BioC 3.4: CHECK report for GenomicInteractions on morelia

Package: GenomicInteractions

Version: 1.8.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.8.1.tar.gz

StartedAt: 2017-04-15 02:44:32 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 02:50:37 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 364.6 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicInteractions.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 GenomicInteractions_1.8.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GenomicInteractions.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.8.1’
* 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 11.4Mb
  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-3.4-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'
** 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'
* DONE (GenomicInteractions)

name	user	system	elapsed
GInteractions-subsetByFeatures-methods	0.447	0.036	0.484
GenomicInteractions-class	0.097	0.011	0.108
GenomicInteractions-package	0.001	0.000	0.001
GenomicInteractions	0.050	0.008	0.057
InteractionHelpers	0.084	0.004	0.089
InteractionTrack	0.791	0.005	0.800
annotateInteractions	0.135	0.002	0.138
annotateRegions	0.041	0.001	0.042
asBED-GInteractions-method	0.395	0.007	0.404
availableDisplayPars	0.037	0.002	0.038
calculateDistances	0.086	0.000	0.087
categoriseInteractions	0.144	0.002	0.146
export.bed12	3.140	0.019	3.163
export.bedpe	0.260	0.013	0.272
export.chiasig	0.165	0.009	0.174
export.igraph	0.108	0.002	0.110
getters	0.092	0.000	0.093
makeGenomicInteractionsFromFile	2.430	0.070	2.504
plotAvgViewpoint	0.328	0.005	0.333
plotCisTrans	0.388	0.003	0.391
plotCounts	0.532	0.011	0.545
plotDists	0.316	0.021	0.337
plotInteractionAnnotations	0.424	0.006	0.430
plotSummaryStats	1.349	0.015	1.371
plotViewpoint	0.573	0.015	0.587
resetAnnotations	0.042	0.001	0.044
setters	0.076	0.000	0.076
summariseByFeaturePairs	1.243	0.006	1.250
summariseByFeatures	0.520	0.005	0.526
viewPoint	0.332	0.003	0.335