Multiple platform build/check report for BioC 3.9 - CHECK report for diffloop on celaya2

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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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/diffloop.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.0’
* 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.

Installation output

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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)

Tests output


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 
 16.255   1.381  18.707

Example timings

name	user	system	elapsed
addchr	0.326	0.014	0.340
annotateAnchors	0.198	0.009	0.210
annotateAnchors.bed	0.136	0.008	0.145
annotateAnchors.bigwig	0.073	0.005	0.078
annotateLoops	0.781	0.053	0.839
annotateLoops.dge	1.145	0.021	1.167
bedToGRanges	0.085	0.006	0.091
calcLDSizeFactors	0.002	0.001	0.002
callCCDs	0.001	0.001	0.001
computeBoundaryScores	0.001	0.000	0.001
featureTest	0.002	0.000	0.002
filterLoops	0.057	0.001	0.058
filterSpanningLoops	0.017	0.000	0.018
getHumanGenes	0.065	0.005	0.070
getHumanTSS	0.192	0.025	0.217
getMouseGenes	0.176	0.019	0.197
getMouseTSS	0.174	0.007	0.182
interchromosomal	0.021	0.001	0.022
intrachromosomal	0.017	0.001	0.018
keepCTCFloops	0.091	0.004	0.094
keepEPloops	0.325	0.016	0.341
loopAssoc	0.002	0.001	0.002
loopDistancePlot	0.040	0.000	0.041
loopGenes	0.136	0.001	0.138
loopMetrics	0.004	0.001	0.006
loopPlot	1.369	0.121	1.997
loopWidth	0.017	0.002	0.116
loopsMake	0.002	0.001	0.003
loopsMake.mango	0.001	0.001	0.002
loopsSubset	0.389	0.060	0.855
mangoCorrection	0.147	0.026	0.216
manyLoopPlots	0.163	0.008	0.317
mergeAnchors	0.195	0.001	0.347
numAnchors	0.019	0.000	0.034
numLoops	0.005	0.001	0.014
padGRanges	0.155	0.014	0.293
pcaPlot	0.028	0.002	0.038
plotTopLoops	1.246	0.025	2.150
quickAssoc	0.072	0.001	0.132
quickAssocVoom	0.068	0.002	0.120
removeRegion	0.315	0.013	0.393
removeSelfLoops	0.012	0.001	0.020
rmchr	0.317	0.027	0.629
sampleNames-loops-method	0.004	0.000	0.005
slidingWindowTest	0.002	0.000	0.003
splitSamples	0.080	0.001	0.082
subsetLoops	0.014	0.001	0.015
subsetRegion	0.672	0.009	1.122
subsetRegionAB	0.425	0.010	0.793
summary-loops-method	0.126	0.001	0.227
topLoops	0.073	0.001	0.088
union-loops-loops-method	0.200	0.002	0.208
updateLDGroups	0.003	0.001	0.093

CHECK report for diffloop on celaya2

Summary

Command output

Installation output

Tests output

Example timings