Multiple platform build/check report for BioC 3.19 - CHECK results for karyoploteR on lconway

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4753
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4518
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/meat/karyoploteR.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-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 Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.30.0’
* 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     44.847  4.028  49.454
kpPlotGenes       26.196  0.679  27.212
mergeTranscripts  21.237  0.336  21.786
kpPlotHorizon     18.267  0.180  18.594
kpPlotRegions     14.120  0.119  14.337
kpPlotBAMCoverage  9.615  0.387  10.111
kpPlotTranscripts  7.886  0.089   8.044
kpPlotManhattan    5.552  0.222   5.848
* 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/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-x86_64/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: x86_64-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 
 21.888   1.254  23.408

Example timings

name	user	system	elapsed
addGeneNames	3.851	0.145	4.045
autotrack	0.001	0.001	0.002
colByCategory	0.003	0.001	0.003
colByChr	0.626	0.036	0.670
colByRegion	1.319	0.175	1.510
colByValue	0.230	0.007	0.242
darker	0.001	0.000	0.001
filterParams	0.001	0.000	0.001
findIntersections	0.150	0.002	0.153
getChromosomeNamesBoundingBox	0.057	0.003	0.060
getColorSchemas	0.001	0.003	0.004
getCytobandColors	0.001	0.002	0.003
getCytobands	0.002	0.001	0.002
getDataPanelBoundingBox	0.058	0.002	0.061
getDefaultPlotParams	0.092	0.009	0.101
getMainTitleBoundingBox	0.048	0.002	0.050
getTextSize	0.099	0.003	0.104
getVariantsColors	0.000	0.000	0.001
horizonColors	0.003	0.000	0.004
is.color	0.000	0.000	0.001
kpAbline	2.811	1.038	3.909
kpAddBaseNumbers	0.420	0.006	0.431
kpAddChromosomeNames	0.041	0.002	0.043
kpAddChromosomeSeparators	0.533	0.008	0.548
kpAddColorRect	0.235	0.005	0.242
kpAddCytobandLabels	0.456	0.008	0.471
kpAddCytobands	0.047	0.002	0.049
kpAddCytobandsAsLine	0.093	0.003	0.097
kpAddLabels	0.577	0.010	0.593
kpAddMainTitle	0.043	0.002	0.046
kpArea	0.430	0.006	0.437
kpArrows	0.698	0.013	0.717
kpAxis	0.376	0.008	0.389
kpBars	0.240	0.004	0.246
kpDataBackground	0.300	0.006	0.311
kpHeatmap	0.178	0.004	0.184
kpLines	0.376	0.009	0.388
kpPlotBAMCoverage	9.615	0.387	10.111
kpPlotBAMDensity	1.761	0.072	1.852
kpPlotBigWig	1.081	0.037	1.130
kpPlotCoverage	0.568	0.020	0.596
kpPlotDensity	44.847	4.028	49.454
kpPlotGenes	26.196	0.679	27.212
kpPlotHorizon	18.267	0.180	18.594
kpPlotLinks	1.379	0.022	1.412
kpPlotLoess	0.073	0.003	0.078
kpPlotManhattan	5.552	0.222	5.848
kpPlotMarkers	2.144	0.040	2.203
kpPlotNames	0.139	0.002	0.144
kpPlotRainfall	1.008	0.017	1.033
kpPlotRegions	14.120	0.119	14.337
kpPlotRibbon	0.102	0.002	0.105
kpPlotTranscripts	7.886	0.089	8.044
kpPoints	0.340	0.007	0.350
kpPolygon	0.287	0.009	0.301
kpRect	0.956	0.015	0.982
kpSegments	0.652	0.009	0.667
kpText	0.298	0.005	0.305
lighter	0.001	0.001	0.001
makeGenesDataFromTxDb	3.996	0.100	4.131
mergeTranscripts	21.237	0.336	21.786
plotDefaultPlotParams	0.212	0.004	0.219
plotKaryotype	1.313	0.048	1.385
plotPalettes	0.018	0.004	0.024
prepareParameters2	0.041	0.002	0.044
prepareParameters4	0.040	0.002	0.043
processClipping	0.041	0.002	0.044
transparent	0.001	0.001	0.001

CHECK results for karyoploteR on lconway

Summary

Command output

Installation output

Tests output

Example timings