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This page was generated on 2024-03-04 11:39:24 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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

Package 1065/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.29.1  (landing page)
Bernat Gel
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: devel
git_last_commit: 2a860f3
git_last_commit_date: 2024-01-11 06:04:35 -0500 (Thu, 11 Jan 2024)
nebbiolo1Linux (Ubuntu 22.04.3 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 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

CHECK results for karyoploteR on merida1


To the developers/maintainers of the karyoploteR package:
- 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 Troubleshooting Build Report for more information.
- 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: 1.29.1
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_1.29.1.tar.gz
StartedAt: 2024-03-02 05:51:21 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 06:11:21 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 1200.3 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_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.29.1’
* 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 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 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 ... 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         73.108  5.199  97.566
kpPlotGenes           46.883  0.798  56.662
mergeTranscripts      37.585  0.388  45.251
kpPlotHorizon         31.961  0.287  36.792
kpPlotRegions         26.195  0.241  31.814
kpPlotTranscripts     15.125  0.135  18.312
kpPlotBAMCoverage     14.027  0.493  16.821
kpPlotManhattan        9.877  0.580  14.708
makeGenesDataFromTxDb  6.561  0.108   8.167
kpAbline               4.597  1.244   7.295
addGeneNames           5.513  0.189   6.616
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/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) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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, table, tapply,
    union, 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 
 35.262   2.009  46.071 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames5.5130.1896.616
autotrack0.0020.0010.004
colByCategory0.0040.0010.010
colByChr1.2150.0541.487
colByRegion2.3080.1722.881
colByValue0.4060.0110.481
darker0.0010.0000.003
filterParams0.0010.0010.001
findIntersections0.2850.0040.336
getChromosomeNamesBoundingBox0.0950.0030.114
getColorSchemas0.0030.0070.012
getCytobandColors0.0020.0040.005
getCytobands0.0020.0000.003
getDataPanelBoundingBox0.1040.0030.124
getDefaultPlotParams0.2020.0240.267
getMainTitleBoundingBox0.0800.0030.092
getTextSize0.1790.0040.215
getVariantsColors0.0020.0010.002
horizonColors0.0070.0020.010
is.color0.0010.0010.002
kpAbline4.5971.2447.295
kpAddBaseNumbers0.8340.0121.029
kpAddChromosomeNames0.0750.0020.080
kpAddChromosomeSeparators1.1290.0161.968
kpAddColorRect0.3580.0080.572
kpAddCytobandLabels0.9030.0141.400
kpAddCytobands0.0770.0030.109
kpAddCytobandsAsLine0.2500.0070.346
kpAddLabels1.0310.0171.387
kpAddMainTitle0.0730.0030.104
kpArea0.7910.0101.061
kpArrows1.3150.0251.652
kpAxis0.6920.0090.795
kpBars0.4270.0070.493
kpDataBackground0.5690.0100.693
kpHeatmap0.3040.0060.362
kpLines0.6180.0090.784
kpPlotBAMCoverage14.027 0.49316.821
kpPlotBAMDensity2.7270.0973.100
kpPlotBigWig3.0550.0763.629
kpPlotCoverage1.0280.0171.255
kpPlotDensity73.108 5.19997.566
kpPlotGenes46.883 0.79856.662
kpPlotHorizon31.961 0.28736.792
kpPlotLinks2.1900.0483.616
kpPlotLoess0.1240.0061.013
kpPlotManhattan 9.877 0.58014.708
kpPlotMarkers3.5570.0524.004
kpPlotNames0.2420.0060.322
kpPlotRainfall1.7160.0302.298
kpPlotRegions26.195 0.24131.814
kpPlotRibbon0.2000.0050.248
kpPlotTranscripts15.125 0.13518.312
kpPoints0.6160.0100.723
kpPolygon0.5010.0120.721
kpRect1.7840.0212.274
kpSegments1.2540.0111.560
kpText0.6890.0090.867
lighter0.0020.0010.003
makeGenesDataFromTxDb6.5610.1088.167
mergeTranscripts37.585 0.38845.251
plotDefaultPlotParams0.4310.0050.527
plotKaryotype2.5180.0583.033
plotPalettes0.0290.0050.044
prepareParameters20.0780.0030.100
prepareParameters40.0810.0050.100
processClipping0.0780.0030.099
transparent0.0020.0010.002