BioC 3.6: CHECK report for karyoploteR on veracruz1

Package: karyoploteR

Version: 1.1.9

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings karyoploteR_1.1.9.tar.gz

StartedAt: 2017-08-16 04:46:39 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 04:53:49 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 430.2 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_1.1.9.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/karyoploteR.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.1.9’
* 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 51.180  4.111  58.658
getCytobands   5.915  0.215  40.407
* 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)

name	user	system	elapsed
darker	0.002	0.000	0.002
getChromosomeNamesBoundingBox	0.909	0.005	0.943
getCytobandColors	0.002	0.001	0.004
getCytobands	5.915	0.215	40.407
getDefaultPlotParams	0.364	0.005	0.371
getMainTitleBoundingBox	0.030	0.001	0.030
getVariantsColors	0.029	0.001	0.028
kpAbline	1.193	0.080	1.312
kpAddBaseNumbers	0.228	0.007	0.254
kpAddChromosomeNames	0.030	0.003	0.034
kpAddCytobandLabels	0.241	0.026	0.276
kpAddCytobands	0.026	0.001	0.026
kpAddCytobandsAsLine	0.026	0.001	0.029
kpAddLabels	0.149	0.001	0.152
kpAddMainTitle	0.026	0.001	0.028
kpArrows	0.398	0.002	0.414
kpAxis	0.719	0.005	0.730
kpBars	0.114	0.001	0.124
kpDataBackground	0.085	0.001	0.092
kpHeatmap	0.104	0.001	0.110
kpLines	0.142	0.001	0.146
kpPlotBAMDensity	1.611	0.042	1.682
kpPlotCoverage	3.784	0.009	3.896
kpPlotDensity	51.180	4.111	58.658
kpPlotLinks	0.752	0.004	0.781
kpPlotMarkers	0.464	0.002	0.490
kpPlotRainfall	0.638	0.003	0.652
kpPlotRegions	3.384	0.007	3.472
kpPlotRibbon	0.042	0.000	0.044
kpPoints	0.145	0.001	0.152
kpPolygon	0.081	0.001	0.085
kpRect	0.391	0.001	0.402
kpSegments	0.125	0.002	0.132
kpText	0.154	0.001	0.157
lighter	0.001	0.000	0.001
plotDefaultPlotParams	0.106	0.001	0.107
plotKaryotype	1.345	0.016	1.422
prepareParameters2	0.056	0.002	0.061
prepareParameters4	0.023	0.001	0.025