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 01:24:47 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:30:50 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 362.4 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) (2019-03-18 r76245)
* 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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (diffloop)

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
Copyright (C) 2019 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 
 15.236   1.305  16.495 

name	user	system	elapsed
addchr	0.231	0.007	0.239
annotateAnchors	0.190	0.014	0.205
annotateAnchors.bed	0.157	0.031	0.189
annotateAnchors.bigwig	0.089	0.017	0.106
annotateLoops	0.616	0.043	0.661
annotateLoops.dge	0.517	0.026	0.543
bedToGRanges	0.111	0.003	0.115
calcLDSizeFactors	0.003	0.000	0.003
callCCDs	0.002	0.001	0.002
computeBoundaryScores	0.003	0.001	0.003
featureTest	0.002	0.001	0.003
filterLoops	0.094	0.001	0.095
filterSpanningLoops	0.019	0.001	0.020
getHumanGenes	0.085	0.007	0.092
getHumanTSS	0.173	0.009	0.181
getMouseGenes	0.162	0.008	0.169
getMouseTSS	0.134	0.008	0.142
interchromosomal	0.013	0.001	0.014
intrachromosomal	0.016	0.001	0.017
keepCTCFloops	0.953	0.018	0.971
keepEPloops	0.348	0.030	0.377
loopAssoc	0.002	0.000	0.003
loopDistancePlot	0.033	0.000	0.033
loopGenes	0.150	0.002	0.152
loopMetrics	0.005	0.001	0.006
loopPlot	1.200	0.111	1.310
loopWidth	0.009	0.000	0.009
loopsMake	0.001	0.001	0.002
loopsMake.mango	0.001	0.000	0.002
loopsSubset	0.245	0.004	0.249
mangoCorrection	0.118	0.001	0.119
manyLoopPlots	0.121	0.004	0.125
mergeAnchors	0.182	0.001	0.184
numAnchors	0.016	0.000	0.016
numLoops	0.004	0.001	0.005
padGRanges	0.111	0.009	0.120
pcaPlot	0.014	0.001	0.015
plotTopLoops	1.381	0.211	1.600
quickAssoc	0.048	0.001	0.049
quickAssocVoom	0.066	0.003	0.070
removeRegion	0.293	0.011	0.305
removeSelfLoops	0.007	0.000	0.008
rmchr	0.242	0.010	0.252
sampleNames-loops-method	0.004	0.001	0.005
slidingWindowTest	0.002	0.000	0.003
splitSamples	0.114	0.001	0.114
subsetLoops	0.019	0.001	0.020
subsetRegion	0.605	0.010	0.615
subsetRegionAB	0.363	0.008	0.372
summary-loops-method	0.072	0.001	0.074
topLoops	0.044	0.001	0.045
union-loops-loops-method	0.176	0.001	0.177
updateLDGroups	0.002	0.001	0.003