BioC 3.5: CHECK report for karyoploteR on malbec2

Package: karyoploteR

Version: 1.2.2

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings karyoploteR_1.2.2.tar.gz

StartedAt: 2017-10-18 00:17:48 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:23:35 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 347.4 seconds

RetCode: 0

Status:  OK

CheckDir: karyoploteR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings karyoploteR_1.2.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/karyoploteR.Rcheck’
* using R version 3.4.2 (2017-09-28)
* 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 ‘1.2.2’
* 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 ... NOTE
Namespace in Imports field not imported from: 'bezier'
  All declared Imports should be used.
* 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 23.124  4.800  33.716
getCytobands   5.496  0.068  51.912
* 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: 3 NOTEs
See
  ‘/home/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	0.000	0.000	0.001
getChromosomeNamesBoundingBox	0.800	0.000	0.798
getCytobandColors	0.000	0.000	0.002
getCytobands	5.496	0.068	51.912
getDefaultPlotParams	0.400	0.004	0.403
getMainTitleBoundingBox	0.024	0.000	0.022
kpAbline	0.964	0.056	1.069
kpAddBaseNumbers	0.212	0.000	0.212
kpAddChromosomeNames	0.020	0.000	0.021
kpAddCytobandLabels	0.164	0.000	0.163
kpAddCytobands	0.024	0.000	0.022
kpAddCytobandsAsLine	0.024	0.000	0.024
kpAddLabels	0.088	0.000	0.091
kpAddMainTitle	0.020	0.000	0.021
kpArrows	0.312	0.000	0.314
kpAxis	0.128	0.000	0.129
kpBars	0.084	0.000	0.084
kpDataBackground	0.068	0.000	0.065
kpHeatmap	0.080	0.000	0.081
kpLines	0.172	0.008	0.176
kpPlotBAMDensity	1.764	0.028	2.162
kpPlotCoverage	3.172	0.004	3.179
kpPlotDensity	23.124	4.800	33.716
kpPlotMarkers	0.360	0.000	0.359
kpPlotRegions	2.572	0.000	2.575
kpPlotRibbon	0.032	0.000	0.033
kpPoints	0.112	0.000	0.113
kpPolygon	0.056	0.000	0.053
kpRect	0.300	0.000	0.302
kpSegments	0.104	0.004	0.106
kpText	0.112	0.000	0.113
lighter	0	0	0
plotDefaultPlotParams	0.068	0.004	0.071
plotKaryotype	1.108	0.000	1.122
prepareParameters2	0.056	0.000	0.056
prepareParameters4	0.036	0.000	0.037