Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2022-11-09 13:20:21 -0500 (Wed, 09 Nov 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2022-10-25 r83175) -- "Unsuffered Consequences" 4449
merida1macOS 10.14.6 Mojavex86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 3992
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

CHECK results for breakpointR on merida1


To the developers/maintainers of the breakpointR package:
- Please 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 How and When does the builder pull? When will my changes propagate? 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 219/2151HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
breakpointR 1.17.0  (landing page)
David Porubsky
Snapshot Date: 2022-11-08 13:55:08 -0500 (Tue, 08 Nov 2022)
git_url: https://git.bioconductor.org/packages/breakpointR
git_branch: master
git_last_commit: 7e2ce62
git_last_commit_date: 2022-11-01 11:18:28 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  NO, package depends on 'GenomicRanges' which is not available

Summary

Package: breakpointR
Version: 1.17.0
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_1.17.0.tar.gz
StartedAt: 2022-11-09 01:02:07 -0500 (Wed, 09 Nov 2022)
EndedAt: 2022-11-09 01:12:14 -0500 (Wed, 09 Nov 2022)
EllapsedTime: 607.7 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_1.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/breakpointR.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘breakpointR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘breakpointR’ version ‘1.17.0’
* 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 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 ... OK
* 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 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
genotyping            19.214  0.854  27.241
hotspotter            11.892  0.156  16.431
synchronizeReadDir     9.307  0.174  13.321
runBreakpointr         5.183  0.082   7.162
plotHeatmap            4.260  0.107   5.852
plotBreakpointsPerChr  4.133  0.118   5.549
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* 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: OK


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/4.2/Resources/library’
* installing *source* package ‘breakpointR’ ...
** 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 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: cowplot
Loading required package: breakpointRdata
> 
> test_check("breakpointR") 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 5 ]
> 
> proc.time()
   user  system elapsed 
 32.036   1.145  47.142 

Example timings

breakpointR.Rcheck/breakpointR-Ex.timings

nameusersystemelapsed
breakSeekr2.7680.1683.928
breakpointr000
breakpointr2UCSC1.3180.0441.857
confidenceInterval0.0000.0010.000
confidenceInterval.binomial000
deltaWCalculator0.8520.0111.179
exportRegions3.3230.1464.776
genotype.binom0.0010.0010.002
genotype.fisher0.0120.0000.016
genotyping19.214 0.85427.241
hotspotter11.892 0.15616.431
loadFromFiles2.1410.0682.991
plotBreakpoints3.4910.0884.626
plotBreakpointsPerChr4.1330.1185.549
plotHeatmap4.2600.1075.852
ranges2UCSC0.5290.0200.758
readBamFileAsGRanges0.3720.0300.551
removeReadPileupSpikes2.4440.1323.478
runBreakpointr5.1830.0827.162
summarizeBreaks0.4600.0100.618
synchronizeReadDir 9.307 0.17413.321