1.24.0
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_1.24.0.tar.gz
StartedAt: 2021-12-05 14:49:48 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 14:53:46 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 237.7 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_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/GeneBreak.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.24.0’
* 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                 8.872  0.720   9.602
bpStats-CopyNumberBreakPoints-method            7.289  0.466   7.765
bpPlot-CopyNumberBreakPoints-method             7.190  0.533   7.771
recurrentGenes-CopyNumberBreakPointGenes-method 6.960  0.498   7.467
* 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-class8.8720.7209.602
CopyNumberBreakPoints-class2.2790.1382.419
accessOptions-CopyNumberBreakPoints-method1.3190.0721.392
addGeneAnnotation-CopyNumberBreakPoints-method2.3740.1252.501
bpFilter-CopyNumberBreakPoints-method2.0850.1252.211
bpGenes-CopyNumberBreakPointGenes-method2.6700.1602.833
bpPlot-CopyNumberBreakPoints-method7.1900.5337.771
bpStats-CopyNumberBreakPoints-method7.2890.4667.765
breakpointData-CopyNumberBreakPoints-method1.2460.8642.156
breakpointsPerGene-CopyNumberBreakPointGenes-method2.7200.9713.751
callData-CopyNumberBreakPoints-method1.6630.9052.592
featureChromosomes-CopyNumberBreakPoints-method1.2790.0841.365
featureInfo-CopyNumberBreakPoints-method2.7180.3333.056
featuresPerGene-CopyNumberBreakPointGenes-method2.9950.1243.149
geneChromosomes-CopyNumberBreakPointGenes-method2.6110.1492.762
geneInfo-CopyNumberBreakPointGenes-method2.5430.2042.750
getBreakpoints1.8880.1162.005
namesFeatures-CopyNumberBreakPoints-method1.2340.0991.334
recurrentGenes-CopyNumberBreakPointGenes-method6.9600.4987.467
sampleNames-CopyNumberBreakPoints-method0.9600.0551.015
segmentData-CopyNumberBreakPoints-method1.5900.8922.570