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CHECK report for karyoploteR on malbec2

This page was generated on 2020-10-17 11:55:00 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE karyoploteR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 915/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.14.1
Bernat Gel
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/karyoploteR
Branch: RELEASE_3_11
Last Commit: 33faf71
Last Changed Date: 2020-09-09 11:02:07 -0400 (Wed, 09 Sep 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: karyoploteR
Version: 1.14.1
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings karyoploteR_1.14.1.tar.gz
StartedAt: 2020-10-17 02:33:32 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 02:43:43 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 611.1 seconds
RetCode: 0
Status:  OK 
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings karyoploteR_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/karyoploteR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.14.1’
* 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     47.228  3.953  51.765
kpPlotGenes       29.052  0.064  29.578
mergeTranscripts  21.824  0.015  21.839
kpPlotHorizon     20.566  0.008  20.573
kpPlotRegions     16.798  0.004  16.809
kpPlotCoverage    16.707  0.000  16.709
kpPlotTranscripts 12.294  0.007  12.301
kpPlotBAMCoverage  6.714  0.155   6.873
kpPlotManhattan    5.380  0.048   5.429
getCytobands       1.005  0.034  19.073
* 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-3.11-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.11-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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("karyoploteR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 181 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 19.256   0.543  22.514 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames3.7090.0363.745
autotrack0.0020.0000.001
colByCategory0.0030.0000.003
colByChr0.6220.0360.658
colByRegion1.0000.0001.006
colByValue0.3170.0000.318
darker0.0020.0000.002
filterParams0.0010.0000.001
findIntersections0.1820.0080.190
getChromosomeNamesBoundingBox0.0740.0000.074
getColorSchemas0.0030.0000.003
getCytobandColors0.0000.0010.002
getCytobands 1.005 0.03419.073
getDataPanelBoundingBox0.0780.0000.077
getDefaultPlotParams0.1260.0000.126
getMainTitleBoundingBox0.0550.0000.056
getTextSize0.1480.0000.147
getVariantsColors0.0010.0000.001
horizonColors0.0030.0030.006
is.color0.0000.0010.001
kpAbline2.6350.1342.878
kpAddBaseNumbers0.6990.0000.698
kpAddChromosomeNames0.0530.0000.054
kpAddChromosomeSeparators0.9150.0360.950
kpAddColorRect0.3130.0000.313
kpAddCytobandLabels0.7540.0000.754
kpAddCytobands0.0570.0000.058
kpAddCytobandsAsLine0.1190.0000.118
kpAddLabels0.2490.0080.257
kpAddMainTitle0.0350.0000.035
kpArea0.3950.0000.394
kpArrows0.7760.0040.780
kpAxis0.5650.0030.567
kpBars0.3330.0000.333
kpDataBackground0.4530.0000.453
kpHeatmap0.2490.0000.249
kpLines0.4870.0000.488
kpPlotBAMCoverage6.7140.1556.873
kpPlotBAMDensity2.6900.0402.729
kpPlotBigWig2.0730.0162.129
kpPlotCoverage16.707 0.00016.709
kpPlotDensity47.228 3.95351.765
kpPlotGenes29.052 0.06429.578
kpPlotHorizon20.566 0.00820.573
kpPlotLinks1.0930.0001.094
kpPlotLoess0.0690.0000.070
kpPlotManhattan5.3800.0485.429
kpPlotMarkers2.6630.0042.668
kpPlotNames0.1930.0000.192
kpPlotRainfall1.3550.0041.360
kpPlotRegions16.798 0.00416.809
kpPlotRibbon0.1610.0000.162
kpPlotTranscripts12.294 0.00712.301
kpPoints0.5600.0040.565
kpPolygon0.4830.0000.483
kpRect1.2820.0001.283
kpSegments1.0010.0001.001
kpText0.40.00.4
lighter0.0010.0000.001
makeGenesDataFromTxDb3.5270.0003.528
mergeTranscripts21.824 0.01521.839
plotDefaultPlotParams1.2790.0561.335
plotKaryotype1.1080.0001.108
plotPalettes0.0260.0000.026
prepareParameters20.0380.0000.038
prepareParameters40.0330.0000.034
processClipping0.0350.0000.035
transparent0.0010.0000.001