Package: diffloop

Version: 1.15.0

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_1.15.0.tar.gz

StartedAt: 2020-01-16 03:48:02 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 03:55:06 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 423.3 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_1.15.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/diffloop.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.15.0’
* 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-3.11-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/4.0/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) (2019-12-14 r77572) -- "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 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 21.236   1.810  26.830 

name	user	system	elapsed
addchr	0.389	0.010	0.399
annotateAnchors	0.244	0.014	0.261
annotateAnchors.bed	1.039	0.011	1.051
annotateAnchors.bigwig	0.093	0.004	0.097
annotateLoops	0.848	0.050	0.901
annotateLoops.dge	0.576	0.031	0.607
bedToGRanges	0.134	0.005	0.139
calcLDSizeFactors	0.003	0.001	0.004
callCCDs	0.002	0.001	0.002
computeBoundaryScores	0.002	0.000	0.003
featureTest	0.002	0.000	0.001
filterLoops	0.168	0.018	0.187
filterSpanningLoops	0.035	0.006	0.042
getHumanGenes	0.126	0.018	0.144
getHumanTSS	0.215	0.010	0.225
getMouseGenes	0.128	0.007	0.134
getMouseTSS	0.218	0.011	0.228
interchromosomal	0.020	0.001	0.020
intrachromosomal	0.025	0.001	0.026
keepCTCFloops	0.164	0.002	0.166
keepEPloops	0.556	0.015	0.572
loopAssoc	0.002	0.000	0.003
loopDistancePlot	0.041	0.001	0.041
loopGenes	0.185	0.003	0.189
loopMetrics	0.005	0.001	0.006
loopPlot	1.189	0.101	1.291
loopWidth	0.026	0.006	0.032
loopsMake	0.001	0.002	0.004
loopsMake.mango	0.001	0.001	0.002
loopsSubset	0.711	0.127	0.837
mangoCorrection	0.231	0.041	0.272
manyLoopPlots	0.136	0.017	0.154
mergeAnchors	0.237	0.001	0.238
numAnchors	0.020	0.001	0.021
numLoops	0.005	0.001	0.005
padGRanges	0.195	0.015	0.210
pcaPlot	0.029	0.002	0.031
plotTopLoops	1.546	0.023	1.580
quickAssoc	0.057	0.001	0.058
quickAssocVoom	0.096	0.003	0.098
removeRegion	0.367	0.009	0.375
removeSelfLoops	0.014	0.001	0.015
rmchr	0.310	0.012	0.322
sampleNames-loops-method	0.004	0.001	0.004
slidingWindowTest	0.002	0.001	0.003
splitSamples	0.131	0.001	0.132
subsetLoops	0.027	0.001	0.028
subsetRegion	0.860	0.011	0.870
subsetRegionAB	0.520	0.008	0.529
summary-loops-method	0.146	0.002	0.148
topLoops	0.072	0.002	0.075
union-loops-loops-method	0.574	0.091	0.665
updateLDGroups	0.002	0.001	0.003