Package: karyoploteR

Version: 1.9.15

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_1.9.15.tar.gz

StartedAt: 2019-04-09 01:46:24 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:54:51 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 507.4 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_1.9.15.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.9.15’
* 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     60.781  5.138  66.416
kpPlotGenes       23.977  0.503  24.692
mergeTranscripts  18.487  0.128  18.758
kpPlotCoverage    10.966  0.064  11.136
kpPlotRegions     10.711  0.025  10.854
kpPlotTranscripts  7.540  0.029   7.651
kpPlotBAMCoverage  5.932  0.283   6.287
getCytobands       4.450  0.202  27.755
* 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’ ...
** 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
* DONE (karyoploteR)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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, colMeans, colSums, 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, rowMeans, rowSums,
    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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 16.730   0.841  17.743 

name	user	system	elapsed
addGeneNames	2.870	0.098	2.978
autotrack	0.001	0.000	0.001
colByChr	0.354	0.009	0.366
colByRegion	0.877	0.134	1.017
darker	0.001	0.000	0.001
filterParams	0.001	0.001	0.001
getChromosomeNamesBoundingBox	0.033	0.003	0.037
getCytobandColors	0.002	0.000	0.002
getCytobands	4.450	0.202	27.755
getDataPanelBoundingBox	0.037	0.001	0.038
getDefaultPlotParams	0.085	0.006	0.094
getMainTitleBoundingBox	0.028	0.000	0.028
getTextSize	0.066	0.001	0.067
getVariantsColors	0.001	0.000	0.002
is.color	0.002	0.000	0.002
kpAbline	1.978	0.223	2.221
kpAddBaseNumbers	0.298	0.003	0.303
kpAddChromosomeNames	0.034	0.001	0.035
kpAddChromosomeSeparators	0.398	0.003	0.410
kpAddCytobandLabels	0.282	0.003	0.289
kpAddCytobands	0.035	0.001	0.037
kpAddCytobandsAsLine	0.151	0.021	0.176
kpAddLabels	0.065	0.001	0.066
kpAddMainTitle	0.026	0.000	0.027
kpArea	0.308	0.002	0.312
kpArrows	0.492	0.007	0.513
kpAxis	0.242	0.012	0.258
kpBars	0.138	0.004	0.143
kpDataBackground	0.186	0.010	0.205
kpHeatmap	0.120	0.008	0.132
kpLines	0.301	0.020	0.322
kpPlotBAMCoverage	5.932	0.283	6.287
kpPlotBAMDensity	1.882	0.052	1.953
kpPlotBigWig	0.646	0.017	0.667
kpPlotCoverage	10.966	0.064	11.136
kpPlotDensity	60.781	5.138	66.416
kpPlotGenes	23.977	0.503	24.692
kpPlotLinks	1.007	0.005	1.025
kpPlotLoess	0.060	0.001	0.062
kpPlotMarkers	1.471	0.004	1.499
kpPlotNames	0.088	0.001	0.089
kpPlotRainfall	0.697	0.003	0.706
kpPlotRegions	10.711	0.025	10.854
kpPlotRibbon	0.081	0.002	0.083
kpPlotTranscripts	7.540	0.029	7.651
kpPoints	0.222	0.002	0.226
kpPolygon	0.204	0.002	0.211
kpRect	0.637	0.003	0.642
kpSegments	0.492	0.002	0.496
kpText	0.245	0.002	0.248
lighter	0.000	0.000	0.001
makeGenesDataFromTxDb	3.904	0.084	4.019
mergeTranscripts	18.487	0.128	18.758
plotDefaultPlotParams	0.110	0.001	0.113
plotKaryotype	1.215	0.021	1.252
prepareParameters2	0.048	0.001	0.050
prepareParameters4	0.030	0.001	0.031
processClipping	0.029	0.001	0.030
transparent	0.001	0.001	0.001