Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:22:50 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for diffloop on merida1


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? 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 530/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffloop 1.24.0  (landing page)
Caleb Lareau
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/diffloop
git_branch: RELEASE_3_15
git_last_commit: d5d5f0f
git_last_commit_date: 2022-04-26 11:32:08 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: diffloop
Version: 1.24.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:diffloop.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings diffloop_1.24.0.tar.gz
StartedAt: 2022-10-19 01:42:04 -0400 (Wed, 19 Oct 2022)
EndedAt: 2022-10-19 01:49:39 -0400 (Wed, 19 Oct 2022)
EllapsedTime: 455.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: diffloop.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:diffloop.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings diffloop_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/diffloop.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.24.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'diffloop' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.15-bioc/meat/diffloop.Rcheck/00install.out’ for details.
* 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 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/diffloop.Rcheck/00check.log’
for details.



Installation output

diffloop.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/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
Warning: Package 'diffloop' is deprecated and will be removed from Bioconductor
  version 3.16
** testing if installed package can be loaded from final location
Warning: Package 'diffloop' is deprecated and will be removed from Bioconductor
  version 3.16
** testing if installed package keeps a record of temporary installation path
* DONE (diffloop)

Tests output

diffloop.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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)
Warning message:
Package 'diffloop' is deprecated and will be removed from Bioconductor
  version 3.16 
> 
> test_check("diffloop")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 4 ]
> 
> proc.time()
   user  system elapsed 
 22.002   0.819  28.439 

Example timings

diffloop.Rcheck/diffloop-Ex.timings

nameusersystemelapsed
addchr0.3130.0300.343
annotateAnchors0.2840.0080.293
annotateAnchors.bed0.1600.0010.162
annotateAnchors.bigwig0.1030.0010.104
annotateLoops0.8050.0150.822
annotateLoops.dge1.3200.0111.333
bedToGRanges0.0980.0020.099
calcLDSizeFactors0.0030.0000.002
callCCDs0.0020.0000.001
computeBoundaryScores0.0020.0010.002
featureTest0.0010.0010.003
filterLoops0.1070.0010.107
filterSpanningLoops0.0230.0010.023
getHumanGenes0.1220.0020.123
getHumanTSS0.2420.0050.247
getMouseGenes0.2200.0060.227
getMouseTSS0.2450.0030.248
interchromosomal0.0230.0010.024
intrachromosomal0.0230.0000.023
keepCTCFloops0.1670.0040.171
keepEPloops0.4930.0120.506
loopAssoc0.0020.0000.002
loopDistancePlot0.0350.0000.037
loopGenes0.1830.0020.184
loopMetrics0.0040.0000.004
loopPlot0.9500.0430.994
loopWidth0.0230.0030.026
loopsMake0.0010.0020.002
loopsMake.mango0.0000.0000.001
loopsSubset0.5790.0530.631
mangoCorrection0.1540.0010.156
manyLoopPlots0.1200.0030.124
mergeAnchors0.2120.0010.213
numAnchors0.0170.0010.017
numLoops0.0050.0010.005
padGRanges0.1560.0030.160
pcaPlot0.0190.0010.020
plotTopLoops1.4740.0191.498
quickAssoc0.0700.0010.072
quickAssocVoom0.0600.0010.061
removeRegion0.2600.0090.269
removeSelfLoops0.0120.0010.012
rmchr0.2100.0090.220
sampleNames-loops-method0.0040.0010.004
slidingWindowTest0.0010.0010.002
splitSamples0.1350.0010.136
subsetLoops0.0280.0010.029
subsetRegion0.8410.0120.854
subsetRegionAB0.4250.0090.435
summary-loops-method0.1290.0010.130
topLoops0.0780.0010.078
union-loops-loops-method0.4280.0010.430
updateLDGroups0.0020.0000.003