Package: karyoploteR

Version: 1.4.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings karyoploteR_1.4.2.tar.gz

StartedAt: 2018-04-12 05:30:24 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 05:37:18 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 414.6 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 --no-vignettes --timings karyoploteR_1.4.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/karyoploteR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.2’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
kpPlotDensity 48.226  3.987  52.996
getCytobands   6.748  0.225  44.986
* 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-3.6-bioc/meat/karyoploteR.Rcheck/00check.log’
for details.

* installing *source* package ‘karyoploteR’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (karyoploteR)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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: memoise
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, 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
Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: rtracklayer
> 
> test_check("karyoploteR")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 128 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 13.563   0.438  14.394 

name	user	system	elapsed
darker	0.001	0.000	0.002
filterParams	0.015	0.001	0.015
getChromosomeNamesBoundingBox	0.464	0.006	0.472
getCytobandColors	0.002	0.001	0.003
getCytobands	6.748	0.225	44.986
getDefaultPlotParams	0.571	0.007	0.752
getMainTitleBoundingBox	0.046	0.002	0.059
getVariantsColors	0.025	0.001	0.026
kpAbline	1.286	0.129	1.900
kpAddBaseNumbers	0.472	0.003	0.488
kpAddChromosomeNames	0.039	0.000	0.040
kpAddCytobandLabels	0.479	0.002	0.602
kpAddCytobands	0.037	0.001	0.038
kpAddCytobandsAsLine	0.038	0.001	0.038
kpAddLabels	0.240	0.001	0.306
kpAddMainTitle	0.041	0.001	0.065
kpArrows	0.449	0.001	0.478
kpAxis	0.358	0.001	0.369
kpBars	0.257	0.002	0.266
kpDataBackground	0.251	0.001	0.254
kpHeatmap	0.197	0.001	0.198
kpLines	0.240	0.002	0.254
kpPlotBAMDensity	1.727	0.035	1.788
kpPlotCoverage	4.042	0.013	4.124
kpPlotDensity	48.226	3.987	52.996
kpPlotLinks	0.753	0.004	0.763
kpPlotLoess	0.055	0.000	0.055
kpPlotMarkers	1.907	0.029	1.977
kpPlotRainfall	0.606	0.003	0.619
kpPlotRegions	3.646	0.009	3.680
kpPlotRibbon	0.074	0.001	0.075
kpPoints	0.205	0.001	0.208
kpPolygon	0.200	0.002	0.203
kpRect	0.488	0.001	0.494
kpSegments	0.221	0.002	0.225
kpText	0.248	0.002	0.250
lighter	0.001	0.000	0.001
plotDefaultPlotParams	0.179	0.001	0.181
plotKaryotype	1.212	0.019	1.254
prepareParameters2	0.040	0.001	0.042
prepareParameters4	0.029	0.001	0.031