Package: diffloop

Version: 1.11.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffloop.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffloop_1.11.0.tar.gz

StartedAt: 2019-04-09 00:29:59 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:34:27 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 268.3 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 --install=check:diffloop.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffloop_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/diffloop.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.11.0’
* 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 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 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/diffloop.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL diffloop
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘diffloop’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (diffloop)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(diffloop)
> 
> test_check("diffloop")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 4 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 11.586   0.559  12.211 

name	user	system	elapsed
addchr	0.159	0.004	0.167
annotateAnchors	0.128	0.004	0.134
annotateAnchors.bed	0.100	0.011	0.111
annotateAnchors.bigwig	0.066	0.007	0.074
annotateLoops	0.445	0.024	0.477
annotateLoops.dge	0.388	0.009	0.399
bedToGRanges	0.075	0.001	0.076
calcLDSizeFactors	0.001	0.001	0.002
callCCDs	0.001	0.000	0.001
computeBoundaryScores	0.001	0.000	0.001
featureTest	0.001	0.000	0.001
filterLoops	0.059	0.000	0.059
filterSpanningLoops	0.012	0.001	0.012
getHumanGenes	0.081	0.003	0.085
getHumanTSS	0.124	0.003	0.128
getMouseGenes	0.156	0.006	0.163
getMouseTSS	0.148	0.005	0.154
interchromosomal	0.011	0.000	0.012
intrachromosomal	0.011	0.000	0.011
keepCTCFloops	0.795	0.005	0.806
keepEPloops	0.260	0.008	0.269
loopAssoc	0.001	0.001	0.001
loopDistancePlot	0.030	0.000	0.031
loopGenes	0.117	0.001	0.121
loopMetrics	0.002	0.000	0.003
loopPlot	0.843	0.054	0.908
loopWidth	0.014	0.000	0.015
loopsMake	0.001	0.001	0.001
loopsMake.mango	0.001	0.000	0.001
loopsSubset	0.259	0.003	0.263
mangoCorrection	0.099	0.001	0.102
manyLoopPlots	0.103	0.003	0.108
mergeAnchors	0.161	0.001	0.168
numAnchors	0.015	0.000	0.016
numLoops	0.004	0.001	0.004
padGRanges	0.146	0.006	0.157
pcaPlot	0.022	0.001	0.025
plotTopLoops	1.169	0.101	1.353
quickAssoc	0.041	0.000	0.041
quickAssocVoom	0.046	0.000	0.047
removeRegion	0.147	0.004	0.152
removeSelfLoops	0.009	0.001	0.009
rmchr	0.142	0.005	0.148
sampleNames-loops-method	0.003	0.000	0.004
slidingWindowTest	0.001	0.000	0.002
splitSamples	0.069	0.000	0.070
subsetLoops	0.013	0.000	0.013
subsetRegion	0.421	0.006	0.432
subsetRegionAB	0.239	0.004	0.251
summary-loops-method	0.093	0.000	0.094
topLoops	0.048	0.000	0.050
union-loops-loops-method	0.133	0.002	0.141
updateLDGroups	0.002	0.000	0.002