Back to Multiple platform build/check report for BioC 3.14
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2022-01-24 13:04:54 -0500 (Mon, 24 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
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 Chicago on nebbiolo2


To the developers/maintainers of the Chicago package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Chicago.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 296/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Chicago 1.22.0  (landing page)
Mikhail Spivakov
Snapshot Date: 2022-01-23 01:55:04 -0500 (Sun, 23 Jan 2022)
git_url: https://git.bioconductor.org/packages/Chicago
git_branch: RELEASE_3_14
git_last_commit: c377e14
git_last_commit_date: 2021-10-26 12:23:53 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    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: Chicago
Version: 1.22.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Chicago.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Chicago_1.22.0.tar.gz
StartedAt: 2022-01-23 06:54:09 -0500 (Sun, 23 Jan 2022)
EndedAt: 2022-01-23 06:56:00 -0500 (Sun, 23 Jan 2022)
EllapsedTime: 111.3 seconds
RetCode: 0
Status:   OK  
CheckDir: Chicago.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:Chicago.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings Chicago_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/Chicago.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.22.0’
* 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 ... 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 17.902  1.689  16.703
exportResults      14.292  0.740  15.023
* 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

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL Chicago
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-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 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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 1.22.0
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
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 11 ]
> 
> proc.time()
   user  system elapsed 
  3.311   0.178   3.168 

Example timings

Chicago.Rcheck/Chicago-Ex.timings

nameusersystemelapsed
cdUnitTest0.0560.0000.057
chicagoData0.0010.0000.001
chicagoPipeline0.0580.0000.044
copyCD0.0100.0040.008
defaultSettings0.0000.0000.001
estimateBrownianComponent0.2410.0160.210
estimateDistFun0.0340.0000.022
estimateTechnicalNoise0.0940.0040.077
exportResults14.292 0.74015.023
getPvals0.0500.0000.037
getScores0.0630.0040.045
getSkOnly0.1230.0120.081
mergeSamples0.1570.0000.105
modifySettings0.0390.0080.045
normaliseBaits0.0960.0160.088
normaliseOtherEnds17.902 1.68916.703
overlapFragWithFeatures0.0630.0000.064
peakEnrichment4Features0.8280.0200.818
plotBaits0.1510.0000.151
plotDistFun0.0470.0040.050
readAndMerge0.1070.0000.069
readSample0.0420.0000.032
setExperiment0.0270.0000.020