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This page was generated on 2023-09-26 11:35:39 -0400 (Tue, 26 Sep 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4625
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4378
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4394
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 1041/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.26.0  (landing page)
Bernat Gel
Snapshot Date: 2023-09-25 14:00:11 -0400 (Mon, 25 Sep 2023)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: RELEASE_3_17
git_last_commit: 473f8eb
git_last_commit_date: 2023-04-25 10:52:09 -0400 (Tue, 25 Apr 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 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for karyoploteR on nebbiolo1


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: 1.26.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings karyoploteR_1.26.0.tar.gz
StartedAt: 2023-09-25 22:24:36 -0400 (Mon, 25 Sep 2023)
EndedAt: 2023-09-25 22:32:53 -0400 (Mon, 25 Sep 2023)
EllapsedTime: 496.6 seconds
RetCode: 0
Status:   OK  
CheckDir: karyoploteR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings karyoploteR_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/karyoploteR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.26.0’
* 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 ... 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 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     30.854  6.136  37.057
kpPlotGenes       19.989  0.692  20.681
mergeTranscripts  15.497  0.156  15.652
kpPlotHorizon     13.273  0.236  13.508
kpPlotRegions     10.772  0.115  10.887
kpPlotBAMCoverage  6.963  0.275   7.238
kpPlotTranscripts  6.088  0.032   6.120
kpPlotManhattan    5.152  0.096   5.248
* 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 ...
  ‘karyoploteR.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/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 version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 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 181 ]

══ 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 181 ]
> 
> proc.time()
   user  system elapsed 
 17.574   0.962  18.524 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames2.7920.0432.836
autotrack0.0010.0000.001
colByCategory0.0030.0000.003
colByChr0.4380.0390.478
colByRegion0.9350.0370.971
colByValue0.1810.0030.185
darker0.0010.0000.001
filterParams0.0000.0010.000
findIntersections0.1040.0190.122
getChromosomeNamesBoundingBox0.0390.0080.047
getColorSchemas0.0030.0000.003
getCytobandColors0.0010.0000.001
getCytobands0.0010.0000.002
getDataPanelBoundingBox0.0410.0030.045
getDefaultPlotParams0.0600.0160.076
getMainTitleBoundingBox0.0310.0030.034
getTextSize0.0630.0210.083
getVariantsColors0.0010.0000.001
horizonColors0.0040.0000.004
is.color0.0000.0010.001
kpAbline0.9230.0420.965
kpAddBaseNumbers0.3140.0000.314
kpAddChromosomeNames0.0290.0000.028
kpAddChromosomeSeparators0.3840.0190.404
kpAddColorRect0.1530.0050.157
kpAddCytobandLabels0.3220.0000.322
kpAddCytobands0.0280.0000.028
kpAddCytobandsAsLine0.0580.0000.058
kpAddLabels0.4000.0000.401
kpAddMainTitle0.0300.0000.031
kpArea0.3080.0030.312
kpArrows0.5440.0000.544
kpAxis0.2590.0000.259
kpBars0.1570.0040.161
kpDataBackground0.1950.0030.200
kpHeatmap0.1220.0010.122
kpLines0.240.000.24
kpPlotBAMCoverage6.9630.2757.238
kpPlotBAMDensity1.8230.0361.858
kpPlotBigWig0.7650.0120.778
kpPlotCoverage0.3910.0030.395
kpPlotDensity30.854 6.13637.057
kpPlotGenes19.989 0.69220.681
kpPlotHorizon13.273 0.23613.508
kpPlotLinks0.9270.0360.964
kpPlotLoess0.0620.0000.061
kpPlotManhattan5.1520.0965.248
kpPlotMarkers1.6020.0081.611
kpPlotNames0.1040.0040.108
kpPlotRainfall0.7260.0040.730
kpPlotRegions10.772 0.11510.887
kpPlotRibbon0.0800.0000.081
kpPlotTranscripts6.0880.0326.120
kpPoints0.2580.0000.258
kpPolygon0.2050.0120.216
kpRect0.7410.0120.752
kpSegments0.4970.0120.509
kpText0.2490.0040.252
lighter0.0010.0000.001
makeGenesDataFromTxDb3.0470.0883.135
mergeTranscripts15.497 0.15615.652
plotDefaultPlotParams0.1530.0000.153
plotKaryotype0.9050.0080.924
plotPalettes0.0160.0040.019
prepareParameters20.0340.0000.034
prepareParameters40.0300.0040.033
processClipping0.0340.0000.034
transparent0.0010.0000.001