BioC 3.1: CHECK report for rols on zin2
This page was generated on 2015-10-09 09:24:58 -0700 (Fri, 09 Oct 2015).
rols 1.10.0 Laurent Gatto
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/rols | Last Changed Rev: 102591 / Revision: 109384 | Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015) |
| 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 |  |
petty | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK |  |
Summary
Package: rols |
Version: 1.10.0 |
Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings rols_1.10.0.tar.gz |
StartedAt: 2015-10-09 05:07:12 -0700 (Fri, 09 Oct 2015) |
EndedAt: 2015-10-09 05:08:12 -0700 (Fri, 09 Oct 2015) |
EllapsedTime: 60.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: rols.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings rols_1.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/rols.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rols/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rols’ version ‘1.10.0’
* 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 ‘rols’ can be installed ... [3s/3s] 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 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
Found the following possibly unsafe calls:
File ‘rols/R/queries.R’:
unlockBinding("ontologies", .rolsEnv)
* 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 ... [8s/26s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
allIds 4.668 0.008 7.597
CVParam-class 0.681 0.019 9.272
* 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-3.1-bioc/meat/rols.Rcheck/00check.log’
for details.
rols.Rcheck/00install.out:
* installing *source* package ‘rols’ ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘SSOAP’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class “connection” in package ‘BiocGenerics’ seems equivalent to one from package ‘SSOAP’: not turning on duplicate class definitions for this class.
* DONE (rols)
rols.Rcheck/rols-Ex.timings:
name | user | system | elapsed
|
CVParam-class | 0.681 | 0.019 | 9.272 |
|
allIds | 4.668 | 0.008 | 7.597 |
|
childrenRelations | 0.046 | 0.000 | 0.342 |
|
isIdObsolete | 0.153 | 0.008 | 1.664 |
|
olsQuery | 0.226 | 0.000 | 1.469 |
|
olsVersion | 0.003 | 0.004 | 0.303 |
|
ontologies | 0.016 | 0.000 | 0.017 |
|
ontologyLoadDate | 0.057 | 0.000 | 0.646 |
|
ontologyNames | 0.016 | 0.000 | 0.016 |
|
parents | 0.049 | 0.000 | 0.343 |
|
rootId | 0.132 | 0.000 | 1.050 |
|
term | 0.102 | 0.001 | 0.998 |
|
termMetadata | 0.101 | 0.004 | 0.700 |
|