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This page was generated on 2024-03-28 11:32:23 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4376
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 1071/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
karyoploteR 1.28.0  (landing page)
Bernat Gel
Snapshot Date: 2024-03-26 09:00:03 -0400 (Tue, 26 Mar 2024)
git_url: https://git.bioconductor.org/packages/karyoploteR
git_branch: RELEASE_3_18
git_last_commit: 20fa00f
git_last_commit_date: 2023-10-24 10:55:15 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for karyoploteR on kjohnson1


To the developers/maintainers of the karyoploteR package:
- 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: 1.28.0
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_1.28.0.tar.gz
StartedAt: 2024-03-27 17:13:47 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 17:23:29 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 582.4 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/karyoploteR.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.28.0’
* 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 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     53.205  3.868  57.481
kpPlotGenes       21.432  0.477  21.972
mergeTranscripts  15.716  0.188  15.907
kpPlotHorizon     12.860  0.059  12.972
kpPlotRegions     10.560  0.043  10.607
kpPlotBAMCoverage  9.497  0.226   9.785
kpPlotManhattan    6.563  0.155   6.740
kpPlotTranscripts  6.105  0.042   6.148
* 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
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/karyoploteR.Rcheck/00check.log’
for details.



Installation output

karyoploteR.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL karyoploteR
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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 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 
 22.141   0.818  23.019 

Example timings

karyoploteR.Rcheck/karyoploteR-Ex.timings

nameusersystemelapsed
addGeneNames4.2750.1264.441
autotrack0.0010.0010.002
colByCategory0.0030.0000.003
colByChr0.4610.0120.479
colByRegion1.1500.1101.274
colByValue0.2060.0070.221
darker0.0010.0000.001
filterParams0.0010.0000.001
findIntersections0.1240.0020.128
getChromosomeNamesBoundingBox0.0620.0020.064
getColorSchemas0.0020.0020.004
getCytobandColors0.0010.0020.002
getCytobands0.0020.0000.002
getDataPanelBoundingBox0.0490.0020.051
getDefaultPlotParams0.0690.0070.076
getMainTitleBoundingBox0.0390.0010.040
getTextSize0.0790.0020.081
getVariantsColors0.0010.0000.002
horizonColors0.0030.0000.004
is.color0.0010.0010.001
kpAbline2.5090.6063.160
kpAddBaseNumbers0.3050.0050.309
kpAddChromosomeNames0.0310.0020.032
kpAddChromosomeSeparators0.3810.0040.386
kpAddColorRect0.1810.0020.183
kpAddCytobandLabels0.3360.0040.342
kpAddCytobands0.0310.0010.033
kpAddCytobandsAsLine0.0660.0030.067
kpAddLabels0.3770.0060.384
kpAddMainTitle0.0300.0010.032
kpArea0.2930.0050.298
kpArrows0.5420.0090.556
kpAxis0.2460.0040.252
kpBars0.1830.0030.188
kpDataBackground0.1870.0020.190
kpHeatmap0.1230.0030.136
kpLines0.3020.0040.307
kpPlotBAMCoverage9.4970.2269.785
kpPlotBAMDensity2.3170.0442.368
kpPlotBigWig0.8570.0450.903
kpPlotCoverage0.4640.0200.495
kpPlotDensity53.205 3.86857.481
kpPlotGenes21.432 0.47721.972
kpPlotHorizon12.860 0.05912.972
kpPlotLinks0.6220.0110.644
kpPlotLoess0.0690.0030.072
kpPlotManhattan6.5630.1556.740
kpPlotMarkers1.7170.0231.741
kpPlotNames0.1080.0030.111
kpPlotRainfall0.7980.0120.810
kpPlotRegions10.560 0.04310.607
kpPlotRibbon0.0840.0030.087
kpPlotTranscripts6.1050.0426.148
kpPoints0.2530.0080.261
kpPolygon0.2010.0050.207
kpRect0.7790.0140.794
kpSegments0.5210.0140.536
kpText0.2380.0070.246
lighter0.0010.0000.001
makeGenesDataFromTxDb3.5320.0953.631
mergeTranscripts15.716 0.18815.907
plotDefaultPlotParams0.1380.0020.140
plotKaryotype1.0240.0521.080
plotPalettes0.0270.0070.033
prepareParameters20.0330.0050.038
prepareParameters40.1270.0160.144
processClipping0.0400.0020.041
transparent0.0010.0000.001