Mikhail Spivakov
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Chicago |
| Branch: RELEASE_3_8 |
| Last Commit: 1a21c85 |
| Last Changed Date: 2019-01-04 13:09:11 -0400 (Fri, 04 Jan 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:59:07 -0400 (Tue, 16 Apr 2019).
| Package 239/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Chicago 1.10.1 Mikhail Spivakov
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: Chicago |
| Version: 1.10.1 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Chicago.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Chicago_1.10.1.tar.gz |
| StartedAt: 2019-04-15 22:53:57 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:56:10 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 132.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: Chicago.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Chicago.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Chicago_1.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/Chicago.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.1’
* 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
normaliseOtherEnds 25.560 20.093 14.745
peakEnrichment4Features 9.150 7.559 2.218
exportResults 14.497 1.511 14.322
* 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
‘/Users/biocbuild/bbs-3.8-bioc/meat/Chicago.Rcheck/00check.log’
for details.
Chicago.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Chicago ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘Chicago’ ... ** 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 * DONE (Chicago)
Chicago.Rcheck/tests/testthat.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 1.10.1
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
9.487 6.762 4.460
Chicago.Rcheck/Chicago-Ex.timings
| name | user | system | elapsed | |
| cdUnitTest | 0.170 | 0.185 | 0.069 | |
| chicagoData | 0.003 | 0.003 | 0.001 | |
| chicagoPipeline | 1.337 | 0.263 | 0.210 | |
| copyCD | 0.088 | 0.002 | 0.009 | |
| defaultSettings | 0.009 | 0.001 | 0.002 | |
| estimateBrownianComponent | 1.230 | 0.920 | 0.283 | |
| estimateDistFun | 0.190 | 0.143 | 0.047 | |
| estimateTechnicalNoise | 0.459 | 0.427 | 0.127 | |
| exportResults | 14.497 | 1.511 | 14.322 | |
| getPvals | 0.087 | 0.030 | 0.024 | |
| getScores | 1.890 | 0.177 | 0.189 | |
| getSkOnly | 2.921 | 1.909 | 1.358 | |
| mergeSamples | 0.581 | 0.713 | 0.185 | |
| modifySettings | 0.115 | 0.139 | 0.036 | |
| normaliseBaits | 0.598 | 0.603 | 0.172 | |
| normaliseOtherEnds | 25.560 | 20.093 | 14.745 | |
| overlapFragWithFeatures | 0.461 | 0.602 | 0.130 | |
| peakEnrichment4Features | 9.150 | 7.559 | 2.218 | |
| plotBaits | 1.802 | 1.355 | 0.377 | |
| plotDistFun | 0.252 | 0.007 | 0.020 | |
| readAndMerge | 1.278 | 0.297 | 0.152 | |
| readSample | 0.177 | 0.236 | 0.051 | |
| setExperiment | 0.054 | 0.085 | 0.017 | |