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This page was generated on 2025-08-28 11:40 -0400 (Thu, 28 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4824
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4604
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4545
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4579
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 805/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.38.0  (landing page)
Evert van den Broek
Snapshot Date: 2025-08-25 13:40 -0400 (Mon, 25 Aug 2025)
git_url: https://git.bioconductor.org/packages/GeneBreak
git_branch: RELEASE_3_21
git_last_commit: 092168b
git_last_commit_date: 2025-04-15 10:55:57 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for GeneBreak on merida1

To the developers/maintainers of the GeneBreak package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: GeneBreak
Version: 1.38.0
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_1.38.0.tar.gz
StartedAt: 2025-08-26 03:53:47 -0400 (Tue, 26 Aug 2025)
EndedAt: 2025-08-26 03:59:12 -0400 (Tue, 26 Aug 2025)
EllapsedTime: 324.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneBreak.Rcheck
Warnings: 0

Command output

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### Running 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_1.38.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/GeneBreak.Rcheck’
* using R version 4.5.1 RC (2025-06-05 r88288)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GeneBreak/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneBreak’ version ‘1.38.0’
* 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 code 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                     10.502  1.022  12.183
bpPlot-CopyNumberBreakPoints-method                  9.402  0.739  10.893
bpStats-CopyNumberBreakPoints-method                 8.787  0.805  10.235
recurrentGenes-CopyNumberBreakPointGenes-method      8.027  0.643   9.549
breakpointsPerGene-CopyNumberBreakPointGenes-method  3.502  2.196   5.913
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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-3.21-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
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘GeneBreak’ ...
** this is package ‘GeneBreak’ version ‘1.38.0’
** 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-class10.502 1.02212.183
CopyNumberBreakPoints-class2.4350.1572.710
accessOptions-CopyNumberBreakPoints-method1.6580.0841.819
addGeneAnnotation-CopyNumberBreakPoints-method2.7000.1562.985
bpFilter-CopyNumberBreakPoints-method1.9150.1692.221
bpGenes-CopyNumberBreakPointGenes-method3.0110.1743.325
bpPlot-CopyNumberBreakPoints-method 9.402 0.73910.893
bpStats-CopyNumberBreakPoints-method 8.787 0.80510.235
breakpointData-CopyNumberBreakPoints-method1.8611.5263.403
breakpointsPerGene-CopyNumberBreakPointGenes-method3.5022.1965.913
callData-CopyNumberBreakPoints-method1.9401.5873.562
featureChromosomes-CopyNumberBreakPoints-method0.9420.1101.065
featureInfo-CopyNumberBreakPoints-method3.1670.5383.751
featuresPerGene-CopyNumberBreakPointGenes-method2.9160.1723.098
geneChromosomes-CopyNumberBreakPointGenes-method2.8870.1503.090
geneInfo-CopyNumberBreakPointGenes-method2.6770.2862.974
getBreakpoints2.3730.1302.544
namesFeatures-CopyNumberBreakPoints-method1.3550.1601.714
recurrentGenes-CopyNumberBreakPointGenes-method8.0270.6439.549
sampleNames-CopyNumberBreakPoints-method1.2870.1061.418
segmentData-CopyNumberBreakPoints-method1.6081.6593.388