Mac ARM64 build report for BioC 3.20 - CHECK results for karyoploteR on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4381
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_1.31.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/karyoploteR.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* 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 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.31.0’
* 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     52.089  3.799  56.156
kpPlotGenes       20.843  0.446  21.345
mergeTranscripts  15.602  0.188  15.795
kpPlotHorizon     13.446  0.082  13.542
kpPlotRegions     11.014  0.074  11.088
kpPlotBAMCoverage  9.675  0.237   9.921
kpPlotManhattan    6.486  0.133   6.620
kpPlotTranscripts  6.056  0.033   6.091
* 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-3.20-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 Patched (2024-04-24 r86482) -- "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':

    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 
 20.574   0.825  21.423

Example timings

name	user	system	elapsed
addGeneNames	3.728	0.097	3.833
autotrack	0.001	0.000	0.001
colByCategory	0.003	0.001	0.003
colByChr	0.234	0.018	0.256
colByRegion	0.881	0.091	0.976
colByValue	0.198	0.006	0.203
darker	0.001	0.000	0.001
filterParams	0	0	0
findIntersections	0.114	0.001	0.115
getChromosomeNamesBoundingBox	0.057	0.002	0.059
getColorSchemas	0.001	0.002	0.004
getCytobandColors	0.000	0.001	0.003
getCytobands	0.002	0.000	0.002
getDataPanelBoundingBox	0.045	0.001	0.047
getDefaultPlotParams	0.067	0.007	0.074
getMainTitleBoundingBox	0.036	0.002	0.038
getTextSize	0.072	0.002	0.074
getVariantsColors	0.000	0.000	0.001
horizonColors	0.003	0.001	0.003
is.color	0.001	0.000	0.001
kpAbline	2.348	0.628	2.988
kpAddBaseNumbers	0.319	0.006	0.324
kpAddChromosomeNames	0.031	0.001	0.032
kpAddChromosomeSeparators	0.370	0.005	0.376
kpAddColorRect	0.170	0.002	0.172
kpAddCytobandLabels	0.304	0.004	0.309
kpAddCytobands	0.031	0.001	0.032
kpAddCytobandsAsLine	0.066	0.002	0.069
kpAddLabels	0.382	0.007	0.389
kpAddMainTitle	0.032	0.001	0.034
kpArea	0.317	0.006	0.323
kpArrows	0.558	0.011	0.570
kpAxis	0.266	0.004	0.271
kpBars	0.170	0.003	0.172
kpDataBackground	0.196	0.002	0.198
kpHeatmap	0.127	0.002	0.130
kpLines	0.303	0.004	0.307
kpPlotBAMCoverage	9.675	0.237	9.921
kpPlotBAMDensity	2.366	0.058	2.465
kpPlotBigWig	0.837	0.031	0.874
kpPlotCoverage	0.440	0.018	0.457
kpPlotDensity	52.089	3.799	56.156
kpPlotGenes	20.843	0.446	21.345
kpPlotHorizon	13.446	0.082	13.542
kpPlotLinks	1.119	0.025	1.145
kpPlotLoess	0.067	0.002	0.068
kpPlotManhattan	6.486	0.133	6.620
kpPlotMarkers	1.627	0.030	1.658
kpPlotNames	0.098	0.002	0.099
kpPlotRainfall	0.769	0.008	0.777
kpPlotRegions	11.014	0.074	11.088
kpPlotRibbon	0.084	0.003	0.087
kpPlotTranscripts	6.056	0.033	6.091
kpPoints	0.234	0.003	0.237
kpPolygon	0.202	0.009	0.211
kpRect	0.774	0.004	0.779
kpSegments	0.511	0.004	0.515
kpText	0.259	0.009	0.267
lighter	0.001	0.001	0.001
makeGenesDataFromTxDb	3.230	0.086	3.318
mergeTranscripts	15.602	0.188	15.795
plotDefaultPlotParams	0.138	0.001	0.140
plotKaryotype	1.144	0.059	1.206
plotPalettes	0.027	0.003	0.029
prepareParameters2	0.034	0.002	0.036
prepareParameters4	0.034	0.002	0.035
processClipping	0.034	0.002	0.036
transparent	0.001	0.000	0.001

CHECK results for karyoploteR on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings