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This page was generated on 2025-06-17 22:14 -0400 (Tue, 17 Jun 2025).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.5.0 (2025-04-11) -- "How About a Twenty-Six" 886
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Package 124/221HostnameOS / ArchINSTALLBUILDCHECK
karyoploteR 1.35.2  (landing page)
Bernat Gel
Snapshot Date: 2025-06-17 18:00 -0400 (Tue, 17 Jun 2025)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: devel
git_last_commit: 827cc95
git_last_commit_date: 2025-06-06 03:55:36 -0400 (Fri, 06 Jun 2025)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  


CHECK results for karyoploteR on teran2

To the developers/maintainers of the karyoploteR package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: karyoploteR
Version: 1.35.2
Command: /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings karyoploteR_1.35.2.tar.gz
StartedAt: 2025-06-17 21:05:48 -0400 (Tue, 17 Jun 2025)
EndedAt: 2025-06-17 21:13:22 -0400 (Tue, 17 Jun 2025)
EllapsedTime: 454.1 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/rapidbuild/bbs-3.22-bioc-rapid/R/site-library --timings karyoploteR_1.35.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/karyoploteR.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.35.2’
* package encoding: UTF-8
* 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
* checking code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... NOTE
checkRd: (-1) kpPlotBAMCoverage.Rd:48: Lost braces
    48 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotBAMDensity.Rd:48: Lost braces
    48 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotCoverage.Rd:46: Lost braces
    46 |  There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                         ^
checkRd: (-1) kpPlotDensity.Rd:42: Lost braces
    42 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotManhattan.Rd:80: Lost braces
    80 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotMarkers.Rd:81: Lost braces
    81 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotRainfall.Rd:47: Lost braces
    47 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPoints.Rd:54: Lost braces
    54 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpRect.Rd:55: Lost braces
    55 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) plotKaryotype.Rd:61: Lost braces
    61 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  getCytobands.Rd: GenomicRanges, memoise, forget
  kpPlotBAMCoverage.Rd: bamsignals
  kpPlotBAMDensity.Rd: Rsamtools
  kpPlotBigWig.Rd: BigWigFile
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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     25.801  4.696  33.108
kpPlotGenes       14.188  0.102  15.731
kpPlotHorizon     10.997  0.089  12.649
mergeTranscripts  11.061  0.023  11.107
kpPlotRegions      7.764  0.002   7.773
kpPlotBAMCoverage  4.775  0.208   5.072
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/meat/karyoploteR.Rcheck/00check.log’
for details.


Installation output

karyoploteR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/rapidbuild/bbs-3.22-bioc-rapid/R/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/rapidbuild/bbs-3.22-bioc-rapid/R/site-library’
* installing *source* package ‘karyoploteR’ ...
** this is package ‘karyoploteR’ version ‘1.35.2’
** 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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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: generics

Attaching package: 'generics'

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

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


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, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    findMatches

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 177 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_plotKaryotype.R:27:1', 'test_plotKaryotype.R:34:1',
  'test_plotKaryotype.R:44:1'

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 177 ]
> 
> proc.time()
   user  system elapsed 
 17.585   1.134  18.747 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames2.5400.0762.891
autotrack0.0010.0000.001
colByCategory0.0020.0000.002
colByChr0.3480.0010.357
colByRegion0.7110.0770.798
colByValue0.1310.0000.131
darker0.0010.0000.001
filterParams0.0000.0000.001
findIntersections0.0820.0010.081
getChromosomeNamesBoundingBox0.0330.0010.034
getColorSchemas0.0000.0010.001
getCytobandColors0.0000.0000.001
getCytobands0.0010.0000.001
getDataPanelBoundingBox0.0300.0000.031
getDefaultPlotParams0.0480.0020.049
getMainTitleBoundingBox0.0250.0000.025
getTextSize0.0520.0000.052
getVariantsColors0.0000.0000.001
horizonColors0.0030.0000.003
is.color000
kpAbline0.6670.0290.732
kpAddBaseNumbers0.2720.0030.277
kpAddChromosomeNames0.0250.0000.024
kpAddChromosomeSeparators0.3070.0000.323
kpAddColorRect0.1030.0010.105
kpAddCytobandLabels0.2850.0010.287
kpAddCytobands0.0260.0000.026
kpAddCytobandsAsLine0.0510.0000.055
kpAddLabels0.3070.0010.348
kpAddMainTitle0.0270.0000.026
kpArea0.2260.0000.242
kpArrows0.4010.0010.412
kpAxis0.1990.0020.202
kpBars0.1200.0000.121
kpDataBackground1.3610.0001.421
kpHeatmap0.0920.0000.093
kpLines0.1740.0000.174
kpPlotBAMCoverage4.7750.2085.072
kpPlotBAMDensity1.1990.0201.274
kpPlotBigWig1.7880.0372.005
kpPlotCoverage0.2770.0010.278
kpPlotDensity25.801 4.69633.108
kpPlotGenes14.188 0.10215.731
kpPlotHorizon10.997 0.08912.649
kpPlotLinks0.6490.0010.726
kpPlotLoess0.0740.0020.076
kpPlotManhattan3.3760.0443.507
kpPlotMarkers1.1660.0021.173
kpPlotNames0.0750.0000.076
kpPlotRainfall0.5160.0000.518
kpPlotRegions7.7640.0027.773
kpPlotRibbon0.0580.0010.059
kpPlotTranscripts4.4300.0014.433
kpPoints0.2110.0000.216
kpPolygon0.1470.0010.148
kpRect0.5180.0020.520
kpSegments0.3580.0010.359
kpText0.1750.0000.175
lighter0.0000.0000.001
makeGenesDataFromTxDb1.9290.0081.938
mergeTranscripts11.061 0.02311.107
plotDefaultPlotParams0.1060.0000.107
plotKaryotype0.7160.0030.720
plotPalettes0.0130.0010.014
prepareParameters20.0230.0000.024
prepareParameters40.0240.0000.024
processClipping0.0240.0000.024
transparent0.0000.0000.001