Package: Chicago

Version: 1.6.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Chicago_1.6.0.tar.gz

StartedAt: 2018-04-11 22:07:52 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:09:34 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 101.6 seconds

RetCode: 0

Status:  OK

CheckDir: Chicago.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Chicago_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Chicago.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.6.0’
* 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:
  .BBSoptions
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 ‘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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
normaliseOtherEnds 13.436   1.40  12.682
exportResults      10.788   0.24  11.480
* 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-3.6-bioc/meat/Chicago.Rcheck/00check.log’
for details.

* installing *source* package ‘Chicago’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Chicago)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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 1.6.0
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 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  7.604   0.096   4.976 

name	user	system	elapsed
cdUnitTest	0.04	0.00	0.04
chicagoData	0.000	0.000	0.001
chicagoPipeline	0.284	0.008	0.157
copyCD	0.008	0.000	0.006
defaultSettings	0	0	0
estimateBrownianComponent	1.012	0.008	0.760
estimateDistFun	0.26	0.00	0.09
estimateTechnicalNoise	0.520	0.000	0.136
exportResults	10.788	0.240	11.480
getPvals	0.204	0.000	0.049
getScores	0.048	0.000	0.040
getSkOnly	0.576	0.008	0.327
mergeSamples	0.420	0.020	0.147
modifySettings	0.008	0.004	0.012
normaliseBaits	0.508	0.000	0.128
normaliseOtherEnds	13.436	1.400	12.682
overlapFragWithFeatures	0.140	0.000	0.112
peakEnrichment4Features	1.148	0.000	1.104
plotBaits	0.144	0.000	0.143
plotDistFun	0.012	0.000	0.010
readAndMerge	0.424	0.032	0.156
readSample	0.200	0.000	0.067
setExperiment	0.004	0.004	0.009