Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-12 13:23:08 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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 merida1


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: 2022-08-11 13:55:06 -0400 (Thu, 11 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings karyoploteR_1.22.0.tar.gz
StartedAt: 2022-08-12 03:50:21 -0400 (Fri, 12 Aug 2022)
EndedAt: 2022-08-12 04:04:24 -0400 (Fri, 12 Aug 2022)
EllapsedTime: 843.1 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings karyoploteR_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/karyoploteR.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (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         70.394  3.808  75.071
kpPlotGenes           43.604  0.504  44.387
mergeTranscripts      34.458  0.160  34.983
kpPlotHorizon         32.528  0.171  32.917
kpPlotRegions         23.887  0.063  24.906
kpPlotTranscripts     13.585  0.040  13.806
kpPlotBAMCoverage      8.170  0.422   8.665
kpPlotManhattan        8.312  0.174   8.570
makeGenesDataFromTxDb  6.131  0.073   6.313
* 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
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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-apple-darwin17.0 (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 
 31.472   1.313  33.016 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames3.5360.0843.647
autotrack0.0020.0000.001
colByCategory0.0040.0010.004
colByChr1.1190.0521.181
colByRegion2.2690.1372.425
colByValue0.3700.0050.379
darker0.0020.0000.002
filterParams0.0000.0000.001
findIntersections0.2660.0010.268
getChromosomeNamesBoundingBox0.0850.0020.087
getColorSchemas0.0020.0020.005
getCytobandColors0.0010.0020.003
getCytobands0.0020.0000.002
getDataPanelBoundingBox0.0920.0010.095
getDefaultPlotParams0.1390.0070.147
getMainTitleBoundingBox0.0610.0010.063
getTextSize0.1780.0180.197
getVariantsColors0.0010.0000.002
horizonColors0.0070.0020.009
is.color0.0010.0010.001
kpAbline4.2050.7244.981
kpAddBaseNumbers0.7620.0040.775
kpAddChromosomeNames0.0650.0010.067
kpAddChromosomeSeparators0.9900.0051.003
kpAddColorRect0.3240.0030.330
kpAddCytobandLabels0.8490.0190.874
kpAddCytobands0.0610.0020.064
kpAddCytobandsAsLine0.1280.0020.136
kpAddLabels0.9650.0060.979
kpAddMainTitle0.0620.0010.064
kpArea0.7500.0070.770
kpArrows1.2200.0181.245
kpAxis0.6440.0040.655
kpBars0.3800.0020.386
kpDataBackground0.4920.0020.501
kpHeatmap0.2890.0010.293
kpLines0.7010.0320.737
kpPlotBAMCoverage8.1700.4228.665
kpPlotBAMDensity2.6560.0612.738
kpPlotBigWig1.8550.0581.934
kpPlotCoverage0.9270.0130.946
kpPlotDensity70.394 3.80875.071
kpPlotGenes43.604 0.50444.387
kpPlotHorizon32.528 0.17132.917
kpPlotLinks2.0750.0122.106
kpPlotLoess0.1290.0020.134
kpPlotManhattan8.3120.1748.570
kpPlotMarkers3.5800.0263.753
kpPlotNames0.2260.0010.239
kpPlotRainfall1.5610.0111.653
kpPlotRegions23.887 0.06324.906
kpPlotRibbon0.1820.0030.186
kpPlotTranscripts13.585 0.04013.806
kpPoints0.5530.0030.557
kpPolygon0.4500.0050.463
kpRect1.5580.0041.577
kpSegments1.1720.0031.181
kpText0.5360.0060.547
lighter0.0010.0000.001
makeGenesDataFromTxDb6.1310.0736.313
mergeTranscripts34.458 0.16034.983
plotDefaultPlotParams0.3270.0020.332
plotKaryotype2.1000.0222.142
plotPalettes0.0270.0030.030
prepareParameters20.0560.0010.057
prepareParameters40.0640.0010.066
processClipping0.0630.0010.065
transparent0.0010.0000.001