Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-01-22 11:05:43 -0500 (Sat, 22 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4163
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4058
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 4000
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4117
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 nebbiolo1


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 510/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffloop 1.23.1  (landing page)
Caleb Lareau
Snapshot Date: 2022-01-21 13:55:18 -0500 (Fri, 21 Jan 2022)
git_url: https://git.bioconductor.org/packages/diffloop
git_branch: master
git_last_commit: a71bf82
git_last_commit_date: 2021-11-20 03:59:02 -0500 (Sat, 20 Nov 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    NA    NA  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  NO, package depends on 'GenomicRanges' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: diffloop
Version: 1.23.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:diffloop.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings diffloop_1.23.1.tar.gz
StartedAt: 2022-01-21 18:58:51 -0500 (Fri, 21 Jan 2022)
EndedAt: 2022-01-21 19:02:35 -0500 (Fri, 21 Jan 2022)
EllapsedTime: 223.8 seconds
RetCode: 0
Status:   OK  
CheckDir: diffloop.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:diffloop.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings diffloop_1.23.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/diffloop.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-pc-linux-gnu (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 ‘1.23.1’
* 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
  ‘/home/biocbuild/bbs-3.15-bioc/meat/diffloop.Rcheck/00check.log’
for details.



Installation output

diffloop.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL diffloop
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
 10.975   0.500  11.461 

Example timings

diffloop.Rcheck/diffloop-Ex.timings

nameusersystemelapsed
addchr0.1760.0040.179
annotateAnchors0.1910.0240.216
annotateAnchors.bed0.1340.0120.146
annotateAnchors.bigwig0.0840.0100.095
annotateLoops0.4540.0230.485
annotateLoops.dge0.3580.0080.401
bedToGRanges0.0540.0000.054
calcLDSizeFactors0.0020.0000.002
callCCDs0.0010.0000.001
computeBoundaryScores0.0010.0000.001
featureTest0.0010.0000.001
filterLoops0.0540.0000.054
filterSpanningLoops0.0100.0000.009
getHumanGenes0.0820.0000.082
getHumanTSS0.1650.0000.164
getMouseGenes0.1180.0000.121
getMouseTSS0.1120.0040.117
interchromosomal0.0070.0040.011
intrachromosomal0.010.000.01
keepCTCFloops0.0940.0040.098
keepEPloops0.2950.0080.318
loopAssoc0.0010.0000.002
loopDistancePlot0.0220.0000.022
loopGenes0.1250.0000.124
loopMetrics0.0010.0030.003
loopPlot0.6250.0000.626
loopWidth0.0140.0000.014
loopsMake0.0010.0000.001
loopsMake.mango0.0000.0000.001
loopsSubset0.2390.1400.379
mangoCorrection0.1060.0640.170
manyLoopPlots0.0710.0000.072
mergeAnchors0.1090.0200.128
numAnchors0.010.000.01
numLoops0.0030.0000.003
padGRanges0.1130.0040.117
pcaPlot0.0120.0000.013
plotTopLoops0.8750.0120.887
quickAssoc0.0340.0000.034
quickAssocVoom0.0300.0000.031
removeRegion0.1480.0000.148
removeSelfLoops0.0060.0000.006
rmchr0.130.000.13
sampleNames-loops-method0.0020.0000.003
slidingWindowTest0.0010.0000.001
splitSamples0.0580.0040.062
subsetLoops0.0150.0000.014
subsetRegion0.4020.0750.477
subsetRegionAB0.2570.0020.259
summary-loops-method0.0550.0160.071
topLoops0.0320.0080.040
union-loops-loops-method0.2060.0120.217
updateLDGroups0.0000.0020.001