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This page was generated on 2023-11-28 11:39:19 -0500 (Tue, 28 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4601
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-11-14 r85524 ucrt) -- "Unsuffered Consequences" 4343
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" 4368
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" 4253
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 1053/2225HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.29.0  (landing page)
Bernat Gel
Snapshot Date: 2023-11-27 14:00:14 -0500 (Mon, 27 Nov 2023)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: devel
git_last_commit: f426285
git_last_commit_date: 2023-10-24 10:55:15 -0500 (Tue, 24 Oct 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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 kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: karyoploteR
Version: 1.29.0
Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings karyoploteR_1.29.0.tar.gz
StartedAt: 2023-11-28 05:25:37 -0000 (Tue, 28 Nov 2023)
EndedAt: 2023-11-28 05:36:19 -0000 (Tue, 28 Nov 2023)
EllapsedTime: 641.2 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library --no-vignettes --timings karyoploteR_1.29.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2023-11-01 r85459)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.29.0’
* 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 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 ... 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     48.475  2.302  51.157
kpPlotGenes       29.488  0.304  29.901
mergeTranscripts  22.908  0.162  23.118
kpPlotHorizon     20.024  0.119  20.189
kpPlotRegions     15.834  0.020  15.889
kpPlotBAMCoverage  9.178  0.248   9.445
kpPlotTranscripts  9.010  0.016   9.047
kpPlotManhattan    5.372  0.104   5.488
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-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) (2023-11-01 r85459) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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

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 
 23.305   0.847  24.194 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames4.0830.1164.206
autotrack0.0010.0000.001
colByCategory0.0030.0000.003
colByChr0.7100.0040.715
colByRegion1.3660.1281.496
colByValue0.2550.0120.267
darker0.0010.0000.001
filterParams000
findIntersections0.1560.0200.176
getChromosomeNamesBoundingBox0.0590.0000.059
getColorSchemas0.0010.0000.002
getCytobandColors0.0010.0000.001
getCytobands0.0030.0000.002
getDataPanelBoundingBox0.0660.0000.065
getDefaultPlotParams0.1010.0040.106
getMainTitleBoundingBox0.0470.0040.050
getTextSize0.1180.0000.118
getVariantsColors0.0010.0000.001
horizonColors0.0050.0000.005
is.color0.0010.0000.001
kpAbline1.3580.0681.434
kpAddBaseNumbers0.5260.0230.551
kpAddChromosomeNames0.0470.0000.047
kpAddChromosomeSeparators0.6420.0040.647
kpAddColorRect0.2110.0000.212
kpAddCytobandLabels0.5450.0040.550
kpAddCytobands0.0480.0000.048
kpAddCytobandsAsLine0.1420.0120.154
kpAddLabels0.6070.0000.608
kpAddMainTitle0.0460.0000.045
kpArea0.4620.0000.463
kpArrows0.7470.0120.760
kpAxis0.4670.0120.480
kpBars0.2570.0000.258
kpDataBackground0.3250.0000.333
kpHeatmap0.1860.0000.186
kpLines0.3460.0000.347
kpPlotBAMCoverage9.1780.2489.445
kpPlotBAMDensity1.7350.0281.765
kpPlotBigWig1.0690.0401.113
kpPlotCoverage0.5840.0080.593
kpPlotDensity48.475 2.30251.157
kpPlotGenes29.488 0.30429.901
kpPlotHorizon20.024 0.11920.189
kpPlotLinks1.3800.0081.391
kpPlotLoess0.0770.0070.084
kpPlotManhattan5.3720.1045.488
kpPlotMarkers2.3940.0162.415
kpPlotNames0.1490.0000.149
kpPlotRainfall1.0840.0001.087
kpPlotRegions15.834 0.02015.889
kpPlotRibbon0.1210.0000.121
kpPlotTranscripts9.0100.0169.047
kpPoints0.3570.0040.362
kpPolygon0.3010.0000.303
kpRect1.0630.0001.066
kpSegments0.7310.0160.750
kpText0.3670.0000.368
lighter0.0010.0000.001
makeGenesDataFromTxDb4.2100.0364.254
mergeTranscripts22.908 0.16223.118
plotDefaultPlotParams0.2250.0040.230
plotKaryotype1.3300.0121.344
plotPalettes0.0190.0000.019
prepareParameters20.0470.0000.046
prepareParameters40.0480.0000.048
processClipping0.0400.0080.048
transparent0.0010.0000.001