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CHECK report for Chicago on malbec2

This page was generated on 2019-10-16 12:07:51 -0400 (Wed, 16 Oct 2019).

Package 253/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
Chicago 1.12.0
Mikhail Spivakov
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/Chicago
Branch: RELEASE_3_9
Last Commit: 06a90b9
Last Changed Date: 2019-05-02 11:53:59 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: Chicago
Version: 1.12.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Chicago.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Chicago_1.12.0.tar.gz
StartedAt: 2019-10-16 00:25:33 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 00:28:41 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 187.8 seconds
RetCode: 0
Status:  OK 
CheckDir: Chicago.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:Chicago.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings Chicago_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/Chicago.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.12.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                             user system elapsed
peakEnrichment4Features   183.851  0.803  30.754
plotBaits                  54.503  0.341   9.003
normaliseOtherEnds         39.837  1.324  18.010
exportResults              19.977  0.432  17.104
normaliseBaits             13.290  0.040   2.220
estimateBrownianComponent   8.136  0.051   1.369
getSkOnly                   7.208  0.015   1.223
estimateTechnicalNoise      6.765  0.023   1.182
mergeSamples                6.739  0.031   1.115
readAndMerge                5.735  0.019   0.991
overlapFragWithFeatures     5.710  0.016   1.075
* 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-3.9-bioc/meat/Chicago.Rcheck/00check.log’
for details.



Installation output

Chicago.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Chicago
###
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* installing to library ‘/home/biocbuild/bbs-3.9-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 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 1.12.0
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 
 59.456   0.489  14.240 

Example timings

Chicago.Rcheck/Chicago-Ex.timings

nameusersystemelapsed
cdUnitTest2.1720.0290.341
chicagoData0.0010.0000.000
chicagoPipeline2.3530.0080.353
copyCD0.0250.0000.008
defaultSettings0.0010.0000.001
estimateBrownianComponent8.1360.0511.369
estimateDistFun3.6200.0130.609
estimateTechnicalNoise6.7650.0231.182
exportResults19.977 0.43217.104
getPvals0.3100.0000.073
getScores1.6590.0090.292
getSkOnly7.2080.0151.223
mergeSamples6.7390.0311.115
modifySettings1.3860.0040.205
normaliseBaits13.29 0.04 2.22
normaliseOtherEnds39.837 1.32418.010
overlapFragWithFeatures5.7100.0161.075
peakEnrichment4Features183.851 0.803 30.754
plotBaits54.503 0.341 9.003
plotDistFun0.0120.0000.010
readAndMerge5.7350.0190.991
readSample2.0150.0120.344
setExperiment0.6080.0000.104