BioC 3.3: CHECK report for ontoCAT on oaxaca
This page was generated on 2016-10-13 12:57:25 -0700 (Thu, 13 Oct 2016).
ontoCAT 1.24.0
Natalja Kurbatova
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/ontoCAT | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
Summary
| Package: ontoCAT |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.24.0.tar.gz |
| StartedAt: 2016-10-13 04:20:35 -0700 (Thu, 13 Oct 2016) |
| EndedAt: 2016-10-13 04:45:52 -0700 (Thu, 13 Oct 2016) |
| EllapsedTime: 1517.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ontoCAT.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ontoCAT_1.24.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-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 ‘1.24.0’
* 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 46.866 1.028 139.597
showHierarchyDownToTerm 6.575 0.105 16.844
getEFO 6.395 0.094 6.392
getAllTerms 3.243 0.053 28.803
searchTermPrefix 2.655 0.035 5.162
getAllTermIds 1.775 0.023 7.049
* 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-3.3-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:
| name | user | system | elapsed
|
| Ontology-class | 46.866 | 1.028 | 139.597 |
|
| OntologyTerm-class | 0.016 | 0.000 | 0.017 |
|
| getAccession | 0.009 | 0.001 | 0.009 |
|
| getAllTermChildren | 0.015 | 0.000 | 0.015 |
|
| getAllTermIds | 1.775 | 0.023 | 7.049 |
|
| getAllTermParents | 0.027 | 0.000 | 0.027 |
|
| getAllTerms | 3.243 | 0.053 | 28.803 |
|
| getEFO | 6.395 | 0.094 | 6.392 |
|
| getEFOBranchRootIds | 3.672 | 0.059 | 3.271 |
|
| getLabel | 0.007 | 0.000 | 0.008 |
|
| getOntology | 1.679 | 0.025 | 2.464 |
|
| getOntologyAccession | 0.003 | 0.000 | 0.003 |
|
| getOntologyDescription | 0.005 | 0.000 | 0.005 |
|
| getRootIds | 3.503 | 0.048 | 3.716 |
|
| getRoots | 3.195 | 0.043 | 2.973 |
|
| getTermAndAllChildren | 0.018 | 0.000 | 0.018 |
|
| getTermById | 0.010 | 0.000 | 0.011 |
|
| getTermChildren | 0.017 | 0.001 | 0.017 |
|
| getTermDefinitions | 0.016 | 0.002 | 2.403 |
|
| getTermNameById | 0.006 | 0.000 | 0.006 |
|
| getTermParents | 0.013 | 0.000 | 0.013 |
|
| getTermSynonyms | 0.031 | 0.000 | 0.031 |
|
| hasTerm | 0.006 | 0.000 | 0.007 |
|
| isEFOBranchRoot | 0.014 | 0.001 | 0.475 |
|
| isRoot | 3.155 | 0.044 | 2.966 |
|
| ontoCAT-package | 0.098 | 0.004 | 0.077 |
|
| searchTerm | 3.242 | 0.049 | 3.878 |
|
| searchTermPrefix | 2.655 | 0.035 | 5.162 |
|
| showHierarchyDownToTerm | 6.575 | 0.105 | 16.844 |
|
| showPathsToTerm | 3.158 | 0.043 | 2.943 |
|