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) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:57:57 -0400 (Wed, 16 Oct 2019).
| Package 276/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CHRONOS 1.12.0 Panos Balomenos
| 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: 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 |
############################################################################## ############################################################################## ### ### 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 ### ############################################################################## ############################################################################## * 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
CHRONOS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CHRONOS ### ############################################################################## ############################################################################## * 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)
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
CHRONOS.Rcheck/CHRONOS-Ex.timings
| name | user | system | elapsed | |
| CHRONOSrun | 3.501 | 0.997 | 4.242 | |
| convertMiRNANomenclature | 0.010 | 0.006 | 0.016 | |
| convertNomenclature | 0.000 | 0.000 | 0.001 | |
| createPathwayGraphs | 0.654 | 0.034 | 0.689 | |
| downloadKEGGPathwayList | 0.034 | 0.007 | 0.041 | |
| downloadMiRecords | 0.047 | 0.009 | 0.056 | |
| downloadPathways | 0.000 | 0.000 | 0.001 | |
| extractLinearSubpathways | 2.635 | 0.791 | 2.973 | |
| extractNonLinearSubpathways | 0.276 | 0.034 | 0.327 | |
| getEdgeTypes | 0.003 | 0.000 | 0.003 | |
| importExpressions | 0.104 | 0.056 | 0.159 | |
| pathwayMeasures | 0.241 | 0.013 | 0.254 | |
| scoreSubpathways | 0.207 | 0.020 | 0.228 | |
| subpathwayKEGGmap | 0.030 | 0.007 | 0.037 | |
| subpathwayMiRNAs | 1.364 | 0.031 | 1.394 | |
| visualizeResults | 0.612 | 0.018 | 2.374 | |