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This page was generated on 2023-02-01 11:08:12 -0500 (Wed, 01 Feb 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4511
palomino4Windows Server 2022 Datacenterx644.2.2 (2022-10-31 ucrt) -- "Innocent and Trusting" 4289
lconwaymacOS 12.5.1 Montereyx86_644.2.2 (2022-10-31) -- "Innocent and Trusting" 4318
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 lconway


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? 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 307/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Chicago 1.26.0  (landing page)
Mikhail Spivakov
Snapshot Date: 2023-01-31 14:00:04 -0500 (Tue, 31 Jan 2023)
git_url: https://git.bioconductor.org/packages/Chicago
git_branch: RELEASE_3_16
git_last_commit: 7c0e4a9
git_last_commit_date: 2022-11-01 11:12:33 -0500 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: Chicago
Version: 1.26.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Chicago.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Chicago_1.26.0.tar.gz
StartedAt: 2023-01-31 19:34:20 -0500 (Tue, 31 Jan 2023)
EndedAt: 2023-01-31 19:36:23 -0500 (Tue, 31 Jan 2023)
EllapsedTime: 123.1 seconds
RetCode: 0
Status:   OK  
CheckDir: Chicago.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Chicago.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Chicago_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/Chicago.Rcheck’
* using R version 4.2.2 (2022-10-31)
* using platform: x86_64-apple-darwin17.0 (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 ‘1.26.0’
* 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 14.777  2.020  16.965
exportResults      13.741  0.561  14.372
* 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:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Chicago
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/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 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 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(Chicago)
Loading required package: data.table

Welcome to CHiCAGO - version 1.26.0
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 
  3.127   0.302   3.438 

Example timings

Chicago.Rcheck/Chicago-Ex.timings

nameusersystemelapsed
cdUnitTest0.0490.0070.060
chicagoData0.0010.0000.001
chicagoPipeline0.0340.0040.039
copyCD0.0040.0010.005
defaultSettings0.0000.0010.002
estimateBrownianComponent0.1610.0150.180
estimateDistFun0.0180.0030.021
estimateTechnicalNoise0.0650.0060.073
exportResults13.741 0.56114.372
getPvals0.0320.0010.033
getScores0.0400.0050.045
getSkOnly0.0730.0130.088
mergeSamples0.0970.0170.116
modifySettings0.0430.0080.052
normaliseBaits0.0710.0100.081
normaliseOtherEnds14.777 2.02016.965
overlapFragWithFeatures0.0530.0090.063
peakEnrichment4Features0.8720.1180.996
plotBaits0.1180.0100.130
plotDistFun0.0540.0040.059
readAndMerge0.0580.0050.062
readSample0.0260.0040.029
setExperiment0.0170.0020.020