Package: diffloop

Version: 1.8.0

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_1.8.0.tar.gz

StartedAt: 2018-10-16 20:57:53 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 21:02:19 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 266.0 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_1.8.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/diffloop.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.8.0’
* 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-3.7-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/3.5/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 version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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 
 13.257   0.589  13.955 

name	user	system	elapsed
addchr	0.257	0.022	0.284
annotateAnchors	0.208	0.028	0.239
annotateAnchors.bed	0.080	0.010	0.091
annotateAnchors.bigwig	0.082	0.012	0.094
annotateLoops	0.626	0.029	0.661
annotateLoops.dge	0.424	0.011	0.442
bedToGRanges	0.104	0.004	0.110
calcLDSizeFactors	0.004	0.000	0.004
callCCDs	0.003	0.000	0.003
computeBoundaryScores	0.003	0.001	0.004
featureTest	0.004	0.000	0.004
filterLoops	0.065	0.001	0.067
filterSpanningLoops	0.018	0.001	0.019
getHumanGenes	0.093	0.001	0.095
getHumanTSS	0.168	0.007	0.176
getMouseGenes	0.216	0.005	0.223
getMouseTSS	0.166	0.004	0.172
interchromosomal	0.024	0.001	0.025
intrachromosomal	0.023	0.001	0.023
keepCTCFloops	0.194	0.004	0.199
keepEPloops	0.359	0.007	0.376
loopAssoc	0.004	0.001	0.004
loopDistancePlot	0.024	0.001	0.024
loopGenes	0.130	0.001	0.132
loopMetrics	0.005	0.001	0.006
loopPlot	1.080	0.038	1.136
loopWidth	0.017	0.000	0.018
loopsMake	0.002	0.000	0.003
loopsMake.mango	0.002	0.000	0.002
loopsSubset	0.257	0.001	0.264
mangoCorrection	0.109	0.001	0.110
manyLoopPlots	0.096	0.003	0.098
mergeAnchors	0.182	0.002	0.186
numAnchors	0.029	0.002	0.032
numLoops	0.006	0.000	0.006
padGRanges	0.216	0.005	0.225
pcaPlot	0.023	0.000	0.023
plotTopLoops	1.207	0.045	1.265
quickAssoc	0.060	0.005	0.067
quickAssocVoom	0.055	0.003	0.060
removeRegion	0.235	0.021	0.257
removeSelfLoops	0.013	0.002	0.014
rmchr	0.218	0.011	0.234
sampleNames-loops-method	0.005	0.001	0.006
slidingWindowTest	0.003	0.000	0.004
splitSamples	0.109	0.001	0.109
subsetLoops	0.025	0.001	0.026
subsetRegion	0.624	0.007	0.636
subsetRegionAB	0.344	0.006	0.358
summary-loops-method	0.097	0.001	0.098
topLoops	0.073	0.001	0.074
union-loops-loops-method	0.191	0.004	0.198
updateLDGroups	0.003	0.000	0.003