Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2021-10-22 12:03:58 -0400 (Fri, 22 Oct 2021).

CHECK results for diffloop on nebbiolo2

To the developers/maintainers of the diffloop package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/diffloop.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 506/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffloop 1.21.0  (landing page)
Caleb Lareau
Snapshot Date: 2021-10-21 14:50:08 -0400 (Thu, 21 Oct 2021)
git_url: https://git.bioconductor.org/packages/diffloop
git_branch: master
git_last_commit: 496ff39
git_last_commit_date: 2021-05-19 12:20:17 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: diffloop
Version: 1.21.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:diffloop.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings diffloop_1.21.0.tar.gz
StartedAt: 2021-10-21 19:51:08 -0400 (Thu, 21 Oct 2021)
EndedAt: 2021-10-21 19:55:03 -0400 (Thu, 21 Oct 2021)
EllapsedTime: 234.8 seconds
RetCode: 0
Status:   OK  
CheckDir: diffloop.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:diffloop.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings diffloop_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/diffloop.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘1.21.0’
* 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
  ‘/home/biocbuild/bbs-3.14-bioc/meat/diffloop.Rcheck/00check.log’
for details.



Installation output

diffloop.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL diffloop
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 11.280   0.439  11.705 

Example timings

diffloop.Rcheck/diffloop-Ex.timings

nameusersystemelapsed
addchr0.2310.0280.260
annotateAnchors0.1260.0000.127
annotateAnchors.bed0.0750.0000.075
annotateAnchors.bigwig0.0520.0000.052
annotateLoops0.5550.0000.555
annotateLoops.dge0.3870.0160.403
bedToGRanges0.0660.0000.065
calcLDSizeFactors0.0010.0000.002
callCCDs0.0010.0000.001
computeBoundaryScores0.0010.0000.001
featureTest0.0000.0000.001
filterLoops0.0530.0000.054
filterSpanningLoops0.0090.0000.010
getHumanGenes0.0780.0000.079
getHumanTSS0.1790.0000.179
getMouseGenes0.1220.0000.121
getMouseTSS0.3280.0030.332
interchromosomal0.0120.0000.013
intrachromosomal0.0110.0000.012
keepCTCFloops0.1260.0000.127
keepEPloops0.5850.0440.629
loopAssoc0.0010.0000.001
loopDistancePlot0.0230.0000.023
loopGenes0.1130.0080.120
loopMetrics0.0030.0000.002
loopPlot0.5780.0240.602
loopWidth0.0110.0000.011
loopsMake0.0010.0000.001
loopsMake.mango0.0010.0000.001
loopsSubset0.2420.0070.250
mangoCorrection0.0930.0120.106
manyLoopPlots0.0690.0000.069
mergeAnchors0.1050.0120.117
numAnchors0.0090.0000.010
numLoops0.0030.0000.002
padGRanges0.1440.0110.156
pcaPlot0.0130.0000.013
plotTopLoops0.9190.0080.927
quickAssoc0.0340.0000.035
quickAssocVoom0.0310.0000.031
removeRegion0.1780.0080.187
removeSelfLoops0.0060.0000.007
rmchr0.1570.0120.169
sampleNames-loops-method0.0000.0030.002
slidingWindowTest0.0010.0000.001
splitSamples0.0710.0200.091
subsetLoops0.0140.0040.018
subsetRegion0.5250.0280.553
subsetRegionAB0.2950.0040.299
summary-loops-method0.0710.0000.072
topLoops0.0470.0000.047
union-loops-loops-method0.2040.0000.205
updateLDGroups0.0010.0000.002