Package: karyoploteR

Version: 1.10.5

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_1.10.5.tar.gz

StartedAt: 2019-10-16 04:00:37 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:11:47 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 669.3 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_1.10.5.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/karyoploteR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.5’
* 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 or elapsed time > 5s
                        user system elapsed
kpPlotDensity         67.378 10.400  78.121
kpPlotGenes           31.294  0.851  32.168
mergeTranscripts      25.807  0.374  26.459
kpPlotRegions         14.317  0.064  14.594
kpPlotCoverage        13.055  0.152  13.208
kpPlotTranscripts      9.983  0.048  10.234
kpPlotBAMCoverage      7.056  0.561   7.629
getCytobands           6.171  0.429  35.199
makeGenesDataFromTxDb  5.451  0.196   5.692
* 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-3.9-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/3.6/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 version 3.6.1 (2019-07-05) -- "Action of the Toes"
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: 132 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 22.058   1.749  23.792 

name	user	system	elapsed
addGeneNames	4.397	0.212	4.610
autotrack	0.002	0.001	0.003
colByChr	0.627	0.037	0.664
colByRegion	1.374	0.262	1.637
darker	0.003	0.001	0.003
filterParams	0.001	0.000	0.001
getChromosomeNamesBoundingBox	0.043	0.007	0.051
getCytobandColors	0.002	0.002	0.005
getCytobands	6.171	0.429	35.199
getDataPanelBoundingBox	0.057	0.002	0.059
getDefaultPlotParams	0.098	0.013	0.111
getMainTitleBoundingBox	0.048	0.002	0.049
getTextSize	0.086	0.002	0.089
getVariantsColors	0.001	0.001	0.002
is.color	0.002	0.000	0.003
kpAbline	2.540	0.450	2.998
kpAddBaseNumbers	0.356	0.021	0.380
kpAddChromosomeNames	0.043	0.001	0.044
kpAddChromosomeSeparators	0.630	0.039	0.671
kpAddCytobandLabels	0.380	0.004	0.385
kpAddCytobands	0.037	0.002	0.040
kpAddCytobandsAsLine	0.066	0.003	0.069
kpAddLabels	0.142	0.002	0.145
kpAddMainTitle	0.033	0.001	0.034
kpArea	0.374	0.004	0.379
kpArrows	0.655	0.010	0.666
kpAxis	0.294	0.004	0.298
kpBars	0.165	0.002	0.167
kpDataBackground	0.190	0.002	0.192
kpHeatmap	0.224	0.013	0.236
kpLines	0.301	0.005	0.306
kpPlotBAMCoverage	7.056	0.561	7.629
kpPlotBAMDensity	2.038	0.095	2.134
kpPlotBigWig	0.938	0.041	0.982
kpPlotCoverage	13.055	0.152	13.208
kpPlotDensity	67.378	10.400	78.121
kpPlotGenes	31.294	0.851	32.168
kpPlotLinks	1.237	0.007	1.244
kpPlotLoess	0.079	0.002	0.087
kpPlotMarkers	1.781	0.005	1.786
kpPlotNames	0.096	0.001	0.099
kpPlotRainfall	0.854	0.012	0.867
kpPlotRegions	14.317	0.064	14.594
kpPlotRibbon	0.100	0.002	0.102
kpPlotTranscripts	9.983	0.048	10.234
kpPoints	0.286	0.003	0.289
kpPolygon	0.271	0.004	0.289
kpRect	1.107	0.007	1.120
kpSegments	0.664	0.003	0.745
kpText	0.225	0.002	0.228
lighter	0.002	0.000	0.003
makeGenesDataFromTxDb	5.451	0.196	5.692
mergeTranscripts	25.807	0.374	26.459
plotDefaultPlotParams	0.169	0.007	0.176
plotKaryotype	1.709	0.052	1.767
prepareParameters2	0.060	0.003	0.063
prepareParameters4	0.041	0.002	0.042
processClipping	0.035	0.001	0.037
transparent	0.001	0.000	0.002