Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-08-15 13:22:45 -0400 (Mon, 15 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4365
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4118
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4183
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: 2022-08-14 13:55:13 -0400 (Sun, 14 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: /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: 2022-08-15 01:33:07 -0400 (Mon, 15 Aug 2022)
EndedAt: 2022-08-15 01:41:05 -0400 (Mon, 15 Aug 2022)
EllapsedTime: 478.2 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 
 22.615   0.882  29.443 

Example timings

diffloop.Rcheck/diffloop-Ex.timings

nameusersystemelapsed
addchr0.3280.0100.339
annotateAnchors0.2600.0060.267
annotateAnchors.bed0.1810.0140.195
annotateAnchors.bigwig0.1210.0090.130
annotateLoops0.8110.0210.837
annotateLoops.dge0.6500.0080.660
bedToGRanges0.1170.0020.120
calcLDSizeFactors0.0020.0000.003
callCCDs0.0020.0000.002
computeBoundaryScores0.0020.0010.003
featureTest0.0010.0000.003
filterLoops0.1200.0000.121
filterSpanningLoops0.0240.0000.025
getHumanGenes0.1310.0010.133
getHumanTSS1.1040.0031.109
getMouseGenes0.1930.0030.196
getMouseTSS0.2460.0030.250
interchromosomal0.0250.0000.026
intrachromosomal0.0220.0000.022
keepCTCFloops0.1680.0040.172
keepEPloops0.5110.0120.523
loopAssoc0.0020.0010.002
loopDistancePlot0.0330.0010.034
loopGenes0.1930.0020.194
loopMetrics0.0040.0010.004
loopPlot0.9930.0571.051
loopWidth0.0250.0030.028
loopsMake0.0010.0010.002
loopsMake.mango0.0010.0000.001
loopsSubset0.5760.0630.639
mangoCorrection0.1930.0020.195
manyLoopPlots0.1250.0040.130
mergeAnchors0.2210.0010.223
numAnchors0.0170.0000.018
numLoops0.0050.0000.005
padGRanges0.1680.0040.172
pcaPlot0.0190.0010.020
plotTopLoops1.5830.0191.606
quickAssoc0.0650.0010.066
quickAssocVoom0.0630.0010.065
removeRegion0.2630.0080.271
removeSelfLoops0.0110.0010.011
rmchr0.2270.0090.235
sampleNames-loops-method0.0030.0010.004
slidingWindowTest0.0020.0010.002
splitSamples0.1390.0010.139
subsetLoops0.0350.0010.036
subsetRegion0.8870.0120.901
subsetRegionAB0.4630.0090.472
summary-loops-method0.1390.0010.139
topLoops0.0750.0010.075
union-loops-loops-method0.4460.0020.448
updateLDGroups0.0020.0010.002