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"	4378
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     52.232  3.708  56.169
kpPlotGenes       21.209  0.449  21.665
mergeTranscripts  15.625  0.183  15.810
kpPlotHorizon     13.645  0.059  13.708
kpPlotRegions     10.641  0.062  10.704
kpPlotBAMCoverage  9.202  0.215   9.433
kpPlotTranscripts  6.204  0.035   6.239
kpPlotManhattan    6.089  0.134   6.240
* 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 
 20.754   0.802  21.584

Example timings

name	user	system	elapsed
addGeneNames	3.515	0.104	3.639
autotrack	0.001	0.001	0.001
colByCategory	0.002	0.001	0.003
colByChr	0.441	0.018	0.462
colByRegion	1.076	0.110	1.187
colByValue	0.195	0.005	0.200
darker	0.001	0.000	0.001
filterParams	0.001	0.000	0.000
findIntersections	0.112	0.001	0.113
getChromosomeNamesBoundingBox	0.058	0.001	0.059
getColorSchemas	0.001	0.002	0.004
getCytobandColors	0.001	0.001	0.002
getCytobands	0.002	0.000	0.002
getDataPanelBoundingBox	0.044	0.001	0.046
getDefaultPlotParams	0.075	0.007	0.082
getMainTitleBoundingBox	0.036	0.001	0.037
getTextSize	0.076	0.002	0.079
getVariantsColors	0.001	0.000	0.001
horizonColors	0.003	0.001	0.003
is.color	0.001	0.000	0.001
kpAbline	2.341	0.600	2.957
kpAddBaseNumbers	0.317	0.005	0.322
kpAddChromosomeNames	0.032	0.002	0.033
kpAddChromosomeSeparators	0.389	0.004	0.393
kpAddColorRect	0.185	0.002	0.187
kpAddCytobandLabels	0.324	0.005	0.329
kpAddCytobands	0.033	0.001	0.034
kpAddCytobandsAsLine	0.070	0.003	0.073
kpAddLabels	0.414	0.006	0.422
kpAddMainTitle	0.033	0.002	0.035
kpArea	0.323	0.004	0.326
kpArrows	0.541	0.005	0.548
kpAxis	0.259	0.004	0.264
kpBars	0.155	0.002	0.158
kpDataBackground	0.189	0.002	0.191
kpHeatmap	0.116	0.002	0.118
kpLines	0.279	0.004	0.283
kpPlotBAMCoverage	9.202	0.215	9.433
kpPlotBAMDensity	2.393	0.060	2.558
kpPlotBigWig	0.829	0.046	0.877
kpPlotCoverage	0.470	0.013	0.483
kpPlotDensity	52.232	3.708	56.169
kpPlotGenes	21.209	0.449	21.665
kpPlotHorizon	13.645	0.059	13.708
kpPlotLinks	1.112	0.011	1.124
kpPlotLoess	0.066	0.002	0.068
kpPlotManhattan	6.089	0.134	6.240
kpPlotMarkers	1.325	0.019	1.348
kpPlotNames	0.105	0.002	0.107
kpPlotRainfall	0.767	0.008	0.775
kpPlotRegions	10.641	0.062	10.704
kpPlotRibbon	0.084	0.003	0.086
kpPlotTranscripts	6.204	0.035	6.239
kpPoints	0.254	0.012	0.265
kpPolygon	0.212	0.005	0.222
kpRect	0.745	0.012	0.757
kpSegments	0.503	0.012	0.514
kpText	0.254	0.006	0.261
lighter	0.001	0.000	0.001
makeGenesDataFromTxDb	3.321	0.081	3.401
mergeTranscripts	15.625	0.183	15.810
plotDefaultPlotParams	0.148	0.002	0.150
plotKaryotype	1.138	0.046	1.187
plotPalettes	0.020	0.008	0.028
prepareParameters2	0.037	0.001	0.038
prepareParameters4	0.039	0.002	0.041
processClipping	0.036	0.002	0.038
transparent	0.001	0.000	0.001

CHECK results for karyoploteR on kjohnson1

Summary

Command output

Installation output

Tests output

Example timings