BioC 3.4: CHECK report for diffloop on malbec1

Package: diffloop

Version: 1.2.2

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings diffloop_1.2.2.tar.gz

StartedAt: 2017-04-14 22:06:19 -0400 (Fri, 14 Apr 2017)

EndedAt: 2017-04-14 22:09:37 -0400 (Fri, 14 Apr 2017)

EllapsedTime: 197.4 seconds

RetCode: 0

Status:  OK

CheckDir: diffloop.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 diffloop_1.2.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/diffloop.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 ‘diffloop/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘diffloop’ 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 ‘diffloop’ can be installed ... OK
* checking installed package size ... OK
* 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 loading without being on the library search path ... 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 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: OK

* installing *source* package ‘diffloop’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (diffloop)

name	user	system	elapsed
addchr	0.184	0.008	0.193
annotateAnchors	0.124	0.000	0.124
annotateAnchors.bed	0.048	0.000	0.049
annotateAnchors.bigwig	0.06	0.00	0.06
annotateLoops	0.680	0.000	0.681
annotateLoops.dge	0.776	0.008	0.784
bedToGRanges	0.064	0.000	0.063
calcLDSizeFactors	0.004	0.000	0.002
callCCDs	0.000	0.000	0.002
computeBoundaryScores	0.004	0.000	0.001
featureTest	0.000	0.000	0.001
filterLoops	0.100	0.004	0.101
filterSpanningLoops	0.024	0.000	0.024
getHumanGenes	0.064	0.004	0.070
getHumanTSS	0.160	0.000	0.163
getMouseGenes	0.088	0.000	0.086
getMouseTSS	0.148	0.000	0.147
interchromosomal	0.016	0.000	0.018
intrachromosomal	0.016	0.000	0.016
keepCTCFloops	0.092	0.000	0.094
keepEPloops	0.288	0.000	0.289
loopAssoc	0.004	0.000	0.001
loopDistancePlot	0.012	0.000	0.014
loopGenes	0.088	0.000	0.090
loopMetrics	0.004	0.000	0.002
loopPlot	0.568	0.004	0.573
loopWidth	0.020	0.000	0.019
loopsMake	0.004	0.000	0.013
loopsMake.mango	0.000	0.000	0.001
loopsSubset	0.156	0.008	0.162
mangoCorrection	0.072	0.000	0.071
manyLoopPlots	0.076	0.004	0.080
mergeAnchors	0.116	0.000	0.116
numAnchors	0.012	0.000	0.010
numLoops	0.004	0.000	0.003
padGRanges	0.112	0.016	0.128
pcaPlot	0.024	0.000	0.024
plotTopLoops	0.824	0.012	0.838
quickAssoc	0.012	0.000	0.009
quickAssocVoom	0.008	0.000	0.009
removeRegion	0.168	0.000	0.166
removeSelfLoops	0.008	0.000	0.008
rmchr	0.144	0.008	0.153
sampleNames-loops-method	0.000	0.000	0.002
slidingWindowTest	0.004	0.000	0.001
splitSamples	0.088	0.000	0.086
subsetLoops	0.020	0.004	0.023
subsetRegion	0.308	0.004	0.312
subsetRegionAB	0.316	0.004	0.317
summary-loops-method	0.068	0.000	0.068
topLoops	0.008	0.000	0.008
union-loops-loops-method	0.124	0.000	0.123
updateLDGroups	0.000	0.000	0.002