Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-21 13:05:18 -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 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? 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: /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: 2022-01-20 08:08:36 -0500 (Thu, 20 Jan 2022)
EndedAt: 2022-01-20 08:15:40 -0500 (Thu, 20 Jan 2022)
EllapsedTime: 423.7 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 4.1.2 (2021-11-01)
* 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     35.701  4.369  40.111
kpPlotGenes       23.812  0.268  24.080
kpPlotHorizon     20.271  0.172  20.443
mergeTranscripts  17.262  0.080  17.342
kpPlotRegions     12.884  0.044  12.929
kpPlotBAMCoverage  6.903  0.304   7.263
kpPlotTranscripts  7.105  0.020   7.124
kpPlotManhattan    5.392  0.056   5.448
* 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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 181 ]
> 
> proc.time()
   user  system elapsed 
 15.769   0.796  16.551 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames1.9200.0591.980
autotrack0.0010.0000.001
colByCategory0.0020.0000.002
colByChr0.4720.0000.471
colByRegion1.0950.1241.219
colByValue0.2210.0000.221
darker0.0010.0000.001
filterParams0.0000.0000.001
findIntersections0.1680.0120.180
getChromosomeNamesBoundingBox0.0490.0000.049
getColorSchemas0.0020.0000.001
getCytobandColors0.0010.0000.001
getCytobands0.0010.0000.001
getDataPanelBoundingBox0.0470.0000.047
getDefaultPlotParams0.0840.0030.087
getMainTitleBoundingBox0.0380.0010.039
getTextSize0.0770.0000.078
getVariantsColors0.0010.0000.001
horizonColors0.0030.0000.003
is.color0.0010.0000.000
kpAbline1.9260.0792.007
kpAddBaseNumbers0.2990.0040.303
kpAddChromosomeNames0.0360.0000.036
kpAddChromosomeSeparators0.3910.0000.390
kpAddColorRect0.1340.0160.149
kpAddCytobandLabels0.4400.0040.444
kpAddCytobands0.0390.0000.040
kpAddCytobandsAsLine0.0740.0000.074
kpAddLabels0.3890.0000.388
kpAddMainTitle0.0360.0000.036
kpArea0.3340.0040.339
kpArrows0.6540.0120.666
kpAxis0.2550.0040.258
kpBars0.1820.0000.182
kpDataBackground0.1880.0000.187
kpHeatmap0.1330.0000.132
kpLines0.2810.0120.293
kpPlotBAMCoverage6.9030.3047.263
kpPlotBAMDensity1.8890.0241.913
kpPlotBigWig1.0630.0001.063
kpPlotCoverage0.4240.0160.440
kpPlotDensity35.701 4.36940.111
kpPlotGenes23.812 0.26824.080
kpPlotHorizon20.271 0.17220.443
kpPlotLinks1.0360.0001.035
kpPlotLoess0.0680.0000.067
kpPlotManhattan5.3920.0565.448
kpPlotMarkers1.5130.0281.540
kpPlotNames0.1730.0000.173
kpPlotRainfall0.7850.0000.785
kpPlotRegions12.884 0.04412.929
kpPlotRibbon0.0840.0040.087
kpPlotTranscripts7.1050.0207.124
kpPoints0.3080.0240.332
kpPolygon0.2280.0000.227
kpRect0.8450.0000.845
kpSegments0.6110.0000.611
kpText0.2790.0000.279
lighter0.0010.0000.001
makeGenesDataFromTxDb3.2030.0243.226
mergeTranscripts17.262 0.08017.342
plotDefaultPlotParams0.1370.0000.137
plotKaryotype0.9080.0080.917
plotPalettes0.0180.0000.018
prepareParameters20.0370.0000.037
prepareParameters40.0350.0040.038
processClipping0.040.000.04
transparent0.0010.0000.000