Panos Balomenos
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/CHRONOS |
| Branch: RELEASE_3_6 |
| Last Commit: d88bc83 |
| Last Changed Date: 2017-10-30 12:41:16 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:14:59 -0400 (Thu, 12 Apr 2018).
| Package 234/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CHRONOS 1.6.0 Panos Balomenos
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | [ OK ] | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
| Package: CHRONOS |
| Version: 1.6.0 |
| Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CHRONOS_1.6.0.tar.gz |
| StartedAt: 2018-04-11 22:15:55 -0400 (Wed, 11 Apr 2018) |
| EndedAt: 2018-04-11 22:17:53 -0400 (Wed, 11 Apr 2018) |
| EllapsedTime: 117.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CHRONOS.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CHRONOS_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/CHRONOS.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘CHRONOS/DESCRIPTION’ ... OK * this is package ‘CHRONOS’ version ‘1.6.0’ * 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 loading without being on the library search path ... 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 installed files from ‘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
* installing *source* package ‘CHRONOS’ ... ** R ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (CHRONOS)
CHRONOS.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.
> 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...done.
Summarising scores...done.
done.
RUNIT TEST PROTOCOL -- Wed Apr 11 22:17:50 2018
***********************************************
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
14.020 0.920 17.632
CHRONOS.Rcheck/CHRONOS-Ex.timings
| name | user | system | elapsed | |
| CHRONOSrun | 3.232 | 0.304 | 3.412 | |
| convertMiRNANomenclature | 0.040 | 0.000 | 0.041 | |
| convertNomenclature | 0 | 0 | 0 | |
| createPathwayGraphs | 0.452 | 0.024 | 0.479 | |
| downloadKEGGPathwayList | 0.024 | 0.004 | 0.028 | |
| downloadMiRecords | 0.028 | 0.000 | 0.028 | |
| downloadPathways | 0.488 | 0.000 | 1.964 | |
| extractLinearSubpathways | 1.252 | 0.180 | 1.280 | |
| extractNonLinearSubpathways | 0.696 | 0.040 | 0.742 | |
| getEdgeTypes | 0.000 | 0.000 | 0.002 | |
| importExpressions | 0.132 | 0.008 | 0.139 | |
| pathwayMeasures | 0.148 | 0.000 | 0.150 | |
| scoreSubpathways | 0.316 | 0.024 | 0.347 | |
| subpathwayKEGGmap | 0.04 | 0.00 | 0.04 | |
| subpathwayMiRNAs | 3.036 | 0.020 | 3.080 | |
| visualizeResults | 0.524 | 0.000 | 2.097 | |