BioC 3.6: CHECK report for diffloop on malbec1

Package: diffloop

Version: 1.5.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings diffloop_1.5.0.tar.gz

StartedAt: 2017-08-15 22:38:23 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:42:02 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 218.5 seconds

RetCode: 0

Status:  OK

CheckDir: diffloop.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings diffloop_1.5.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/diffloop.Rcheck’
* using R version 3.4.1 (2017-06-30)
* 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 ‘1.5.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/diffloop.Rcheck/00check.log’
for details.

* 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	0.788	0.000	0.787
annotateAnchors	0.292	0.024	0.317
annotateAnchors.bed	0.084	0.000	0.083
annotateAnchors.bigwig	0.036	0.004	0.038
annotateLoops	1.140	0.000	1.141
annotateLoops.dge	0.348	0.008	0.354
bedToGRanges	0.076	0.000	0.077
calcLDSizeFactors	0.000	0.000	0.002
callCCDs	0.000	0.000	0.001
computeBoundaryScores	0.000	0.000	0.002
featureTest	0.000	0.000	0.001
filterLoops	0.104	0.000	0.106
filterSpanningLoops	0.016	0.000	0.015
getHumanGenes	0.056	0.000	0.055
getHumanTSS	0.188	0.000	0.186
getMouseGenes	0.080	0.000	0.081
getMouseTSS	0.144	0.000	0.142
interchromosomal	0.016	0.000	0.017
intrachromosomal	0.016	0.000	0.017
keepCTCFloops	0.108	0.000	0.108
keepEPloops	0.264	0.000	0.264
loopAssoc	0.000	0.000	0.001
loopDistancePlot	0.072	0.000	0.075
loopGenes	0.092	0.000	0.093
loopMetrics	0.004	0.000	0.002
loopPlot	1.124	0.000	1.124
loopWidth	0.016	0.000	0.015
loopsMake	0.004	0.000	0.410
loopsMake.mango	0.000	0.000	0.001
loopsSubset	0.436	0.000	0.471
mangoCorrection	0.164	0.000	0.162
manyLoopPlots	0.328	0.000	0.331
mergeAnchors	0.200	0.000	0.202
numAnchors	0.004	0.004	0.009
numLoops	0.004	0.000	0.002
padGRanges	0.116	0.000	0.117
pcaPlot	0.112	0.000	0.110
plotTopLoops	2.516	0.024	2.542
quickAssoc	0.040	0.000	0.039
quickAssocVoom	0.216	0.000	0.216
removeRegion	0.144	0.004	0.149
removeSelfLoops	0.004	0.000	0.007
rmchr	0.128	0.000	0.129
sampleNames-loops-method	0.004	0.000	0.003
slidingWindowTest	0.004	0.000	0.002
splitSamples	0.072	0.000	0.073
subsetLoops	0.020	0.000	0.019
subsetRegion	0.412	0.008	0.419
subsetRegionAB	0.180	0.008	0.188
summary-loops-method	0.080	0.000	0.079
topLoops	0.044	0.000	0.045
union-loops-loops-method	0.108	0.000	0.106
updateLDGroups	0.000	0.000	0.002