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This page was generated on 2021-12-06 13:05:55 -0500 (Mon, 06 Dec 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 509/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffloop 1.22.0  (landing page)
Caleb Lareau
Snapshot Date: 2021-12-05 01:55:05 -0500 (Sun, 05 Dec 2021)
git_url: https://git.bioconductor.org/packages/diffloop
git_branch: RELEASE_3_14
git_last_commit: 684b6b0
git_last_commit_date: 2021-10-26 12:27:40 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: 1.22.0
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_1.22.0.tar.gz
StartedAt: 2021-12-05 13:55:10 -0500 (Sun, 05 Dec 2021)
EndedAt: 2021-12-05 14:01:03 -0500 (Sun, 05 Dec 2021)
EllapsedTime: 352.7 seconds
RetCode: 0
Status:   OK  
CheckDir: diffloop.Rcheck
Warnings: 0

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_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/diffloop.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.22.0’
* 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
  ‘/Users/biocbuild/bbs-3.14-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/4.1/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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
 16.412   0.710  17.110 

Example timings

diffloop.Rcheck/diffloop-Ex.timings

nameusersystemelapsed
addchr0.3130.0120.325
annotateAnchors0.2070.0030.210
annotateAnchors.bed0.1150.0020.116
annotateAnchors.bigwig0.0890.0070.096
annotateLoops0.8220.0240.848
annotateLoops.dge0.4890.0110.499
bedToGRanges0.1170.0050.123
calcLDSizeFactors0.0010.0010.002
callCCDs0.0010.0010.001
computeBoundaryScores0.0010.0000.002
featureTest0.0010.0000.001
filterLoops0.0840.0010.085
filterSpanningLoops0.0130.0000.014
getHumanGenes0.0610.0010.062
getHumanTSS0.2740.0030.278
getMouseGenes0.2250.0030.228
getMouseTSS0.2070.0040.211
interchromosomal0.0210.0010.022
intrachromosomal0.0160.0010.017
keepCTCFloops0.1900.0050.196
keepEPloops0.5280.0160.551
loopAssoc0.0020.0000.002
loopDistancePlot0.0420.0010.044
loopGenes0.1740.0010.175
loopMetrics0.0040.0010.004
loopPlot0.8510.0450.896
loopWidth0.0230.0020.025
loopsMake0.0010.0010.001
loopsMake.mango0.0010.0010.001
loopsSubset0.4510.0470.498
mangoCorrection0.1650.0010.166
manyLoopPlots0.0940.0030.097
mergeAnchors0.1980.0010.199
numAnchors0.0110.0010.011
numLoops0.0040.0010.004
padGRanges0.1580.0040.161
pcaPlot0.0190.0010.020
plotTopLoops1.3460.0211.369
quickAssoc0.0510.0000.052
quickAssocVoom0.0500.0010.051
removeRegion0.2140.0070.222
removeSelfLoops0.0060.0000.006
rmchr0.1950.0070.202
sampleNames-loops-method0.0030.0010.004
slidingWindowTest0.0020.0010.002
splitSamples0.1180.0020.119
subsetLoops0.0260.0010.026
subsetRegion0.7340.0140.750
subsetRegionAB0.4150.0110.427
summary-loops-method0.1240.0010.126
topLoops0.0680.0010.070
union-loops-loops-method0.2840.0010.285
updateLDGroups0.0010.0000.002