Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:07:57 -0500 (Fri, 21 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4079
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4140
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? here 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: 2022-01-20 01:55:04 -0500 (Thu, 20 Jan 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 -0500 (Wed, 19 Jan 2022)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  YES
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  YES
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  YES

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: 2022-01-20 14:20:46 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 14:33:05 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 739.2 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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 4.1.2 (2021-11-01)
* 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         70.622  3.514  74.478
kpPlotGenes           44.197  0.527  44.768
kpPlotHorizon         38.923  0.107  39.113
mergeTranscripts      34.408  0.144  34.606
kpPlotRegions         26.807  0.065  26.929
kpPlotTranscripts     13.467  0.047  13.534
kpPlotManhattan        8.365  0.202   8.700
kpPlotBAMCoverage      7.474  0.309   7.800
makeGenesDataFromTxDb  5.836  0.063   5.911
* 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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]
> 
> proc.time()
   user  system elapsed 
 26.743   1.165  27.918 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames3.0710.1003.172
autotrack0.0010.0000.001
colByCategory0.0040.0010.004
colByChr0.7750.0300.808
colByRegion2.0040.1102.119
colByValue0.4170.0070.425
darker0.0010.0010.001
filterParams0.0000.0010.001
findIntersections0.3570.0280.385
getChromosomeNamesBoundingBox0.0920.0070.100
getColorSchemas0.0020.0040.006
getCytobandColors0.0010.0020.003
getCytobands0.0020.0000.002
getDataPanelBoundingBox0.0900.0110.101
getDefaultPlotParams0.1660.0280.195
getMainTitleBoundingBox0.0780.0090.087
getTextSize0.1440.0180.161
getVariantsColors0.0010.0000.001
horizonColors0.0060.0020.009
is.color0.0020.0010.002
kpAbline3.7200.6194.345
kpAddBaseNumbers0.6370.0040.662
kpAddChromosomeNames0.0700.0020.072
kpAddChromosomeSeparators0.7810.0050.788
kpAddColorRect0.2430.0020.245
kpAddCytobandLabels0.7930.0310.826
kpAddCytobands0.0700.0020.070
kpAddCytobandsAsLine0.1110.0020.114
kpAddLabels0.8230.0050.831
kpAddMainTitle0.0760.0020.078
kpArea0.7630.0340.798
kpArrows1.3690.0361.406
kpAxis0.5810.0040.587
kpBars0.3840.0020.386
kpDataBackground0.4280.0020.432
kpHeatmap0.2770.0020.280
kpLines0.5600.0040.564
kpPlotBAMCoverage7.4740.3097.800
kpPlotBAMDensity2.3950.0572.456
kpPlotBigWig2.0570.0282.089
kpPlotCoverage1.0040.0041.011
kpPlotDensity70.622 3.51474.478
kpPlotGenes44.197 0.52744.768
kpPlotHorizon38.923 0.10739.113
kpPlotLinks2.1300.0122.145
kpPlotLoess0.1180.0020.121
kpPlotManhattan8.3650.2028.700
kpPlotMarkers3.0730.0193.103
kpPlotNames0.2750.0020.278
kpPlotRainfall1.5980.0111.613
kpPlotRegions26.807 0.06526.929
kpPlotRibbon0.1600.0030.164
kpPlotTranscripts13.467 0.04713.534
kpPoints0.5260.0030.530
kpPolygon0.5510.0280.580
kpRect1.7330.0051.742
kpSegments1.3850.0051.394
kpText0.5730.0040.577
lighter0.0010.0000.002
makeGenesDataFromTxDb5.8360.0635.911
mergeTranscripts34.408 0.14434.606
plotDefaultPlotParams0.3170.0020.319
plotKaryotype2.0430.0302.077
plotPalettes0.0230.0030.026
prepareParameters20.0740.0030.076
prepareParameters40.0770.0030.081
processClipping0.0670.0020.068
transparent0.0010.0000.002