Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:05:31 -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 nebbiolo2


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: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings karyoploteR_1.20.3.tar.gz
StartedAt: 2022-04-12 07:57:47 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 08:05:00 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 433.4 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings karyoploteR_1.20.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/karyoploteR.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.20.3’
* 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     36.640  4.556  41.196
kpPlotGenes       23.209  0.196  23.404
kpPlotHorizon     19.481  0.080  19.561
mergeTranscripts  17.341  0.076  17.418
kpPlotRegions     13.560  0.128  13.689
kpPlotTranscripts  8.464  0.136   8.601
kpPlotBAMCoverage  7.118  0.464   7.584
kpPlotManhattan    5.488  0.087   5.576
* 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-3.14-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.3 (2022-03-10) -- "One Push-Up"
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 
 16.191   0.888  17.065 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames1.8180.0481.866
autotrack0.0010.0010.001
colByCategory0.0020.0000.002
colByChr0.4150.0310.447
colByRegion1.2160.0801.296
colByValue0.2400.0010.239
darker000
filterParams000
findIntersections0.190.000.19
getChromosomeNamesBoundingBox0.0510.0030.055
getColorSchemas0.0010.0010.001
getCytobandColors0.0010.0000.001
getCytobands0.0010.0000.002
getDataPanelBoundingBox0.0520.0000.052
getDefaultPlotParams0.1010.0000.100
getMainTitleBoundingBox0.0430.0030.046
getTextSize0.0930.0110.105
getVariantsColors0.0010.0000.001
horizonColors0.0040.0010.004
is.color0.0010.0000.001
kpAbline2.0310.2392.271
kpAddBaseNumbers0.2990.0050.305
kpAddChromosomeNames0.0360.0000.036
kpAddChromosomeSeparators0.3830.0120.396
kpAddColorRect0.1320.0080.140
kpAddCytobandLabels0.3640.0240.388
kpAddCytobands0.0350.0000.035
kpAddCytobandsAsLine0.0750.0000.075
kpAddLabels0.4160.0000.416
kpAddMainTitle0.0590.0000.059
kpArea0.3540.0040.358
kpArrows0.6880.0120.701
kpAxis0.2760.0000.276
kpBars0.1930.0000.194
kpDataBackground0.2040.0000.204
kpHeatmap0.1360.0000.136
kpLines0.3110.0120.322
kpPlotBAMCoverage7.1180.4647.584
kpPlotBAMDensity1.9160.0321.947
kpPlotBigWig1.0230.0361.059
kpPlotCoverage0.4210.0040.425
kpPlotDensity36.640 4.55641.196
kpPlotGenes23.209 0.19623.404
kpPlotHorizon19.481 0.08019.561
kpPlotLinks1.1630.0001.162
kpPlotLoess0.0710.0000.072
kpPlotManhattan5.4880.0875.576
kpPlotMarkers1.5300.0361.567
kpPlotNames0.1230.0000.123
kpPlotRainfall0.7810.0000.781
kpPlotRegions13.560 0.12813.689
kpPlotRibbon0.0870.0000.087
kpPlotTranscripts8.4640.1368.601
kpPoints0.2600.0040.264
kpPolygon0.2310.0000.231
kpRect0.8140.0040.818
kpSegments0.6380.0040.642
kpText0.2790.0000.280
lighter0.0010.0000.000
makeGenesDataFromTxDb3.2960.0123.308
mergeTranscripts17.341 0.07617.418
plotDefaultPlotParams0.1380.0000.138
plotKaryotype0.9430.0000.942
plotPalettes0.0180.0000.018
prepareParameters20.0370.0000.037
prepareParameters40.0370.0000.037
processClipping0.0370.0000.037
transparent0.0010.0000.000