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 03:00:44 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:11:26 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 641.8 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) (2019-03-18 r76245)
* 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         66.741 10.189  77.191
kpPlotGenes           30.395  1.249  31.993
mergeTranscripts      23.224  0.254  23.487
kpPlotRegions         13.745  0.086  13.938
kpPlotCoverage        10.745  0.153  10.899
kpPlotTranscripts      8.410  0.038   8.456
kpPlotBAMCoverage      7.026  0.545   7.582
makeGenesDataFromTxDb  4.829  0.307   5.135
getCytobands           4.717  0.359  30.439
* 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 Under development (unstable) (2019-03-18 r76245) -- "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, 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 
 20.985   1.820  22.767 

name	user	system	elapsed
addGeneNames	3.735	0.176	3.911
autotrack	0.001	0.000	0.001
colByChr	0.460	0.023	0.484
colByRegion	1.277	0.260	1.539
darker	0.002	0.001	0.002
filterParams	0.001	0.001	0.002
getChromosomeNamesBoundingBox	0.036	0.007	0.044
getCytobandColors	0.002	0.001	0.004
getCytobands	4.717	0.359	30.439
getDataPanelBoundingBox	0.058	0.001	0.059
getDefaultPlotParams	0.103	0.012	0.115
getMainTitleBoundingBox	0.036	0.002	0.039
getTextSize	0.079	0.002	0.080
getVariantsColors	0.001	0.001	0.001
is.color	0.001	0.000	0.001
kpAbline	2.636	0.425	3.072
kpAddBaseNumbers	0.392	0.003	0.396
kpAddChromosomeNames	0.033	0.001	0.035
kpAddChromosomeSeparators	0.456	0.004	0.461
kpAddCytobandLabels	0.416	0.004	0.421
kpAddCytobands	0.035	0.001	0.036
kpAddCytobandsAsLine	0.085	0.003	0.088
kpAddLabels	0.105	0.002	0.107
kpAddMainTitle	0.233	0.061	0.294
kpArea	0.364	0.003	0.368
kpArrows	0.596	0.017	0.614
kpAxis	0.332	0.005	0.338
kpBars	0.213	0.019	0.234
kpDataBackground	0.250	0.012	0.263
kpHeatmap	0.161	0.025	0.186
kpLines	0.334	0.016	0.350
kpPlotBAMCoverage	7.026	0.545	7.582
kpPlotBAMDensity	1.972	0.103	2.109
kpPlotBigWig	0.960	0.014	0.977
kpPlotCoverage	10.745	0.153	10.899
kpPlotDensity	66.741	10.189	77.191
kpPlotGenes	30.395	1.249	31.993
kpPlotLinks	1.296	0.009	1.307
kpPlotLoess	0.071	0.001	0.073
kpPlotMarkers	1.749	0.005	1.788
kpPlotNames	0.106	0.001	0.108
kpPlotRainfall	0.730	0.008	0.757
kpPlotRegions	13.745	0.086	13.938
kpPlotRibbon	0.101	0.002	0.104
kpPlotTranscripts	8.410	0.038	8.456
kpPoints	0.244	0.003	0.247
kpPolygon	0.240	0.003	0.244
kpRect	0.927	0.007	0.933
kpSegments	0.485	0.004	0.490
kpText	0.308	0.003	0.311
lighter	0.001	0.000	0.002
makeGenesDataFromTxDb	4.829	0.307	5.135
mergeTranscripts	23.224	0.254	23.487
plotDefaultPlotParams	0.118	0.001	0.119
plotKaryotype	1.471	0.030	1.540
prepareParameters2	0.067	0.003	0.070
prepareParameters4	0.048	0.002	0.050
processClipping	0.047	0.001	0.049
transparent	0.001	0.000	0.002