BioC 3.4: CHECK report for GenomicInteractions on malbec1

Package: GenomicInteractions

Version: 1.8.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.8.1.tar.gz

StartedAt: 2017-04-14 22:48:18 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:53:16 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 297.6 seconds

RetCode: 0

Status:  OK

CheckDir: GenomicInteractions.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.8.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GenomicInteractions.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (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 10.9Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    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
  ‘/home/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	0.276	0.008	0.287
GenomicInteractions-class	0.076	0.004	0.081
GenomicInteractions-package	0.000	0.000	0.001
GenomicInteractions	0.044	0.000	0.044
InteractionHelpers	0.068	0.000	0.068
InteractionTrack	0.480	0.000	0.478
annotateInteractions	0.124	0.000	0.122
annotateRegions	0.032	0.000	0.033
asBED-GInteractions-method	0.236	0.008	0.244
availableDisplayPars	0.020	0.000	0.019
calculateDistances	0.048	0.000	0.049
categoriseInteractions	0.096	0.000	0.098
export.bed12	2.140	0.004	2.148
export.bedpe	0.188	0.004	0.192
export.chiasig	0.176	0.000	0.179
export.igraph	0.076	0.000	0.079
getters	0.064	0.000	0.063
makeGenomicInteractionsFromFile	1.820	0.016	1.839
plotAvgViewpoint	0.212	0.000	0.212
plotCisTrans	0.280	0.000	0.279
plotCounts	0.324	0.008	0.333
plotDists	0.296	0.004	0.299
plotInteractionAnnotations	0.384	0.004	0.394
plotSummaryStats	0.780	0.000	0.777
plotViewpoint	0.364	0.012	0.376
resetAnnotations	0.032	0.000	0.031
setters	0.048	0.000	0.048
summariseByFeaturePairs	0.808	0.000	0.807
summariseByFeatures	0.364	0.000	0.366
viewPoint	0.18	0.00	0.18