Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJ[K]LMNOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:08:13 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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 karyoploteR on machv2


To the developers/maintainers of the karyoploteR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/karyoploteR.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 975/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.20.3  (landing page)
Bernat Gel
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: RELEASE_3_14
git_last_commit: 1a34c68
git_last_commit_date: 2022-01-19 05:36:06 -0400 (Wed, 19 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: karyoploteR
Version: 1.20.3
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings karyoploteR_1.20.3.tar.gz
StartedAt: 2022-04-12 14:41:36 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 14:54:04 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 748.2 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings karyoploteR_1.20.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/karyoploteR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.20.3’
* 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 ‘karyoploteR’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘regioneR’ ‘GenomicRanges’
A package should be listed in only one of these fields.
* 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 R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                        user system elapsed
kpPlotDensity         71.849  3.517  75.762
kpPlotGenes           44.500  0.385  44.949
kpPlotHorizon         39.671  0.202  39.971
mergeTranscripts      35.827  0.141  36.016
kpPlotRegions         27.755  0.085  27.901
kpPlotTranscripts     15.521  0.052  15.613
kpPlotManhattan        8.167  0.190   8.375
kpPlotBAMCoverage      7.481  0.346   7.836
makeGenesDataFromTxDb  6.177  0.069   6.267
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘karyoploteR’ ...
** 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 (karyoploteR)

Tests output

karyoploteR.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
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(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("karyoploteR")
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]
> 
> proc.time()
   user  system elapsed 
 27.149   1.190  28.367 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames3.0990.0883.189
autotrack0.0010.0000.001
colByCategory0.0030.0010.004
colByChr0.9260.0450.997
colByRegion2.2140.1422.379
colByValue0.3620.0060.370
darker0.0020.0010.002
filterParams0.0000.0000.001
findIntersections0.3430.0020.345
getChromosomeNamesBoundingBox0.0800.0020.083
getColorSchemas0.0010.0030.004
getCytobandColors0.0000.0020.002
getCytobands0.0010.0000.001
getDataPanelBoundingBox0.0830.0010.085
getDefaultPlotParams0.1720.0240.196
getMainTitleBoundingBox0.0810.0090.091
getTextSize0.1590.0130.173
getVariantsColors0.0010.0010.002
horizonColors0.0050.0020.006
is.color0.0010.0010.001
kpAbline3.6560.6034.266
kpAddBaseNumbers0.6550.0040.659
kpAddChromosomeNames0.0570.0010.059
kpAddChromosomeSeparators0.8130.0030.818
kpAddColorRect0.2560.0020.257
kpAddCytobandLabels0.7540.0090.765
kpAddCytobands0.0570.0010.058
kpAddCytobandsAsLine0.1230.0020.126
kpAddLabels0.7170.0050.724
kpAddMainTitle0.0690.0010.071
kpArea0.6960.0060.703
kpArrows1.3550.0101.367
kpAxis0.5820.0040.587
kpBars0.3150.0020.317
kpDataBackground0.3290.0020.332
kpHeatmap0.2380.0020.240
kpLines0.5890.0060.595
kpPlotBAMCoverage7.4810.3467.836
kpPlotBAMDensity2.4860.0572.546
kpPlotBigWig1.8840.0491.937
kpPlotCoverage0.9510.0080.958
kpPlotDensity71.849 3.51775.762
kpPlotGenes44.500 0.38544.949
kpPlotHorizon39.671 0.20239.971
kpPlotLinks2.2260.0122.241
kpPlotLoess0.1170.0020.121
kpPlotManhattan8.1670.1908.375
kpPlotMarkers3.0310.0223.057
kpPlotNames0.3150.0020.317
kpPlotRainfall1.6610.0131.675
kpPlotRegions27.755 0.08527.901
kpPlotRibbon0.1710.0030.176
kpPlotTranscripts15.521 0.05215.613
kpPoints0.6310.0050.637
kpPolygon0.4100.0060.417
kpRect1.7390.0061.749
kpSegments1.1950.0061.203
kpText0.5420.0040.547
lighter0.0010.0000.002
makeGenesDataFromTxDb6.1770.0696.267
mergeTranscripts35.827 0.14136.016
plotDefaultPlotParams0.2930.0020.295
plotKaryotype1.9960.0302.031
plotPalettes0.0240.0020.027
prepareParameters20.0710.0020.073
prepareParameters40.0650.0010.067
processClipping0.0620.0010.064
transparent0.0020.0000.001