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BioC 3.4: CHECK report for ontoCAT on morelia

This page was generated on 2016-09-21 03:50:47 -0700 (Wed, 21 Sep 2016).

Package 846/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ontoCAT 1.25.0
Natalja Kurbatova
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ontoCAT
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: ontoCAT
Version: 1.25.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.25.0.tar.gz
StartedAt: 2016-09-20 10:48:38 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 10:50:27 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 108.7 seconds
RetCode: 0
Status:  OK 
CheckDir: ontoCAT.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ontoCAT.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 ‘ontoCAT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ontoCAT’ version ‘1.25.0’
* 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 ‘ontoCAT’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                          user system elapsed
Ontology-class          63.391  0.999  35.320
showHierarchyDownToTerm  7.443  0.088   6.982
getEFO                   7.413  0.077   6.464
* 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/ontoCAT.Rcheck/00check.log’
for details.


ontoCAT.Rcheck/00install.out:

* installing *source* package ‘ontoCAT’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ontoCAT)

ontoCAT.Rcheck/ontoCAT-Ex.timings:

nameusersystemelapsed
Ontology-class63.391 0.99935.320
OntologyTerm-class0.0100.0010.010
getAccession0.0070.0000.007
getAllTermChildren0.0180.0010.019
getAllTermIds2.5600.0162.130
getAllTermParents0.0200.0000.021
getAllTerms4.0500.0453.680
getEFO7.4130.0776.464
getEFOBranchRootIds3.8620.0453.432
getLabel0.0050.0000.004
getOntology2.1350.0191.793
getOntologyAccession0.0020.0000.003
getOntologyDescription0.0020.0000.002
getRootIds4.1470.0463.647
getRoots3.9110.0423.671
getTermAndAllChildren0.0160.0000.016
getTermById0.0080.0000.008
getTermChildren0.0200.0000.019
getTermDefinitions0.0170.0010.017
getTermNameById0.0040.0000.005
getTermParents0.0110.0000.011
getTermSynonyms0.0330.0010.033
hasTerm0.0040.0000.005
isEFOBranchRoot0.0090.0000.008
isRoot4.0800.0423.888
ontoCAT-package0.2080.0050.121
searchTerm4.4490.0612.875
searchTermPrefix3.5560.0362.921
showHierarchyDownToTerm7.4430.0886.982
showPathsToTerm3.8600.0423.646