Package: karyoploteR

Version: 1.13.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings karyoploteR_1.13.4.tar.gz

StartedAt: 2020-01-16 05:47:21 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 06:00:56 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 814.9 seconds

RetCode: 0

Status:  OK

CheckDir: karyoploteR.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:karyoploteR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings karyoploteR_1.13.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘karyoploteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘karyoploteR’ version ‘1.13.4’
* 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 ... OK
* 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 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         58.950 11.031  70.386
kpPlotGenes           42.538  1.431  44.442
mergeTranscripts      36.678  0.398  37.273
kpPlotHorizon         30.174  0.058  30.297
kpPlotRegions         22.147  0.081  22.543
kpPlotCoverage        22.010  0.117  22.146
kpPlotTranscripts     14.810  0.048  14.862
kpPlotBAMCoverage      7.720  0.596   8.351
makeGenesDataFromTxDb  5.402  0.172   5.577
kpPlotManhattan        5.026  0.201   5.285
getCytobands           1.374  0.123  20.724
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL karyoploteR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, 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, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 
> test_check("karyoploteR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 181 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 27.940   2.273  30.190 

name	user	system	elapsed
addGeneNames	4.777	0.223	5.000
autotrack	0.001	0.001	0.002
colByChr	1.113	0.036	1.150
colByRegion	1.862	0.238	2.102
colByValue	0.411	0.068	0.482
darker	0.003	0.001	0.004
filterParams	0.001	0.001	0.002
findIntersections	0.271	0.048	0.320
getChromosomeNamesBoundingBox	0.081	0.013	0.095
getColorSchemas	0.005	0.004	0.009
getCytobandColors	0.003	0.002	0.005
getCytobands	1.374	0.123	20.724
getDataPanelBoundingBox	0.078	0.009	0.090
getDefaultPlotParams	0.144	0.014	0.158
getMainTitleBoundingBox	0.054	0.002	0.059
getTextSize	0.189	0.002	0.196
getVariantsColors	0.001	0.000	0.003
horizonColors	0.009	0.001	0.010
is.color	0.002	0.001	0.002
kpAbline	3.040	0.465	3.515
kpAddBaseNumbers	0.757	0.006	0.765
kpAddChromosomeNames	0.073	0.004	0.077
kpAddChromosomeSeparators	0.965	0.006	0.974
kpAddCytobandLabels	0.922	0.005	0.930
kpAddCytobands	0.063	0.001	0.065
kpAddCytobandsAsLine	0.128	0.003	0.133
kpAddLabels	0.247	0.002	0.250
kpAddMainTitle	0.046	0.002	0.047
kpArea	0.730	0.007	0.737
kpArrows	1.000	0.015	1.018
kpAxis	0.707	0.007	0.716
kpBars	0.375	0.004	0.379
kpDataBackground	0.528	0.002	0.531
kpHeatmap	0.315	0.002	0.318
kpLines	0.526	0.004	0.530
kpPlotBAMCoverage	7.720	0.596	8.351
kpPlotBAMDensity	2.414	0.129	2.547
kpPlotBigWig	2.087	0.214	2.303
kpPlotCoverage	22.010	0.117	22.146
kpPlotDensity	58.950	11.031	70.386
kpPlotGenes	42.538	1.431	44.442
kpPlotHorizon	30.174	0.058	30.297
kpPlotLinks	2.324	0.011	2.382
kpPlotLoess	0.151	0.002	0.154
kpPlotManhattan	5.026	0.201	5.285
kpPlotMarkers	4.115	0.037	4.208
kpPlotNames	0.240	0.001	0.302
kpPlotRainfall	1.635	0.013	1.650
kpPlotRegions	22.147	0.081	22.543
kpPlotRibbon	0.200	0.002	0.203
kpPlotTranscripts	14.810	0.048	14.862
kpPoints	0.533	0.003	0.538
kpPolygon	0.490	0.004	0.496
kpRect	1.562	0.007	1.570
kpSegments	0.974	0.004	0.979
kpText	0.593	0.007	0.602
lighter	0.002	0.000	0.002
makeGenesDataFromTxDb	5.402	0.172	5.577
mergeTranscripts	36.678	0.398	37.273
plotDefaultPlotParams	0.253	0.001	0.256
plotKaryotype	1.775	0.031	1.815
plotPalettes	0.027	0.003	0.032
prepareParameters2	0.069	0.002	0.071
prepareParameters4	0.209	0.032	0.242
processClipping	0.065	0.001	0.067
transparent	0.002	0.000	0.002