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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:07:51 -0400 (Wed, 16 Oct 2019).
| Package 253/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Chicago 1.12.0 Mikhail Spivakov
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| 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 |
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### Running command:
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### /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.
Chicago.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Chicago ### ############################################################################## ############################################################################## * 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)
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
Chicago.Rcheck/Chicago-Ex.timings
| name | user | system | elapsed | |
| cdUnitTest | 2.172 | 0.029 | 0.341 | |
| chicagoData | 0.001 | 0.000 | 0.000 | |
| chicagoPipeline | 2.353 | 0.008 | 0.353 | |
| copyCD | 0.025 | 0.000 | 0.008 | |
| defaultSettings | 0.001 | 0.000 | 0.001 | |
| estimateBrownianComponent | 8.136 | 0.051 | 1.369 | |
| estimateDistFun | 3.620 | 0.013 | 0.609 | |
| estimateTechnicalNoise | 6.765 | 0.023 | 1.182 | |
| exportResults | 19.977 | 0.432 | 17.104 | |
| getPvals | 0.310 | 0.000 | 0.073 | |
| getScores | 1.659 | 0.009 | 0.292 | |
| getSkOnly | 7.208 | 0.015 | 1.223 | |
| mergeSamples | 6.739 | 0.031 | 1.115 | |
| modifySettings | 1.386 | 0.004 | 0.205 | |
| normaliseBaits | 13.29 | 0.04 | 2.22 | |
| normaliseOtherEnds | 39.837 | 1.324 | 18.010 | |
| overlapFragWithFeatures | 5.710 | 0.016 | 1.075 | |
| peakEnrichment4Features | 183.851 | 0.803 | 30.754 | |
| plotBaits | 54.503 | 0.341 | 9.003 | |
| plotDistFun | 0.012 | 0.000 | 0.010 | |
| readAndMerge | 5.735 | 0.019 | 0.991 | |
| readSample | 2.015 | 0.012 | 0.344 | |
| setExperiment | 0.608 | 0.000 | 0.104 | |