BioC 3.4: CHECK report for diffloop on morelia

Package: diffloop

Version: 1.2.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffloop_1.2.2.tar.gz

StartedAt: 2017-04-15 01:07:08 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:11:35 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 267.2 seconds

RetCode: 0

Status:  OK

CheckDir: diffloop.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 diffloop_1.2.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/diffloop.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 ‘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	0.180	0.007	0.187
annotateAnchors	0.119	0.005	0.124
annotateAnchors.bed	0.049	0.002	0.051
annotateAnchors.bigwig	0.044	0.002	0.047
annotateLoops	0.620	0.014	0.635
annotateLoops.dge	0.697	0.009	0.706
bedToGRanges	0.091	0.002	0.093
calcLDSizeFactors	0.001	0.001	0.002
callCCDs	0.001	0.000	0.001
computeBoundaryScores	0.001	0.000	0.001
featureTest	0.002	0.001	0.002
filterLoops	0.065	0.000	0.065
filterSpanningLoops	0.014	0.000	0.014
getHumanGenes	0.045	0.001	0.047
getHumanTSS	0.151	0.003	0.153
getMouseGenes	0.104	0.001	0.105
getMouseTSS	0.188	0.001	0.189
interchromosomal	0.018	0.000	0.019
intrachromosomal	0.018	0.000	0.018
keepCTCFloops	0.142	0.002	0.144
keepEPloops	0.321	0.004	0.325
loopAssoc	0.001	0.000	0.002
loopDistancePlot	0.015	0.000	0.015
loopGenes	0.096	0.001	0.096
loopMetrics	0.004	0.000	0.004
loopPlot	0.599	0.020	0.776
loopWidth	0.022	0.000	0.022
loopsMake	0.001	0.000	0.001
loopsMake.mango	0.000	0.000	0.001
loopsSubset	0.135	0.002	0.137
mangoCorrection	0.075	0.009	0.085
manyLoopPlots	0.117	0.007	0.165
mergeAnchors	0.099	0.001	0.099
numAnchors	0.012	0.000	0.013
numLoops	0.003	0.000	0.003
padGRanges	0.144	0.001	0.146
pcaPlot	0.021	0.000	0.021
plotTopLoops	0.959	0.010	0.990
quickAssoc	0.013	0.000	0.013
quickAssocVoom	0.014	0.001	0.013
removeRegion	0.205	0.004	0.209
removeSelfLoops	0.008	0.000	0.008
rmchr	0.151	0.003	0.185
sampleNames-loops-method	0.002	0.000	0.002
slidingWindowTest	0.001	0.000	0.002
splitSamples	0.093	0.001	0.095
subsetLoops	0.020	0.000	0.019
subsetRegion	0.319	0.002	0.321
subsetRegionAB	0.248	0.003	0.251
summary-loops-method	0.089	0.001	0.089
topLoops	0.015	0.000	0.014
union-loops-loops-method	0.126	0.001	0.127
updateLDGroups	0.002	0.000	0.002