BioC 3.6: CHECK report for karyoploteR on malbec1

Package: karyoploteR

Version: 1.1.9

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings karyoploteR_1.1.9.tar.gz

StartedAt: 2017-08-16 00:14:12 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 00:20:12 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 359.2 seconds

RetCode: 0

Status:  OK

CheckDir: karyoploteR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings karyoploteR_1.1.9.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/karyoploteR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘1.1.9’
* 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 21.992  14.42  43.537
getCytobands   5.300   0.06  44.651
* 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
  ‘/home/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)

name	user	system	elapsed
darker	0.000	0.000	0.001
getChromosomeNamesBoundingBox	0.772	0.000	0.773
getCytobandColors	0.000	0.000	0.001
getCytobands	5.300	0.060	44.651
getDefaultPlotParams	0.292	0.000	0.295
getMainTitleBoundingBox	0.020	0.000	0.022
getVariantsColors	0.020	0.000	0.018
kpAbline	1.132	0.036	1.204
kpAddBaseNumbers	0.196	0.000	0.196
kpAddChromosomeNames	0.020	0.004	0.024
kpAddCytobandLabels	0.168	0.000	0.169
kpAddCytobands	0.032	0.000	0.033
kpAddCytobandsAsLine	0.020	0.000	0.022
kpAddLabels	0.100	0.000	0.101
kpAddMainTitle	0.02	0.00	0.02
kpArrows	0.288	0.000	0.289
kpAxis	0.168	0.000	0.167
kpBars	0.088	0.000	0.088
kpDataBackground	0.064	0.000	0.064
kpHeatmap	0.076	0.000	0.076
kpLines	0.116	0.000	0.115
kpPlotBAMDensity	1.648	0.004	1.654
kpPlotCoverage	2.924	0.000	2.928
kpPlotDensity	21.992	14.420	43.537
kpPlotLinks	0.596	0.004	0.600
kpPlotMarkers	0.364	0.000	0.366
kpPlotRainfall	0.520	0.000	0.519
kpPlotRegions	2.568	0.000	2.570
kpPlotRibbon	0.036	0.000	0.035
kpPoints	0.112	0.000	0.112
kpPolygon	0.056	0.000	0.054
kpRect	0.292	0.000	0.289
kpSegments	0.092	0.004	0.096
kpText	0.108	0.004	0.114
lighter	0	0	0
plotDefaultPlotParams	0.088	0.000	0.089
plotKaryotype	1.012	0.000	1.033
prepareParameters2	0.056	0.000	0.058
prepareParameters4	0.024	0.000	0.025