Multiple platform build/check report for BioC 3.10 - CHECK report for diffloop on merida1

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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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/diffloop.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.14.0’
* 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-3.10-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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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 
 13.589   0.749  14.421

Example timings

name	user	system	elapsed
addchr	0.299	0.016	0.327
annotateAnchors	0.277	0.003	0.284
annotateAnchors.bed	0.123	0.002	0.124
annotateAnchors.bigwig	0.076	0.004	0.080
annotateLoops	1.343	0.029	1.390
annotateLoops.dge	0.990	0.012	1.016
bedToGRanges	0.107	0.002	0.109
calcLDSizeFactors	0.002	0.001	0.002
callCCDs	0.002	0.000	0.002
computeBoundaryScores	0.001	0.000	0.002
featureTest	0.002	0.001	0.002
filterLoops	0.102	0.003	0.107
filterSpanningLoops	0.020	0.003	0.023
getHumanGenes	0.067	0.002	0.069
getHumanTSS	0.195	0.022	0.218
getMouseGenes	0.123	0.009	0.134
getMouseTSS	0.199	0.022	0.225
interchromosomal	0.029	0.004	0.034
intrachromosomal	0.027	0.004	0.031
keepCTCFloops	0.176	0.010	0.189
keepEPloops	0.405	0.009	0.420
loopAssoc	0.002	0.000	0.002
loopDistancePlot	0.032	0.000	0.032
loopGenes	0.173	0.003	0.176
loopMetrics	0.004	0.001	0.005
loopPlot	1.095	0.074	1.186
loopWidth	0.016	0.003	0.018
loopsMake	0.000	0.001	0.001
loopsMake.mango	0.001	0.000	0.001
loopsSubset	0.414	0.061	0.478
mangoCorrection	0.127	0.018	0.145
manyLoopPlots	0.113	0.003	0.117
mergeAnchors	0.153	0.000	0.154
numAnchors	0.014	0.000	0.015
numLoops	0.005	0.001	0.004
padGRanges	0.140	0.006	0.146
pcaPlot	0.018	0.000	0.019
plotTopLoops	1.137	0.013	1.166
quickAssoc	0.057	0.000	0.057
quickAssocVoom	0.046	0.000	0.048
removeRegion	0.153	0.003	0.156
removeSelfLoops	0.009	0.000	0.009
rmchr	0.169	0.006	0.177
sampleNames-loops-method	0.003	0.001	0.004
slidingWindowTest	0.001	0.000	0.002
splitSamples	0.099	0.000	0.102
subsetLoops	0.026	0.001	0.026
subsetRegion	0.641	0.007	0.657
subsetRegionAB	0.312	0.006	0.321
summary-loops-method	0.113	0.001	0.117
topLoops	0.062	0.001	0.064
union-loops-loops-method	0.276	0.001	0.277
updateLDGroups	0.001	0.000	0.002

CHECK report for diffloop on merida1

Summary

Command output

Installation output

Tests output

Example timings