BioC 3.3: CHECK report for GenomicInteractions on oaxaca

Package: GenomicInteractions

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.6.2.tar.gz

StartedAt: 2016-10-13 01:58:10 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 02:05:07 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 417.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: GenomicInteractions.Rcheck

Warnings: 1

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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_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GenomicInteractions.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.6.2’
* 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 ‘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 ... WARNING
Rd files with duplicated alias 'GenomicInteractions':
  ‘GenomicInteractions-package.Rd’ ‘GenomicInteractions.Rd’
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-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	0.373	0.026	0.400
GenomicInteractions-class	0.101	0.000	0.101
GenomicInteractions	0.058	0.001	0.058
InteractionHelpers	0.065	0.004	0.069
InteractionTrack	0.638	0.006	0.670
annotateInteractions	0.124	0.006	0.129
annotateRegions	0.045	0.002	0.047
asBED-GInteractions-method	0.366	0.008	0.376
availableDisplayPars	0.025	0.001	0.026
calculateDistances	0.063	0.000	0.064
categoriseInteractions	0.114	0.004	0.118
export.bed12	2.976	0.019	2.998
export.bedpe	0.649	0.008	0.658
export.chiasig	0.155	0.007	0.162
export.igraph	0.071	0.002	0.150
getters	0.081	0.000	0.082
makeGenomicInteractionsFromFile	2.846	0.063	2.934
plotAvgViewpoint	0.325	0.003	0.332
plotCisTrans	0.331	0.004	0.338
plotCounts	0.501	0.016	0.521
plotDists	0.284	0.004	0.289
plotInteractionAnnotations	0.335	0.006	0.341
plotSummaryStats	0.934	0.005	0.973
plotViewpoint	0.598	0.016	0.672
resetAnnotations	0.043	0.001	0.045
setters	0.073	0.001	0.073
summariseByFeaturePairs	1.201	0.007	1.210
summariseByFeatures	0.484	0.005	0.490
viewPoint	0.308	0.004	0.317