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CHECK report for diffloop on merida2

This page was generated on 2018-10-17 08:56:32 -0400 (Wed, 17 Oct 2018).

Package 388/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
diffloop 1.8.0
Caleb Lareau
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/diffloop
Branch: RELEASE_3_7
Last Commit: 30215fe
Last Changed Date: 2018-04-30 10:35:42 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: diffloop
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffloop.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffloop_1.8.0.tar.gz
StartedAt: 2018-10-16 20:57:53 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 21:02:19 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 266.0 seconds
RetCode: 0
Status:  OK 
CheckDir: diffloop.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:diffloop.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings diffloop_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/diffloop.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.8.0’
* 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-3.7-bioc/meat/diffloop.Rcheck/00check.log’
for details.



Installation output

diffloop.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘diffloop’ ...
** 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
* DONE (diffloop)

Tests output

diffloop.Rcheck/tests/testthat.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 4 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 13.257   0.589  13.955 

Example timings

diffloop.Rcheck/diffloop-Ex.timings

nameusersystemelapsed
addchr0.2570.0220.284
annotateAnchors0.2080.0280.239
annotateAnchors.bed0.0800.0100.091
annotateAnchors.bigwig0.0820.0120.094
annotateLoops0.6260.0290.661
annotateLoops.dge0.4240.0110.442
bedToGRanges0.1040.0040.110
calcLDSizeFactors0.0040.0000.004
callCCDs0.0030.0000.003
computeBoundaryScores0.0030.0010.004
featureTest0.0040.0000.004
filterLoops0.0650.0010.067
filterSpanningLoops0.0180.0010.019
getHumanGenes0.0930.0010.095
getHumanTSS0.1680.0070.176
getMouseGenes0.2160.0050.223
getMouseTSS0.1660.0040.172
interchromosomal0.0240.0010.025
intrachromosomal0.0230.0010.023
keepCTCFloops0.1940.0040.199
keepEPloops0.3590.0070.376
loopAssoc0.0040.0010.004
loopDistancePlot0.0240.0010.024
loopGenes0.1300.0010.132
loopMetrics0.0050.0010.006
loopPlot1.0800.0381.136
loopWidth0.0170.0000.018
loopsMake0.0020.0000.003
loopsMake.mango0.0020.0000.002
loopsSubset0.2570.0010.264
mangoCorrection0.1090.0010.110
manyLoopPlots0.0960.0030.098
mergeAnchors0.1820.0020.186
numAnchors0.0290.0020.032
numLoops0.0060.0000.006
padGRanges0.2160.0050.225
pcaPlot0.0230.0000.023
plotTopLoops1.2070.0451.265
quickAssoc0.0600.0050.067
quickAssocVoom0.0550.0030.060
removeRegion0.2350.0210.257
removeSelfLoops0.0130.0020.014
rmchr0.2180.0110.234
sampleNames-loops-method0.0050.0010.006
slidingWindowTest0.0030.0000.004
splitSamples0.1090.0010.109
subsetLoops0.0250.0010.026
subsetRegion0.6240.0070.636
subsetRegionAB0.3440.0060.358
summary-loops-method0.0970.0010.098
topLoops0.0730.0010.074
union-loops-loops-method0.1910.0040.198
updateLDGroups0.0030.0000.003