BioC 3.6: CHECK report for ontoCAT on veracruz1

Package: ontoCAT

Version: 1.29.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.29.0.tar.gz

StartedAt: 2017-08-16 06:25:27 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 06:27:27 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 120.0 seconds

RetCode: 0

Status:  OK

CheckDir: ontoCAT.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.29.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/ontoCAT.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.29.0’
* 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          65.701  1.319  38.517
showHierarchyDownToTerm  8.146  0.029   8.294
getEFO                   6.766  0.037   6.329
getRootIds               5.113  0.028   4.237
* 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-3.6-bioc/meat/ontoCAT.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
Ontology-class	65.701	1.319	38.517
OntologyTerm-class	0.009	0.000	0.009
getAccession	0.006	0.000	0.006
getAllTermChildren	0.011	0.000	0.011
getAllTermIds	2.694	0.017	1.815
getAllTermParents	0.020	0.000	0.022
getAllTerms	3.787	0.047	3.069
getEFO	6.766	0.037	6.329
getEFOBranchRootIds	4.756	0.012	4.611
getLabel	0.005	0.000	0.006
getOntology	3.621	0.036	1.962
getOntologyAccession	0.002	0.000	0.002
getOntologyDescription	0.002	0.000	0.002
getRootIds	5.113	0.028	4.237
getRoots	3.992	0.010	3.993
getTermAndAllChildren	0.016	0.000	0.020
getTermById	0.008	0.000	0.008
getTermChildren	0.015	0.000	0.015
getTermDefinitions	0.009	0.000	0.008
getTermNameById	0.004	0.000	0.004
getTermParents	0.014	0.001	0.015
getTermSynonyms	0.031	0.000	0.034
hasTerm	0.004	0.000	0.004
isEFOBranchRoot	0.006	0.000	0.007
isRoot	3.917	0.009	3.966
ontoCAT-package	0.307	0.004	0.118
searchTerm	4.592	0.023	3.090
searchTermPrefix	3.23	0.01	3.11
showHierarchyDownToTerm	8.146	0.029	8.294
showPathsToTerm	3.82	0.01	3.94