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CHECK report for Chicago on malbec1

This page was generated on 2020-08-06 11:38:05 -0400 (Thu, 06 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE Chicago PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 267/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Chicago 1.17.0
Mikhail Spivakov
Snapshot Date: 2020-08-05 14:50:59 -0400 (Wed, 05 Aug 2020)
URL: https://git.bioconductor.org/packages/Chicago
Branch: master
Last Commit: 05d4c19
Last Changed Date: 2020-07-23 06:49:54 -0400 (Thu, 23 Jul 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Chicago
Version: 1.17.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Chicago.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Chicago_1.17.0.tar.gz
StartedAt: 2020-08-06 01:32:37 -0400 (Thu, 06 Aug 2020)
EndedAt: 2020-08-06 01:34:54 -0400 (Thu, 06 Aug 2020)
EllapsedTime: 136.1 seconds
RetCode: 0
Status:  OK 
CheckDir: Chicago.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:Chicago.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings Chicago_1.17.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/Chicago.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Chicago/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Chicago’ version ‘1.17.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Chicago’ 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                     user system elapsed
normaliseOtherEnds 39.052  1.348  18.818
exportResults      15.660  0.300  15.980
* 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: OK


Installation output

Chicago.Rcheck/00install.out

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL Chicago
###
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘Chicago’ ...
** using staged installation
** R
** data
** 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 (Chicago)

Tests output

Chicago.Rcheck/tests/testthat.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 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(Chicago)
Loading required package: data.table

Welcome to CHiCAGO - version 1.17.0
If you are new to CHiCAGO, please consider reading the vignette through the command: vignette("Chicago").
NOTE: Default values of tlb.minProxOEPerBin and tlb.minProxB2BPerBin changed as of Version 1.1.5. No action is required unless you specified non-default values, or wish to re-run the pipeline on old chicagoData objects. See news(package="Chicago")
> 
> test_check("Chicago")
Read 4 items
Read 4 items
Read 4 items
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  7.692   0.180   5.487 

Example timings

Chicago.Rcheck/Chicago-Ex.timings

nameusersystemelapsed
cdUnitTest0.0920.0080.232
chicagoData0.0000.0000.001
chicagoPipeline0.1120.0200.094
copyCD0.0080.0000.008
defaultSettings0.0040.0000.002
estimateBrownianComponent1.3000.0080.500
estimateDistFun0.4480.0040.146
estimateTechnicalNoise0.4840.0080.173
exportResults15.66 0.3015.98
getPvals0.2280.0040.077
getScores0.1240.0080.092
getSkOnly1.9440.0081.423
mergeSamples1.0800.0040.385
modifySettings0.0800.0040.085
normaliseBaits0.3440.0000.172
normaliseOtherEnds39.052 1.34818.818
overlapFragWithFeatures0.1040.0000.445
peakEnrichment4Features1.3680.0681.361
plotBaits0.2680.0240.299
plotDistFun0.0720.0000.071
readAndMerge1.5360.0080.499
readSample0.3320.0040.134
setExperiment0.0480.0000.043