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This page was generated on 2025-04-02 19:28 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 790/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneBreak 1.36.0  (landing page)
Evert van den Broek
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/GeneBreak
git_branch: RELEASE_3_20
git_last_commit: 82f97c3
git_last_commit_date: 2024-10-29 10:04:34 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for GeneBreak on nebbiolo2

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: 1.36.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneBreak_1.36.0.tar.gz
StartedAt: 2025-03-31 22:22:23 -0400 (Mon, 31 Mar 2025)
EndedAt: 2025-03-31 22:25:01 -0400 (Mon, 31 Mar 2025)
EllapsedTime: 158.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneBreak.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:GeneBreak.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings GeneBreak_1.36.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/GeneBreak.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘GeneBreak/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneBreak’ version ‘1.36.0’
* 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 loading without being on the library search path ... 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 5.926  0.119   6.046
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/GeneBreak.Rcheck/00check.log’
for details.


Installation output

GeneBreak.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL GeneBreak
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-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-class5.9260.1196.046
CopyNumberBreakPoints-class1.6080.0841.692
accessOptions-CopyNumberBreakPoints-method0.9010.0290.930
addGeneAnnotation-CopyNumberBreakPoints-method1.5200.0331.553
bpFilter-CopyNumberBreakPoints-method1.2070.0181.226
bpGenes-CopyNumberBreakPointGenes-method1.6850.0311.715
bpPlot-CopyNumberBreakPoints-method4.4740.0304.504
bpStats-CopyNumberBreakPoints-method4.3970.0664.464
breakpointData-CopyNumberBreakPoints-method0.9730.0961.069
breakpointsPerGene-CopyNumberBreakPointGenes-method1.7870.0941.882
callData-CopyNumberBreakPoints-method0.7100.0850.795
featureChromosomes-CopyNumberBreakPoints-method0.9500.0410.991
featureInfo-CopyNumberBreakPoints-method1.7520.0401.792
featuresPerGene-CopyNumberBreakPointGenes-method1.6360.0391.675
geneChromosomes-CopyNumberBreakPointGenes-method1.6310.0221.653
geneInfo-CopyNumberBreakPointGenes-method1.9710.0412.012
getBreakpoints1.2000.0261.226
namesFeatures-CopyNumberBreakPoints-method0.8080.0430.851
recurrentGenes-CopyNumberBreakPointGenes-method4.0500.0354.085
sampleNames-CopyNumberBreakPoints-method0.5010.0970.597
segmentData-CopyNumberBreakPoints-method0.7210.1070.828