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This page was generated on 2025-03-20 12:06 -0400 (Thu, 20 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4406
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: 2025-03-17 13:00 -0400 (Mon, 17 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 palomino8

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: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneBreak.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneBreak_1.36.0.tar.gz
StartedAt: 2025-03-18 01:38:16 -0400 (Tue, 18 Mar 2025)
EndedAt: 2025-03-18 01:41:39 -0400 (Tue, 18 Mar 2025)
EllapsedTime: 203.2 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneBreak.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GeneBreak.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings GeneBreak_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/GeneBreak.Rcheck'
* using R version 4.4.3 (2025-02-28 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GeneBreak/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GeneBreak' version '1.36.0'
* 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 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                 7.18   0.95    8.14
recurrentGenes-CopyNumberBreakPointGenes-method 6.39   1.61    8.02
bpStats-CopyNumberBreakPoints-method            6.06   1.52    7.63
bpPlot-CopyNumberBreakPoints-method             5.94   1.05    6.98
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/GeneBreak.Rcheck/00check.log'
for details.


Installation output

GeneBreak.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL GeneBreak
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-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-class7.180.958.14
CopyNumberBreakPoints-class1.750.191.93
accessOptions-CopyNumberBreakPoints-method0.660.150.82
addGeneAnnotation-CopyNumberBreakPoints-method2.230.362.59
bpFilter-CopyNumberBreakPoints-method1.300.241.53
bpGenes-CopyNumberBreakPointGenes-method1.860.402.27
bpPlot-CopyNumberBreakPoints-method5.941.056.98
bpStats-CopyNumberBreakPoints-method6.061.527.63
breakpointData-CopyNumberBreakPoints-method0.890.641.75
breakpointsPerGene-CopyNumberBreakPointGenes-method2.390.783.17
callData-CopyNumberBreakPoints-method1.470.532.37
featureChromosomes-CopyNumberBreakPoints-method0.870.191.07
featureInfo-CopyNumberBreakPoints-method2.190.362.57
featuresPerGene-CopyNumberBreakPointGenes-method1.970.432.41
geneChromosomes-CopyNumberBreakPointGenes-method2.130.352.47
geneInfo-CopyNumberBreakPointGenes-method2.080.362.44
getBreakpoints2.010.292.33
namesFeatures-CopyNumberBreakPoints-method1.040.211.23
recurrentGenes-CopyNumberBreakPointGenes-method6.391.618.02
sampleNames-CopyNumberBreakPoints-method0.700.250.95
segmentData-CopyNumberBreakPoints-method1.550.532.08