Mac ARM64 build report for BioC 3.19 - CHECK results for karyoploteR on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4461
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*

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### Running command:
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###   /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_1.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/karyoploteR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* 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 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.30.0’
* 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 code 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 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 ... NOTE
checkRd: (-1) kpPlotBAMCoverage.Rd:48: Lost braces
    48 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotBAMDensity.Rd:48: Lost braces
    48 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotCoverage.Rd:46: Lost braces
    46 |  There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                         ^
checkRd: (-1) kpPlotDensity.Rd:42: Lost braces
    42 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotManhattan.Rd:80: Lost braces
    80 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotMarkers.Rd:81: Lost braces
    81 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPlotRainfall.Rd:47: Lost braces
    47 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpPoints.Rd:54: Lost braces
    54 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) kpRect.Rd:55: Lost braces
    55 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
checkRd: (-1) plotKaryotype.Rd:61: Lost braces
    61 | There's more information at the \url{https://bernatgel.github.io/karyoploter_tutorial/}{karyoploteR tutorial}.
       |                                                                                        ^
* 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 16.432  1.252  17.739
kpPlotGenes    6.271  0.117   6.391
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-bioc-mac-arm64/meat/karyoploteR.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL karyoploteR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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':

    anyDuplicated, aperm, append, as.data.frame, basename, cbind,
    colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
    get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    Position, rank, rbind, Reduce, 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':

    expand.grid, I, 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 
  6.547   0.231   6.778

Example timings

name	user	system	elapsed
addGeneNames	1.312	0.031	1.345
autotrack	0	0	0
colByCategory	0.001	0.000	0.001
colByChr	0.127	0.006	0.133
colByRegion	0.284	0.019	0.303
colByValue	0.055	0.002	0.056
darker	0.000	0.000	0.001
filterParams	0.001	0.000	0.000
findIntersections	0.032	0.002	0.035
getChromosomeNamesBoundingBox	0.016	0.001	0.017
getColorSchemas	0.001	0.001	0.001
getCytobandColors	0	0	0
getCytobands	0.001	0.000	0.000
getDataPanelBoundingBox	0.012	0.001	0.013
getDefaultPlotParams	0.018	0.003	0.022
getMainTitleBoundingBox	0.009	0.001	0.011
getTextSize	0.029	0.001	0.030
getVariantsColors	0	0	0
horizonColors	0.001	0.000	0.001
is.color	0.001	0.000	0.000
kpAbline	0.642	0.196	0.839
kpAddBaseNumbers	0.084	0.001	0.086
kpAddChromosomeNames	0.009	0.001	0.009
kpAddChromosomeSeparators	0.568	0.007	0.575
kpAddColorRect	0.037	0.001	0.037
kpAddCytobandLabels	0.083	0.001	0.084
kpAddCytobands	0.007	0.000	0.008
kpAddCytobandsAsLine	0.018	0.001	0.018
kpAddLabels	0.108	0.006	0.114
kpAddMainTitle	0.010	0.001	0.010
kpArea	0.091	0.002	0.093
kpArrows	0.131	0.003	0.134
kpAxis	0.070	0.001	0.072
kpBars	0.051	0.000	0.052
kpDataBackground	0.051	0.000	0.051
kpHeatmap	0.032	0.001	0.033
kpLines	0.065	0.000	0.065
kpPlotBAMCoverage	3.200	0.062	3.264
kpPlotBAMDensity	0.737	0.014	0.752
kpPlotBigWig	0.25	0.01	0.26
kpPlotCoverage	0.107	0.002	0.108
kpPlotDensity	16.432	1.252	17.739
kpPlotGenes	6.271	0.117	6.391
kpPlotHorizon	4.449	0.040	4.491
kpPlotLinks	0.257	0.003	0.260
kpPlotLoess	0.018	0.001	0.019
kpPlotManhattan	2.051	0.045	2.121
kpPlotMarkers	0.482	0.007	0.489
kpPlotNames	0.029	0.001	0.031
kpPlotRainfall	0.201	0.007	0.219
kpPlotRegions	3.118	0.038	3.160
kpPlotRibbon	0.025	0.001	0.026
kpPlotTranscripts	1.681	0.011	1.694
kpPoints	0.064	0.002	0.065
kpPolygon	0.054	0.002	0.056
kpRect	0.196	0.008	0.204
kpSegments	0.130	0.004	0.134
kpText	0.066	0.002	0.068
lighter	0.001	0.000	0.001
makeGenesDataFromTxDb	0.875	0.018	0.894
mergeTranscripts	4.124	0.032	4.157
plotDefaultPlotParams	0.039	0.000	0.039
plotKaryotype	0.339	0.018	0.358
plotPalettes	0.009	0.002	0.011
prepareParameters2	0.010	0.001	0.010
prepareParameters4	0.010	0.000	0.011
processClipping	0.010	0.001	0.012
transparent	0	0	0

CHECK results for karyoploteR on kjohnson3

Summary

Command output

Installation output

Tests output

Example timings