Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:06:34 -0400 (Fri, 15 Oct 2021).

CHECK results for diffloop on machv2

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: /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_1.20.0.tar.gz
StartedAt: 2021-10-14 18:24:38 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 18:29:59 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 320.8 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/diffloop.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.20.0’
* 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:
  .git_fetch_output.txt
  .git_merge_output.txt
  .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-3.13-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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 15.453   0.659  16.098 

Example timings

diffloop.Rcheck/diffloop-Ex.timings

nameusersystemelapsed
addchr0.2740.0260.300
annotateAnchors0.1930.0190.214
annotateAnchors.bed0.1260.0030.128
annotateAnchors.bigwig0.0820.0020.085
annotateLoops0.8120.0200.838
annotateLoops.dge0.6220.0100.634
bedToGRanges0.0700.0010.071
calcLDSizeFactors0.0010.0000.002
callCCDs0.0010.0000.001
computeBoundaryScores0.0010.0010.002
featureTest0.0020.0010.002
filterLoops0.1290.0010.129
filterSpanningLoops0.0280.0010.029
getHumanGenes0.0950.0040.100
getHumanTSS0.3090.0040.312
getMouseGenes0.1560.0030.159
getMouseTSS0.2540.0040.257
interchromosomal0.0340.0010.035
intrachromosomal0.0300.0010.031
keepCTCFloops0.1700.0040.174
keepEPloops0.5120.0080.521
loopAssoc0.0010.0010.001
loopDistancePlot0.0490.0020.052
loopGenes0.1680.0010.170
loopMetrics0.0040.0000.005
loopPlot0.8760.0350.912
loopWidth0.0330.0030.036
loopsMake0.0000.0010.002
loopsMake.mango0.0010.0010.001
loopsSubset0.4450.0510.496
mangoCorrection0.200.020.22
manyLoopPlots0.1230.0050.128
mergeAnchors0.1970.0020.200
numAnchors0.0160.0010.017
numLoops0.0040.0000.004
padGRanges0.1720.0050.177
pcaPlot0.0180.0010.019
plotTopLoops1.3040.0211.329
quickAssoc0.0560.0010.057
quickAssocVoom0.0540.0010.055
removeRegion0.2550.0090.264
removeSelfLoops0.0110.0010.013
rmchr0.2650.0090.274
sampleNames-loops-method0.0040.0010.004
slidingWindowTest0.0020.0010.003
splitSamples0.1590.0010.163
subsetLoops0.0520.0010.053
subsetRegion0.7330.0130.745
subsetRegionAB1.2220.0371.261
summary-loops-method0.0960.0010.097
topLoops0.0680.0010.068
union-loops-loops-method0.3650.0010.366
updateLDGroups0.0010.0000.002