BioC 3.5: CHECK report for karyoploteR on toluca2

Package: karyoploteR

Version: 0.99.16

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings karyoploteR_0.99.16.tar.gz

StartedAt: 2017-04-23 05:45:28 -0400 (Sun, 23 Apr 2017)

EndedAt: 2017-04-23 05:52:56 -0400 (Sun, 23 Apr 2017)

EllapsedTime: 448.6 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_0.99.16.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/karyoploteR.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘0.99.16’
* 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 ... NOTE
kpPlotMarkers: no visible global function definition for 'strwidth'
Undefined global functions or variables:
  strwidth
Consider adding
  importFrom("graphics", "strwidth")
to your NAMESPACE file.
* 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  50.895  3.971  56.715
getCytobands    7.293  0.198  40.876
kpPlotCoverage  4.410  0.026   6.582
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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	0.966	0.009	0.981
getCytobandColors	0.002	0.001	0.003
getCytobands	7.293	0.198	40.876
getDefaultPlotParams	0.490	0.005	0.496
getMainTitleBoundingBox	0.032	0.001	0.033
kpAbline	1.350	0.105	1.470
kpAddBaseNumbers	0.301	0.020	0.324
kpAddChromosomeNames	0.028	0.001	0.030
kpAddCytobandLabels	0.238	0.002	0.242
kpAddCytobands	0.027	0.000	0.028
kpAddCytobandsAsLine	0.029	0.001	0.031
kpAddLabels	0.130	0.001	0.131
kpAddMainTitle	0.029	0.000	0.030
kpArrows	0.507	0.005	0.590
kpAxis	0.212	0.001	0.270
kpBars	0.136	0.001	0.710
kpDataBackground	0.099	0.001	0.473
kpHeatmap	0.132	0.002	0.581
kpLines	0.205	0.003	0.755
kpPlotBAMDensity	1.737	0.045	2.317
kpPlotCoverage	4.410	0.026	6.582
kpPlotDensity	50.895	3.971	56.715
kpPlotMarkers	0.633	0.086	0.727
kpPlotRegions	3.727	0.014	3.772
kpPlotRibbon	0.046	0.001	0.047
kpPoints	0.167	0.001	0.171
kpPolygon	0.080	0.001	0.081
kpRect	0.445	0.003	0.455
kpSegments	0.168	0.001	0.173
kpText	0.180	0.002	0.185
lighter	0.001	0.001	0.001
plotDefaultPlotParams	0.106	0.001	0.107
plotKaryotype	1.617	0.021	1.673
prepareParameters2	0.043	0.001	0.045
prepareParameters4	0.030	0.001	0.030