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CHECK report for CHRONOS on celaya2

This page was generated on 2019-10-16 12:57:57 -0400 (Wed, 16 Oct 2019).

Package 276/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CHRONOS 1.12.0
Panos Balomenos
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/CHRONOS
Branch: RELEASE_3_9
Last Commit: 6fbd5ff
Last Changed Date: 2019-05-02 11:54:02 -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: CHRONOS
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CHRONOS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CHRONOS_1.12.0.tar.gz
StartedAt: 2019-10-16 01:28:36 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:31:45 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 188.6 seconds
RetCode: 0
Status:  OK 
CheckDir: CHRONOS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CHRONOS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CHRONOS_1.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/CHRONOS.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CHRONOS/DESCRIPTION’ ... OK
* this is package ‘CHRONOS’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CHRONOS’ 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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

CHRONOS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CHRONOS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘CHRONOS’ ...
** using staged installation
** R
** 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 (CHRONOS)

Tests output

CHRONOS.Rcheck/tests/runTests.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-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.

> BiocGenerics:::testPackage('CHRONOS')
Testing test_CHRONOSrun...Importing entrezgene data...done.
Importing miRNA data...done.
Downloading files...done.
Creating adjacency matrices...done.
Extracting Linear Subpathways...done.
	#98 subpathways initially
Calculating subscores...done.
	#21 subpathways after subscore.
Calculating mirscores......end.
Extracting Non Linear Subpathways...done.
	#24 subpathways initially
Calculating subscores...done.
	#19 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_pathwayToGraph...Creating adjacency matrices...done.
done.
Testing test_subExtractionLinear...Importing entrezgene data...done.
Extracting Linear Subpathways...done.
done.
Testing test_subExtractionNonLinear...Importing entrezgene data...done.
Extracting Non Linear Subpathways...done.
done.
Testing test_subRefinement...Importing entrezgene data...done.
Importing miRNA data...done.
	#98 subpathways initially
Calculating subscores...done.
	#21 subpathways after subscore.
Calculating mirscores......end.
done.
Testing test_subVisualization...Importing entrezgene data...done.
Summarising scores...Note: zip::zip() is deprecated, please use zip::zipr() instead
done.
Summarising scores...done.
done.


RUNIT TEST PROTOCOL -- Wed Oct 16 01:31:35 2019 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
CHRONOS RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> 
> proc.time()
   user  system elapsed 
 13.915   2.999  19.095 

Example timings

CHRONOS.Rcheck/CHRONOS-Ex.timings

nameusersystemelapsed
CHRONOSrun3.5010.9974.242
convertMiRNANomenclature0.0100.0060.016
convertNomenclature0.0000.0000.001
createPathwayGraphs0.6540.0340.689
downloadKEGGPathwayList0.0340.0070.041
downloadMiRecords0.0470.0090.056
downloadPathways0.0000.0000.001
extractLinearSubpathways2.6350.7912.973
extractNonLinearSubpathways0.2760.0340.327
getEdgeTypes0.0030.0000.003
importExpressions0.1040.0560.159
pathwayMeasures0.2410.0130.254
scoreSubpathways0.2070.0200.228
subpathwayKEGGmap0.0300.0070.037
subpathwayMiRNAs1.3640.0311.394
visualizeResults0.6120.0182.374