Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-12 13:21:22 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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 palomino3


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: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 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 20.04.4 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: F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:diffloop.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings diffloop_1.24.0.tar.gz
StartedAt: 2022-08-12 00:23:20 -0400 (Fri, 12 Aug 2022)
EndedAt: 2022-08-12 00:28:02 -0400 (Fri, 12 Aug 2022)
EllapsedTime: 282.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: diffloop.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:diffloop.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings diffloop_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/diffloop.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (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 whether package 'diffloop' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'diffloop' is deprecated and will be removed from Bioconductor
  Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
See 'F:/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
  'F:/biocbuild/bbs-3.15-bioc/meat/diffloop.Rcheck/00check.log'
for details.



Installation output

diffloop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL diffloop
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'diffloop' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
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: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop'
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 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 messages:
1: replacing previous import 'GenomicRanges::windows' by 'grDevices::windows' when loading 'diffloop' 
2: 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 
  13.73    0.62   14.34 

Example timings

diffloop.Rcheck/diffloop-Ex.timings

nameusersystemelapsed
addchr0.250.050.29
annotateAnchors0.170.020.25
annotateAnchors.bed0.080.010.09
annotateAnchors.bigwig0.060.000.06
annotateLoops0.580.030.95
annotateLoops.dge0.470.000.47
bedToGRanges0.100.020.11
calcLDSizeFactors000
callCCDs000
computeBoundaryScores000
featureTest0.010.000.02
filterLoops0.090.000.09
filterSpanningLoops0.020.000.02
getHumanGenes0.080.000.07
getHumanTSS0.120.000.13
getMouseGenes0.180.000.22
getMouseTSS0.140.000.14
interchromosomal0.010.000.01
intrachromosomal0.020.000.02
keepCTCFloops0.090.010.11
keepEPloops0.30.00.3
loopAssoc000
loopDistancePlot0.010.000.01
loopGenes0.110.000.11
loopMetrics000
loopPlot0.520.020.53
loopWidth0.010.000.02
loopsMake000
loopsMake.mango000
loopsSubset0.240.000.23
mangoCorrection0.080.020.10
manyLoopPlots0.060.010.07
mergeAnchors0.140.000.15
numAnchors000
numLoops000
padGRanges0.170.000.17
pcaPlot0.010.000.02
plotTopLoops0.780.000.78
quickAssoc0.040.000.03
quickAssocVoom0.040.000.05
removeRegion0.210.000.20
removeSelfLoops0.010.000.02
rmchr0.190.020.20
sampleNames-loops-method000
slidingWindowTest000
splitSamples0.110.000.10
subsetLoops0.020.010.04
subsetRegion0.660.030.68
subsetRegionAB0.260.050.32
summary-loops-method0.060.000.06
topLoops0.050.000.05
union-loops-loops-method0.170.000.17
updateLDGroups000