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BioC 3.4: CHECK report for CHRONOS on morelia

This page was generated on 2016-09-21 03:55:58 -0700 (Wed, 21 Sep 2016).

Package 199/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CHRONOS 1.1.3
Panos Balomenos
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CHRONOS
Last Changed Rev: 117512 / Revision: 121152
Last Changed Date: 2016-05-15 13:14:22 -0700 (Sun, 15 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: CHRONOS
Version: 1.1.3
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CHRONOS_1.1.3.tar.gz
StartedAt: 2016-09-20 04:30:56 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:32:55 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 118.8 seconds
RetCode: 0
Status:  OK 
CheckDir: CHRONOS.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings CHRONOS_1.1.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/CHRONOS.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CHRONOS/DESCRIPTION’ ... OK
* this is package ‘CHRONOS’ version ‘1.1.3’
* 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 ... NOTE
.betweennessCentrality: no visible global function definition for ‘as’
.nlSubpaths: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/CHRONOS.Rcheck/00check.log’
for details.


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/CHRONOS-Ex.timings:

nameusersystemelapsed
CHRONOSrun3.2890.3773.783
convertMiRNANomenclature0.0090.0030.013
convertNomenclature0.0000.0000.001
createPathwayGraphs0.5310.0080.541
downloadKEGGPathwayList0.0420.0030.047
downloadMiRecords0.0390.0040.043
downloadPathways0.0360.0011.549
extractLinearSubpathways2.7260.3062.447
extractNonLinearSubpathways0.2290.0210.252
getEdgeTypes0.0020.0000.003
importExpressions0.0720.0350.107
pathwayMeasures0.2640.0130.294
scoreSubpathways0.1650.0140.178
subpathwayKEGGmap0.0400.0100.051
subpathwayMiRNAs1.7000.0241.727
visualizeResults0.0730.0101.674