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This page was generated on 2023-02-01 11:09:32 -0500 (Wed, 01 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4483
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-01-10 r83596 ucrt) -- "Unsuffered Consequences" 4249
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences" 4272
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 1005/2164HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.25.0  (landing page)
Bernat Gel
Snapshot Date: 2023-01-31 14:00:20 -0500 (Tue, 31 Jan 2023)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: master
git_last_commit: 051aa8b
git_last_commit_date: 2022-11-01 11:15:07 -0500 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 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: 1.25.0
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_1.25.0.tar.gz
StartedAt: 2023-02-01 02:47:16 -0500 (Wed, 01 Feb 2023)
EndedAt: 2023-02-01 03:06:47 -0500 (Wed, 01 Feb 2023)
EllapsedTime: 1170.5 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_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2023-01-10 r83596)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* R was compiled by
    Apple clang version 12.0.0 (clang-1200.0.32.29)
    GNU Fortran (GCC) 8.2.0
* running under: macOS Mojave 10.14.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.25.0’
* 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         71.328  3.895  98.731
kpPlotGenes           44.853  0.581  60.075
mergeTranscripts      36.755  0.285  49.043
kpPlotHorizon         32.659  0.096  42.827
kpPlotRegions         25.387  0.066  34.546
kpPlotTranscripts     14.434  0.050  19.949
kpPlotManhattan        8.810  0.195  11.769
kpPlotBAMCoverage      8.350  0.405  11.632
makeGenesDataFromTxDb  6.380  0.066   8.135
kpAbline               4.319  0.724   6.493
addGeneNames           4.531  0.084   6.067
* 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-3.17-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/4.3/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 Under development (unstable) (2023-01-10 r83596) -- "Unsuffered Consequences"
Copyright (C) 2023 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, aperm, 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 
 31.860   1.373  44.063 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames4.5310.0846.067
autotrack0.0010.0000.002
colByCategory0.0040.0000.005
colByChr1.1340.0961.607
colByRegion2.2290.1193.122
colByValue0.3900.0050.538
darker0.0010.0000.002
filterParams0.0010.0010.000
findIntersections0.2590.0020.358
getChromosomeNamesBoundingBox0.0800.0020.107
getColorSchemas0.0020.0020.005
getCytobandColors0.0010.0020.003
getCytobands0.0020.0000.002
getDataPanelBoundingBox0.0910.0010.119
getDefaultPlotParams0.1480.0140.217
getMainTitleBoundingBox0.0670.0070.096
getTextSize0.1770.0200.262
getVariantsColors0.0020.0000.002
horizonColors0.0070.0010.014
is.color0.0010.0000.002
kpAbline4.3190.7246.493
kpAddBaseNumbers0.7670.0050.976
kpAddChromosomeNames0.0660.0020.083
kpAddChromosomeSeparators0.9760.0061.302
kpAddColorRect0.3210.0030.425
kpAddCytobandLabels0.8610.0631.104
kpAddCytobands0.0620.0010.075
kpAddCytobandsAsLine0.1260.0030.167
kpAddLabels0.9520.0061.249
kpAddMainTitle0.0690.0010.085
kpArea0.7260.0080.896
kpArrows1.2320.0251.599
kpAxis0.6400.0030.841
kpBars0.3930.0020.508
kpDataBackground0.4870.0030.669
kpHeatmap0.3010.0020.409
kpLines0.5840.0040.754
kpPlotBAMCoverage 8.350 0.40511.632
kpPlotBAMDensity2.6630.0633.515
kpPlotBigWig1.9000.0732.478
kpPlotCoverage0.9310.0211.199
kpPlotDensity71.328 3.89598.731
kpPlotGenes44.853 0.58160.075
kpPlotHorizon32.659 0.09642.827
kpPlotLinks2.0960.0142.660
kpPlotLoess0.1360.0020.172
kpPlotManhattan 8.810 0.19511.769
kpPlotMarkers3.6860.0154.875
kpPlotNames0.2340.0010.309
kpPlotRainfall1.5900.0072.116
kpPlotRegions25.387 0.06634.546
kpPlotRibbon0.1860.0010.279
kpPlotTranscripts14.434 0.05019.949
kpPoints0.5830.0060.773
kpPolygon0.5580.0060.761
kpRect1.6070.0052.078
kpSegments1.1940.0051.557
kpText0.6820.0060.899
lighter0.0020.0010.004
makeGenesDataFromTxDb6.3800.0668.135
mergeTranscripts36.755 0.28549.043
plotDefaultPlotParams0.3290.0020.446
plotKaryotype2.0770.0192.854
plotPalettes0.0260.0020.034
prepareParameters20.0630.0020.092
prepareParameters40.0650.0010.091
processClipping0.0630.0010.084
transparent0.0010.0010.002