Package: diffloop

Version: 1.10.0

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_1.10.0.tar.gz

StartedAt: 2019-04-15 23:32:02 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:36:30 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 268.1 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_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/diffloop.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.10.0’
* 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-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
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 
 12.473   0.547  13.095 

name	user	system	elapsed
addchr	0.199	0.022	0.222
annotateAnchors	0.157	0.020	0.179
annotateAnchors.bed	0.089	0.002	0.092
annotateAnchors.bigwig	0.049	0.001	0.050
annotateLoops	0.438	0.022	0.467
annotateLoops.dge	0.319	0.012	0.334
bedToGRanges	0.084	0.002	0.087
calcLDSizeFactors	0.002	0.000	0.003
callCCDs	0.002	0.001	0.002
computeBoundaryScores	0.001	0.000	0.001
featureTest	0.002	0.001	0.002
filterLoops	0.074	0.000	0.076
filterSpanningLoops	0.014	0.000	0.015
getHumanGenes	0.048	0.002	0.049
getHumanTSS	0.184	0.008	0.196
getMouseGenes	0.122	0.004	0.126
getMouseTSS	0.147	0.006	0.154
interchromosomal	0.013	0.001	0.013
intrachromosomal	0.018	0.000	0.019
keepCTCFloops	0.136	0.004	0.142
keepEPloops	0.369	0.008	0.378
loopAssoc	0.001	0.000	0.002
loopDistancePlot	0.031	0.001	0.032
loopGenes	0.143	0.002	0.146
loopMetrics	0.002	0.000	0.003
loopPlot	0.862	0.043	0.914
loopWidth	0.009	0.000	0.009
loopsMake	0.001	0.000	0.001
loopsMake.mango	0	0	0
loopsSubset	0.190	0.002	0.194
mangoCorrection	0.076	0.001	0.076
manyLoopPlots	0.077	0.002	0.081
mergeAnchors	0.136	0.001	0.139
numAnchors	0.025	0.001	0.026
numLoops	0.004	0.001	0.004
padGRanges	0.188	0.004	0.193
pcaPlot	0.022	0.000	0.023
plotTopLoops	1.065	0.033	1.111
quickAssoc	0.060	0.006	0.069
quickAssocVoom	0.042	0.005	0.048
removeRegion	0.234	0.008	0.243
removeSelfLoops	0.009	0.000	0.009
rmchr	0.153	0.005	0.161
sampleNames-loops-method	0.003	0.000	0.003
slidingWindowTest	0.002	0.001	0.002
splitSamples	0.100	0.000	0.101
subsetLoops	0.021	0.000	0.022
subsetRegion	0.473	0.006	0.484
subsetRegionAB	0.227	0.004	0.233
summary-loops-method	0.094	0.000	0.095
topLoops	0.067	0.006	0.077
union-loops-loops-method	0.178	0.028	0.206
updateLDGroups	0.002	0.001	0.002