Back to Multiple platform build/check report for BioC 3.15
ABCDEFGHIJ[K]LMNOPQRSTUVWXYZ

This page was generated on 2022-08-08 13:19:37 -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 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: 2022-08-07 13:55:12 -0400 (Sun, 07 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
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: 2022-08-07 20:33:46 -0400 (Sun, 07 Aug 2022)
EndedAt: 2022-08-07 20:41:00 -0400 (Sun, 07 Aug 2022)
EllapsedTime: 434.4 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     32.292  5.485  37.785
kpPlotGenes       20.952  0.219  21.173
kpPlotHorizon     15.801  0.248  16.050
mergeTranscripts  15.081  0.056  15.139
kpPlotRegions      9.910  0.044   9.955
kpPlotBAMCoverage  7.615  0.420   8.036
kpPlotTranscripts  5.694  0.032   5.727
kpPlotManhattan    5.105  0.076   5.182
* 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 
 16.523   1.342  17.852 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames1.8190.0631.884
autotrack0.0010.0010.001
colByCategory0.0030.0010.003
colByChr0.4160.0470.464
colByRegion1.0030.0651.066
colByValue0.1810.0040.185
darker0.0010.0000.001
filterParams0.0010.0000.001
findIntersections0.1110.0070.118
getChromosomeNamesBoundingBox0.0430.0010.043
getColorSchemas0.0000.0030.004
getCytobandColors0.0000.0020.002
getCytobands0.0010.0000.002
getDataPanelBoundingBox0.0410.0000.041
getDefaultPlotParams0.0620.0110.073
getMainTitleBoundingBox0.0320.0000.032
getTextSize0.0640.0120.076
getVariantsColors0.0010.0000.001
horizonColors0.0010.0040.004
is.color0.0010.0000.001
kpAbline1.9130.2362.150
kpAddBaseNumbers0.3090.0000.309
kpAddChromosomeNames0.0290.0000.029
kpAddChromosomeSeparators0.3920.0350.428
kpAddColorRect0.1260.0030.130
kpAddCytobandLabels0.3490.0240.372
kpAddCytobands0.0260.0040.031
kpAddCytobandsAsLine0.0610.0000.061
kpAddLabels0.4080.0080.416
kpAddMainTitle0.0250.0030.028
kpArea0.3190.0150.336
kpArrows0.5100.0230.533
kpAxis0.2680.0000.269
kpBars0.1570.0040.160
kpDataBackground0.1950.0000.195
kpHeatmap0.1200.0030.124
kpLines0.3560.0160.372
kpPlotBAMCoverage7.6150.4208.036
kpPlotBAMDensity1.8580.0161.873
kpPlotBigWig0.8190.0200.839
kpPlotCoverage0.3910.0200.412
kpPlotDensity32.292 5.48537.785
kpPlotGenes20.952 0.21921.173
kpPlotHorizon15.801 0.24816.050
kpPlotLinks0.9020.0040.905
kpPlotLoess0.0620.0040.067
kpPlotManhattan5.1050.0765.182
kpPlotMarkers1.5250.0081.533
kpPlotNames0.1030.0000.103
kpPlotRainfall0.7040.0000.705
kpPlotRegions9.9100.0449.955
kpPlotRibbon0.0820.0000.081
kpPlotTranscripts5.6940.0325.727
kpPoints0.2290.0000.229
kpPolygon0.2050.0000.205
kpRect0.6170.0000.617
kpSegments0.4690.0120.481
kpText0.2230.0080.232
lighter0.0010.0000.001
makeGenesDataFromTxDb2.6940.0442.737
mergeTranscripts15.081 0.05615.139
plotDefaultPlotParams0.1380.0000.138
plotKaryotype0.8670.0240.891
plotPalettes0.0180.0000.018
prepareParameters20.0290.0000.030
prepareParameters40.0330.0000.034
processClipping0.0320.0000.032
transparent0.0000.0010.001