Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-08 13:20:12 -0400 (Mon, 08 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4362
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4180
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 CopyNumberPlots on merida1


To the developers/maintainers of the CopyNumberPlots package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CopyNumberPlots.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 409/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CopyNumberPlots 1.12.0  (landing page)
Bernat Gel
Snapshot Date: 2022-08-07 13:55:12 -0400 (Sun, 07 Aug 2022)
git_url: https://git.bioconductor.org/packages/CopyNumberPlots
git_branch: RELEASE_3_15
git_last_commit: b6a4fde
git_last_commit_date: 2022-04-26 11:55:13 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: CopyNumberPlots
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CopyNumberPlots_1.12.0.tar.gz
StartedAt: 2022-08-08 00:49:40 -0400 (Mon, 08 Aug 2022)
EndedAt: 2022-08-08 00:58:51 -0400 (Mon, 08 Aug 2022)
EllapsedTime: 550.5 seconds
RetCode: 0
Status:   OK  
CheckDir: CopyNumberPlots.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CopyNumberPlots.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CopyNumberPlots_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/CopyNumberPlots.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CopyNumberPlots/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CopyNumberPlots’ version ‘1.12.0’
* package encoding: UTF-8
* 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 ‘CopyNumberPlots’ 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 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 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

CopyNumberPlots.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘CopyNumberPlots’ ...
** using staged installation
** R
** inst
** 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 (CopyNumberPlots)

Tests output

CopyNumberPlots.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
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(CopyNumberPlots)
Loading required package: karyoploteR
Loading required package: regioneR
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, 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
> 
> test_check("CopyNumberPlots")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 26 ]
> 
> proc.time()
   user  system elapsed 
 27.901   1.086  29.021 

Example timings

CopyNumberPlots.Rcheck/CopyNumberPlots-Ex.timings

nameusersystemelapsed
EnsemblStyle0.8720.0410.915
UCSCStyle0.6590.0850.746
Ztree2Hclust0.0080.0020.010
colByCopyNumber0.8780.0320.915
computeHclustPlotOrder0.0300.0020.033
getBAFColumn0.0040.0000.004
getChrColumn0.0030.0000.003
getColumn0.0050.0000.004
getCopyNumberColors0.0010.0010.002
getCopyNumberColumn0.0040.0000.004
getEndColumn0.0030.0000.003
getIDColumn0.0030.0010.003
getLOHColumn0.0030.0000.003
getLRRColumn0.0040.0000.003
getPosColumn0.0030.0010.003
getSegmentValueColumn0.0030.0000.004
getStartColumn0.0040.0000.003
loadCopyNumberCalls0.0380.0010.039
loadCopyNumberCallsCNVkit0.0980.0020.101
loadCopyNumberCallsCnmops0.3300.0020.332
loadCopyNumberCallsDECoN0.1550.0020.157
loadCopyNumberCallsDNAcopy1.2580.0101.270
loadCopyNumberCallsPanelcnmops0.6450.0130.662
loadCopyNumberCallsSeg0.0360.0010.036
loadCopyNumberCallspennCNV0.0680.0010.070
loadSNPData0.0880.0010.091
loadSNPDataDNAcopy1.1710.0071.181
loadSNPDataFromVCF0.0010.0010.001
plotBAF1.9360.0481.991
plotCopyNumberCalls0.3470.0340.383
plotCopyNumberCallsAsLines0.3140.0340.352
plotCopyNumberSummary0.3980.0270.429
plotLRR0.7810.0050.790
plotSingleCellCopyNumberCalls0.0950.0020.096
plotSingleCellCopyNumberSummary0.0700.0010.071
prepareLabels0.1590.0000.160
readHDF5Ztree000
removeNAs0.3310.0010.333
transformChr0.0060.0000.006