Package: diffloop

Version: 1.6.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings diffloop_1.6.0.tar.gz

StartedAt: 2018-04-12 02:53:07 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:57:21 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 254.2 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 --no-vignettes --timings diffloop_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/diffloop.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... 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-3.6-bioc/meat/diffloop.Rcheck/00check.log’
for details.

* installing *source* package ‘diffloop’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (diffloop)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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 
  9.581   0.318  10.038 

name	user	system	elapsed
addchr	0.691	0.022	0.892
annotateAnchors	0.528	0.005	0.666
annotateAnchors.bed	0.130	0.002	0.171
annotateAnchors.bigwig	0.058	0.003	0.072
annotateLoops	2.401	0.021	3.050
annotateLoops.dge	0.426	0.009	0.529
bedToGRanges	0.116	0.002	0.126
calcLDSizeFactors	0.003	0.000	0.003
callCCDs	0.002	0.001	0.002
computeBoundaryScores	0.002	0.000	0.002
featureTest	0.001	0.000	0.002
filterLoops	0.131	0.000	0.138
filterSpanningLoops	0.02	0.00	0.02
getHumanGenes	0.067	0.001	0.069
getHumanTSS	0.175	0.005	0.231
getMouseGenes	0.123	0.002	0.157
getMouseTSS	0.181	0.003	0.192
interchromosomal	0.021	0.000	0.022
intrachromosomal	0.020	0.000	0.023
keepCTCFloops	0.166	0.003	0.171
keepEPloops	0.373	0.005	0.477
loopAssoc	0.002	0.000	0.002
loopDistancePlot	0.122	0.001	0.155
loopGenes	0.138	0.001	0.171
loopMetrics	0.004	0.001	0.004
loopPlot	1.566	0.027	1.837
loopWidth	0.029	0.001	0.030
loopsMake	0.001	0.000	0.001
loopsMake.mango	0.001	0.000	0.000
loopsSubset	0.494	0.002	0.497
mangoCorrection	0.133	0.000	0.136
manyLoopPlots	0.341	0.002	0.345
mergeAnchors	0.242	0.000	0.243
numAnchors	0.011	0.000	0.012
numLoops	0.004	0.001	0.004
padGRanges	0.149	0.006	0.157
pcaPlot	0.103	0.001	0.103
plotTopLoops	2.286	0.012	2.336
quickAssoc	0.038	0.001	0.041
quickAssocVoom	0.287	0.001	0.297
removeRegion	0.203	0.005	0.212
removeSelfLoops	0.009	0.000	0.009
rmchr	0.159	0.005	0.164
sampleNames-loops-method	0.003	0.000	0.004
slidingWindowTest	0.001	0.001	0.002
splitSamples	0.092	0.000	0.099
subsetLoops	0.028	0.001	0.030
subsetRegion	0.462	0.005	0.473
subsetRegionAB	0.259	0.005	0.269
summary-loops-method	0.108	0.001	0.112
topLoops	0.053	0.001	0.053
union-loops-loops-method	0.136	0.001	0.137
updateLDGroups	0.002	0.000	0.002