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CHECK report for diffloop on machv2

This page was generated on 2020-10-17 11:58:23 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE diffloop PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 475/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffloop 1.16.0
Caleb Lareau
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/diffloop
Branch: RELEASE_3_11
Last Commit: 672f933
Last Changed Date: 2020-04-27 14:57:23 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: diffloop
Version: 1.16.0
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_1.16.0.tar.gz
StartedAt: 2020-10-17 00:31:50 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:38:52 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 422.0 seconds
RetCode: 0
Status:  OK 
CheckDir: diffloop.Rcheck
Warnings: 0

Command output

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###
### Running 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_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/diffloop.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.16.0’
* 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.



Installation output

diffloop.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL diffloop
###
##############################################################################
##############################################################################


* 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)

Tests output

diffloop.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 
 20.084   0.887  31.153 

Example timings

diffloop.Rcheck/diffloop-Ex.timings

nameusersystemelapsed
addchr0.2830.0290.311
annotateAnchors0.2060.0180.226
annotateAnchors.bed0.1350.0130.147
annotateAnchors.bigwig0.1070.0030.109
annotateLoops0.7050.0150.721
annotateLoops.dge0.4780.0080.486
bedToGRanges0.1100.0020.111
calcLDSizeFactors0.0020.0010.003
callCCDs0.0020.0000.003
computeBoundaryScores0.0020.0000.003
featureTest0.0020.0000.002
filterLoops0.0980.0020.101
filterSpanningLoops0.0260.0010.028
getHumanGenes0.0740.0020.077
getHumanTSS0.2930.0040.297
getMouseGenes0.1510.0030.156
getMouseTSS0.2200.0030.225
interchromosomal0.0270.0010.028
intrachromosomal0.0440.0030.047
keepCTCFloops0.1670.0040.170
keepEPloops0.4260.0070.434
loopAssoc0.0010.0010.002
loopDistancePlot0.0280.0010.029
loopGenes0.1640.0020.165
loopMetrics0.0040.0000.005
loopPlot0.8680.0370.906
loopWidth0.0270.0030.030
loopsMake0.0000.0000.002
loopsMake.mango0.0010.0000.001
loopsSubset0.5320.0060.538
mangoCorrection0.1420.0010.144
manyLoopPlots0.1080.0030.111
mergeAnchors0.1710.0010.171
numAnchors0.0110.0010.012
numLoops0.0040.0010.005
padGRanges0.1660.0070.172
pcaPlot0.0180.0020.020
plotTopLoops1.3380.0541.393
quickAssoc0.0650.0010.067
quickAssocVoom0.0590.0010.059
removeRegion0.2410.0100.251
removeSelfLoops0.0120.0000.013
rmchr0.2060.0130.220
sampleNames-loops-method0.0020.0010.003
slidingWindowTest0.0010.0000.002
splitSamples0.1260.0060.132
subsetLoops0.0370.0010.038
subsetRegion0.6620.0610.724
subsetRegionAB0.3820.0150.398
summary-loops-method0.1070.0010.108
topLoops0.0800.0010.081
union-loops-loops-method0.3430.0020.344
updateLDGroups0.0020.0010.002