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This page was generated on 2025-08-09 12:09 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 240/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
breakpointR 1.27.0  (landing page)
David Porubsky
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/breakpointR
git_branch: devel
git_last_commit: 2477dce
git_last_commit_date: 2025-04-15 11:37:18 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for breakpointR on kjohnson3

To the developers/maintainers of the breakpointR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/breakpointR.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: breakpointR
Version: 1.27.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:breakpointR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings breakpointR_1.27.0.tar.gz
StartedAt: 2025-08-08 18:24:54 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 18:26:30 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 96.2 seconds
RetCode: 0
Status:   OK  
CheckDir: breakpointR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:breakpointR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings breakpointR_1.27.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/breakpointR.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘breakpointR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘breakpointR’ version ‘1.27.0’
* 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 ‘breakpointR’ 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  BreakPoint.Rd: GRanges-class
  breakSeekr.Rd: GRanges-class
  breakpointr2UCSC.Rd: GRanges-class
  collapseBins.Rd: GRanges-class
  confidenceInterval.Rd: GRanges-class
  confidenceInterval.binomial.Rd: GRanges-class
  createCompositeFile.Rd: GRanges-class
  deltaWCalculator.Rd: GRanges-class
  deltaWCalculatorVariousWindows.Rd: GRanges-class
  genotyping.Rd: GRanges-class
  hotspotter.Rd: GRangesList-class, GRanges-class
  insertchr.Rd: GRanges-class
  loadFromFiles.Rd: GRanges-class
  plotHeatmap.Rd: GRanges-class
  ranges2UCSC.Rd: GRanges-class
  readBamFileAsGRanges.Rd: GRanges-class
  removeDoubleSCEs.Rd: GRanges-class
  removeReadPileupSpikes.Rd: GRanges-class
  runBreakpointr.Rd: GRanges-class
  summarizeBreaks.Rd: GRanges-class
  synchronizeReadDir.Rd: GRanges-class
  transCoord.Rd: GRanges-class
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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-3.22-bioc/meat/breakpointR.Rcheck/00check.log’
for details.


Installation output

breakpointR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL breakpointR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘breakpointR’ ...
** this is package ‘breakpointR’ version ‘1.27.0’
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** 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 (breakpointR)

Tests output

breakpointR.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(breakpointR)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: Seqinfo
Loading required package: cowplot
Loading required package: breakpointRdata
> 
> test_check("breakpointR") 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
  5.944   0.229   6.205 

Example timings

breakpointR.Rcheck/breakpointR-Ex.timings

nameusersystemelapsed
breakSeekr0.6670.0240.694
breakpointr000
breakpointr2UCSC0.4530.0080.461
confidenceInterval000
confidenceInterval.binomial000
deltaWCalculator0.1150.0040.119
exportRegions1.0370.0281.077
genotype.binom0.0000.0000.001
genotype.fisher0.0020.0000.002
genotyping3.6470.4934.157
hotspotter1.9320.1612.103
loadFromFiles0.6380.0340.672
plotBreakpoints0.8530.0550.926
plotBreakpointsPerChr0.7870.0550.865
plotHeatmap0.9220.0380.979
ranges2UCSC0.1170.0120.131
readBamFileAsGRanges0.0610.0080.078
removeReadPileupSpikes0.7830.0670.875
runBreakpointr0.6910.0400.738
summarizeBreaks0.1090.0060.118
synchronizeReadDir1.6550.1021.774