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This page was generated on 2023-03-29 11:04:53 -0400 (Wed, 29 Mar 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_64R Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences" 4547
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2023-03-15 r83984 ucrt) -- "Unsuffered Consequences" 4308
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2023-03-16 r83985) -- "Unsuffered Consequences" 4301
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 nebbiolo1


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 1027/2195HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.25.0  (landing page)
Bernat Gel
Snapshot Date: 2023-03-28 14:00:22 -0400 (Tue, 28 Mar 2023)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: devel
git_last_commit: 051aa8b
git_last_commit_date: 2022-11-01 11:15:07 -0400 (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: /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_1.25.0.tar.gz
StartedAt: 2023-03-28 20:42:25 -0400 (Tue, 28 Mar 2023)
EndedAt: 2023-03-28 20:51:09 -0400 (Tue, 28 Mar 2023)
EllapsedTime: 524.3 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_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
    GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* 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 ... 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     31.118  5.335  36.460
kpPlotGenes       20.548  0.288  20.836
mergeTranscripts  16.926  0.336  17.262
kpPlotHorizon     14.754  0.140  14.894
kpPlotRegions     11.024  0.020  11.044
kpPlotBAMCoverage  7.200  0.388   7.589
kpPlotTranscripts  6.209  0.004   6.213
kpPlotManhattan    5.110  0.080   5.191
* 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 Under development (unstable) (2023-03-16 r83996) -- "Unsuffered Consequences"
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 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 
 17.553   0.845  18.388 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames2.8650.1322.997
autotrack0.0010.0000.001
colByCategory0.0030.0000.003
colByChr0.4170.0640.481
colByRegion1.0030.0241.027
colByValue0.1930.0160.209
darker0.0010.0000.001
filterParams000
findIntersections0.0970.0340.131
getChromosomeNamesBoundingBox0.0420.0040.046
getColorSchemas0.0000.0030.003
getCytobandColors0.0000.0020.002
getCytobands0.0000.0020.002
getDataPanelBoundingBox0.0440.0000.044
getDefaultPlotParams0.0550.0200.075
getMainTitleBoundingBox0.0920.0070.099
getTextSize0.0670.0040.071
getVariantsColors0.0000.0000.001
horizonColors0.0030.0000.003
is.color0.0010.0000.001
kpAbline2.0580.2242.284
kpAddBaseNumbers0.3260.0080.334
kpAddChromosomeNames0.0290.0000.029
kpAddChromosomeSeparators0.4120.0040.416
kpAddColorRect0.1500.0120.162
kpAddCytobandLabels0.4040.0120.416
kpAddCytobands0.0330.0000.033
kpAddCytobandsAsLine0.0690.0000.069
kpAddLabels0.4250.0000.425
kpAddMainTitle0.0310.0000.030
kpArea0.3210.0160.337
kpArrows0.5400.0040.543
kpAxis0.2580.0080.265
kpBars0.1650.0000.165
kpDataBackground0.1970.0040.201
kpHeatmap0.1290.0000.129
kpLines0.2390.0080.247
kpPlotBAMCoverage7.2000.3887.589
kpPlotBAMDensity1.8640.0361.900
kpPlotBigWig0.9400.0290.969
kpPlotCoverage0.3920.0000.392
kpPlotDensity31.118 5.33536.460
kpPlotGenes20.548 0.28820.836
kpPlotHorizon14.754 0.14014.894
kpPlotLinks0.9800.0120.991
kpPlotLoess0.0550.0080.064
kpPlotManhattan5.1100.0805.191
kpPlotMarkers1.6720.0121.684
kpPlotNames0.1100.0000.109
kpPlotRainfall0.7200.0080.729
kpPlotRegions11.024 0.02011.044
kpPlotRibbon0.0860.0000.086
kpPlotTranscripts6.2090.0046.213
kpPoints0.2440.0080.252
kpPolygon0.2010.0040.205
kpRect0.7040.0120.717
kpSegments0.5040.0000.504
kpText0.2550.0000.254
lighter0.0010.0000.001
makeGenesDataFromTxDb3.1440.0443.188
mergeTranscripts16.926 0.33617.262
plotDefaultPlotParams0.1430.0040.146
plotKaryotype0.9190.0240.943
plotPalettes0.0190.0000.019
prepareParameters20.030.000.03
prepareParameters40.0280.0030.031
processClipping0.0310.0000.031
transparent0.0010.0000.001