Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:39 -0400 (Fri, 15 Oct 2021).

CHECK results for diffloop on nebbiolo1

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 501/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffloop 1.20.0  (landing page)
Caleb Lareau
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/diffloop
git_branch: RELEASE_3_13
git_last_commit: 900a5e1
git_last_commit_date: 2021-05-19 12:20:17 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: diffloop
Version: 1.20.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:diffloop.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings diffloop_1.20.0.tar.gz
StartedAt: 2021-10-14 09:35:29 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:39:25 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 236.1 seconds
RetCode: 0
Status:   OK  
CheckDir: diffloop.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:diffloop.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings diffloop_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-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 ‘1.20.0’
* 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-3.13-bioc/meat/diffloop.Rcheck/00check.log’
for details.



Installation output

diffloop.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL diffloop
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 
 10.290   0.444  10.717 

Example timings

diffloop.Rcheck/diffloop-Ex.timings

nameusersystemelapsed
addchr0.2210.0200.241
annotateAnchors0.1340.0200.157
annotateAnchors.bed0.1010.0160.118
annotateAnchors.bigwig0.0500.0000.051
annotateLoops1.3930.0161.418
annotateLoops.dge0.3680.0080.376
bedToGRanges0.070.000.07
calcLDSizeFactors0.0020.0000.002
callCCDs0.0020.0000.001
computeBoundaryScores0.0010.0000.001
featureTest0.0010.0000.001
filterLoops0.1020.0080.110
filterSpanningLoops0.0170.0040.022
getHumanGenes0.0830.0000.083
getHumanTSS0.1690.0000.169
getMouseGenes0.1170.0040.124
getMouseTSS0.1790.0080.187
interchromosomal0.0200.0000.021
intrachromosomal0.0190.0000.020
keepCTCFloops0.1200.0040.124
keepEPloops0.3880.0000.388
loopAssoc0.0020.0000.002
loopDistancePlot0.0280.0000.028
loopGenes0.1200.0040.124
loopMetrics0.0030.0000.002
loopPlot0.5450.0280.573
loopWidth0.0170.0040.022
loopsMake0.0010.0000.002
loopsMake.mango0.0010.0000.001
loopsSubset0.2750.0720.347
mangoCorrection0.1280.0190.147
manyLoopPlots0.0620.0000.061
mergeAnchors0.1210.0000.121
numAnchors0.0090.0000.009
numLoops0.0030.0000.003
padGRanges0.1040.0000.105
pcaPlot0.0100.0000.011
plotTopLoops0.9360.0120.948
quickAssoc0.0430.0000.043
quickAssocVoom0.0300.0040.033
removeRegion0.2020.0000.202
removeSelfLoops0.0080.0000.008
rmchr0.1820.0080.191
sampleNames-loops-method0.0030.0000.002
slidingWindowTest0.0010.0000.001
splitSamples0.0960.0000.096
subsetLoops0.0380.0030.040
subsetRegion0.6590.2280.900
subsetRegionAB0.3460.0120.358
summary-loops-method0.0920.0010.094
topLoops0.0470.0000.048
union-loops-loops-method0.2550.0240.278
updateLDGroups0.0020.0000.001