Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-15 13:23:03 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
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: 2022-08-14 13:55:13 -0400 (Sun, 14 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: 2022-08-15 03:45:49 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 03:59:55 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 845.8 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         69.974  3.748  74.578
kpPlotGenes           43.757  0.576  44.622
mergeTranscripts      34.133  0.169  34.588
kpPlotHorizon         32.533  0.176  32.926
kpPlotRegions         23.466  0.063  24.360
kpPlotTranscripts     13.448  0.036  13.706
kpPlotManhattan        8.443  0.184   8.829
kpPlotBAMCoverage      8.081  0.385   8.538
makeGenesDataFromTxDb  5.957  0.056   6.033
* 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 
 31.402   1.308  32.922 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames3.6360.0943.755
autotrack0.0020.0000.002
colByCategory0.0040.0010.005
colByChr1.1000.0491.156
colByRegion2.2540.1382.406
colByValue0.3710.0050.381
darker0.0020.0000.002
filterParams0.0000.0000.001
findIntersections0.2630.0010.265
getChromosomeNamesBoundingBox0.0840.0020.087
getColorSchemas0.0030.0020.004
getCytobandColors0.0010.0020.002
getCytobands0.0020.0000.002
getDataPanelBoundingBox0.0850.0010.087
getDefaultPlotParams0.1440.0070.154
getMainTitleBoundingBox0.0660.0010.067
getTextSize0.1740.0160.193
getVariantsColors0.0010.0000.002
horizonColors0.0070.0020.009
is.color0.0010.0000.001
kpAbline4.2290.7184.976
kpAddBaseNumbers0.7720.0050.796
kpAddChromosomeNames0.0650.0010.068
kpAddChromosomeSeparators0.9660.0050.976
kpAddColorRect0.3210.0020.326
kpAddCytobandLabels0.8600.0220.891
kpAddCytobands0.0630.0010.064
kpAddCytobandsAsLine0.1260.0020.131
kpAddLabels0.9410.0050.952
kpAddMainTitle0.0620.0010.064
kpArea0.7190.0070.729
kpArrows1.2010.0191.233
kpAxis0.6390.0040.646
kpBars0.3940.0020.400
kpDataBackground0.4790.0030.488
kpHeatmap0.2910.0020.296
kpLines0.7000.0350.739
kpPlotBAMCoverage8.0810.3858.538
kpPlotBAMDensity2.6760.0622.761
kpPlotBigWig1.8240.0551.898
kpPlotCoverage0.9120.0100.928
kpPlotDensity69.974 3.74874.578
kpPlotGenes43.757 0.57644.622
kpPlotHorizon32.533 0.17632.926
kpPlotLinks2.0530.0092.082
kpPlotLoess0.1240.0010.127
kpPlotManhattan8.4430.1848.829
kpPlotMarkers3.5460.0243.738
kpPlotNames0.2250.0010.236
kpPlotRainfall1.5720.0091.601
kpPlotRegions23.466 0.06324.360
kpPlotRibbon0.1830.0020.197
kpPlotTranscripts13.448 0.03613.706
kpPoints0.5650.0030.574
kpPolygon0.4520.0040.461
kpRect1.5370.0061.550
kpSegments1.1630.0061.172
kpText0.5440.0040.550
lighter0.0010.0000.001
makeGenesDataFromTxDb5.9570.0566.033
mergeTranscripts34.133 0.16934.588
plotDefaultPlotParams0.3420.0020.349
plotKaryotype2.1190.0202.157
plotPalettes0.0260.0020.029
prepareParameters20.0630.0020.065
prepareParameters40.0660.0020.068
processClipping0.0660.0020.071
transparent0.0010.0000.001