Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-15 13:20:23 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
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 nebbiolo1


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 1000/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.22.0  (landing page)
Bernat Gel
Snapshot Date: 2022-08-14 13:55:13 -0400 (Sun, 14 Aug 2022)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: RELEASE_3_15
git_last_commit: c0d3786
git_last_commit_date: 2022-04-26 11:38:43 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    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: karyoploteR
Version: 1.22.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings karyoploteR_1.22.0.tar.gz
StartedAt: 2022-08-14 20:28:08 -0400 (Sun, 14 Aug 2022)
EndedAt: 2022-08-14 20:35:05 -0400 (Sun, 14 Aug 2022)
EllapsedTime: 417.2 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings karyoploteR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/karyoploteR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (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 ‘1.22.0’
* 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 ‘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     30.505  5.383  35.895
kpPlotGenes       20.013  0.448  20.462
mergeTranscripts  14.948  0.056  15.006
kpPlotHorizon     13.207  0.124  13.332
kpPlotRegions      9.930  0.040   9.971
kpPlotBAMCoverage  7.034  0.392   7.426
kpPlotTranscripts  5.752  0.064   5.816
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 15.855   0.935  16.773 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames1.7460.0801.826
autotrack0.0000.0010.001
colByCategory0.0010.0010.003
colByChr0.4520.0260.478
colByRegion1.0390.0441.084
colByValue0.1880.0160.204
darker0.0010.0000.001
filterParams0.0010.0000.000
findIntersections0.1150.0080.122
getChromosomeNamesBoundingBox0.0430.0000.043
getColorSchemas0.0000.0040.004
getCytobandColors0.0020.0000.002
getCytobands0.0010.0000.002
getDataPanelBoundingBox0.0390.0000.039
getDefaultPlotParams0.0650.0080.072
getMainTitleBoundingBox0.0320.0000.031
getTextSize0.0720.0040.077
getVariantsColors0.0010.0000.001
horizonColors0.0040.0000.004
is.color0.0010.0000.001
kpAbline1.9030.2592.163
kpAddBaseNumbers0.3270.0090.337
kpAddChromosomeNames0.030.000.03
kpAddChromosomeSeparators0.4110.0000.410
kpAddColorRect0.1310.0040.134
kpAddCytobandLabels0.3690.0080.377
kpAddCytobands0.0290.0000.029
kpAddCytobandsAsLine0.0640.0000.064
kpAddLabels0.4000.0440.444
kpAddMainTitle0.0330.0000.033
kpArea0.3020.0320.333
kpArrows0.5190.0240.543
kpAxis0.2700.0040.275
kpBars0.1750.0000.176
kpDataBackground0.2040.0120.215
kpHeatmap0.1440.0000.144
kpLines0.3830.0160.400
kpPlotBAMCoverage7.0340.3927.426
kpPlotBAMDensity1.8310.0521.883
kpPlotBigWig0.8330.0600.895
kpPlotCoverage0.3910.0200.411
kpPlotDensity30.505 5.38335.895
kpPlotGenes20.013 0.44820.462
kpPlotHorizon13.207 0.12413.332
kpPlotLinks0.9810.0160.996
kpPlotLoess0.0610.0000.061
kpPlotManhattan4.9110.0804.991
kpPlotMarkers1.4990.0041.503
kpPlotNames0.0990.0000.098
kpPlotRainfall0.6560.0080.663
kpPlotRegions9.9300.0409.971
kpPlotRibbon0.0800.0000.081
kpPlotTranscripts5.7520.0645.816
kpPoints0.2640.0000.264
kpPolygon0.2120.0000.212
kpRect0.6930.0000.694
kpSegments0.4720.0040.476
kpText0.2210.0000.221
lighter0.0000.0000.001
makeGenesDataFromTxDb2.9300.0672.997
mergeTranscripts14.948 0.05615.006
plotDefaultPlotParams0.1390.0000.139
plotKaryotype0.8440.0240.868
plotPalettes0.0150.0040.019
prepareParameters20.0290.0000.030
prepareParameters40.0300.0000.031
processClipping0.0300.0000.029
transparent0.0000.0000.001