BioC 3.3: CHECK report for ontoCAT on linux2.bioconductor.org
This page was generated on 2015-10-27 12:11:53 -0400 (Tue, 27 Oct 2015).
ontoCAT 1.23.0
Natalja Kurbatova
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ontoCAT | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
Summary
| Package: ontoCAT |
| Version: 1.23.0 |
| Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.23.0.tar.gz |
| StartedAt: 2015-10-27 06:27:53 -0400 (Tue, 27 Oct 2015) |
| EndedAt: 2015-10-27 06:29:36 -0400 (Tue, 27 Oct 2015) |
| EllapsedTime: 103.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ontoCAT.Rcheck |
| Warnings: 0 |
Command output
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###
### Running command:
###
### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings ontoCAT_1.23.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/ontoCAT.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (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 ‘1.23.0’
* 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 ... [2s/2s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [102s/77s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
Ontology-class 52.256 0.736 33.146
getEFO 6.930 0.063 6.270
showHierarchyDownToTerm 6.492 0.020 6.372
getEFOBranchRootIds 5.856 0.020 3.636
* 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
‘/home/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 | 52.256 | 0.736 | 33.146 |
|
| OntologyTerm-class | 0.009 | 0.000 | 0.009 |
|
| getAccession | 0.005 | 0.000 | 0.005 |
|
| getAllTermChildren | 0.013 | 0.000 | 0.013 |
|
| getAllTermIds | 3.134 | 0.004 | 2.623 |
|
| getAllTermParents | 0.068 | 0.000 | 0.036 |
|
| getAllTerms | 4.419 | 0.004 | 4.084 |
|
| getEFO | 6.930 | 0.063 | 6.270 |
|
| getEFOBranchRootIds | 5.856 | 0.020 | 3.636 |
|
| getLabel | 0.005 | 0.000 | 0.005 |
|
| getOntology | 2.261 | 0.008 | 1.998 |
|
| getOntologyAccession | 0.003 | 0.000 | 0.004 |
|
| getOntologyDescription | 0.003 | 0.000 | 0.004 |
|
| getRootIds | 3.113 | 0.012 | 2.923 |
|
| getRoots | 3.875 | 0.016 | 3.853 |
|
| getTermAndAllChildren | 0.014 | 0.000 | 0.015 |
|
| getTermById | 0.007 | 0.000 | 0.006 |
|
| getTermChildren | 0.013 | 0.000 | 0.012 |
|
| getTermDefinitions | 0.012 | 0.000 | 0.012 |
|
| getTermNameById | 0.003 | 0.000 | 0.003 |
|
| getTermParents | 0.012 | 0.000 | 0.012 |
|
| getTermSynonyms | 0.026 | 0.004 | 0.030 |
|
| hasTerm | 0.004 | 0.000 | 0.003 |
|
| isEFOBranchRoot | 0.007 | 0.000 | 0.006 |
|
| isRoot | 3.229 | 0.020 | 3.134 |
|
| ontoCAT-package | 0.057 | 0.004 | 0.061 |
|
| searchTerm | 2.256 | 0.004 | 2.075 |
|
| searchTermPrefix | 3.370 | 0.000 | 3.141 |
|
| showHierarchyDownToTerm | 6.492 | 0.020 | 6.372 |
|
| showPathsToTerm | 3.159 | 0.008 | 3.110 |
|