BioC 3.5: CHECK report for GenomicInteractions on veracruz2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/GenomicInteractions.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 ‘GenomicInteractions/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicInteractions’ version ‘1.10.0’
* 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 ‘GenomicInteractions’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   7.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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-3.5-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.

* installing *source* package ‘GenomicInteractions’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions'
Warning: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions'
Warning: replacing previous import 'BiocGenerics::sd' by 'stats::sd' when loading 'GenomicInteractions'
* DONE (GenomicInteractions)

name	user	system	elapsed
GInteractions-subsetByFeatures-methods	0.616	0.011	0.654
GenomicInteractions-class	0.843	0.003	0.871
GenomicInteractions-package	0.001	0.000	0.001
GenomicInteractions	0.304	0.025	0.332
InteractionHelpers	0.053	0.006	0.060
InteractionTrack	1.096	0.021	1.166
annotateInteractions	0.137	0.004	0.147
annotateRegions	0.037	0.001	0.038
asBED-GInteractions-method	0.313	0.008	0.322
availableDisplayPars	0.029	0.002	0.031
calculateDistances	0.048	0.000	0.048
categoriseInteractions	0.268	0.004	0.283
export.bed12	2.427	0.015	2.498
export.bedpe	0.137	0.004	0.146
export.chiasig	0.094	0.004	0.102
export.igraph	0.090	0.002	0.093
getters	0.075	0.001	0.077
makeGenomicInteractionsFromFile	1.238	0.041	1.309
plotAvgViewpoint	0.214	0.003	0.221
plotCisTrans	1.169	0.010	1.247
plotCounts	1.018	0.004	1.059
plotDists	0.255	0.003	0.270
plotInteractionAnnotations	0.461	0.004	0.471
plotSummaryStats	0.878	0.004	0.895
plotViewpoint	0.449	0.002	0.465
resetAnnotations	0.032	0.001	0.038
setters	0.039	0.000	0.039
summariseByFeaturePairs	0.745	0.005	0.764
summariseByFeatures	0.357	0.003	0.361
viewPoint	0.181	0.002	0.187

BioC 3.5: CHECK report for GenomicInteractions on veracruz2

Summary

Command output