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BioC 2.14: CHECK report for rols on morelia

This page was generated on 2014-10-08 09:05:36 -0700 (Wed, 08 Oct 2014).

Package 680/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rols 1.6.1
Laurent Gatto
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/rols
Last Changed Rev: 95096 / Revision: 95116
Last Changed Date: 2014-10-07 14:02:28 -0700 (Tue, 07 Oct 2014)
zin2 Linux (Ubuntu 12.04.4 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: 1.6.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rols_1.6.1.tar.gz
StartedAt: 2014-10-08 01:18:56 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 01:21:24 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 148.2 seconds
RetCode: 0
Status:  OK 
CheckDir: rols.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rols_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/rols.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.6.1’
* 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 ... [6s/6s] 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 ... [18s/84s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
allIds        9.104  0.034  11.763
CVParam-class 2.205  0.017  21.483
term          0.785  0.004  12.230
isIdObsolete  0.712  0.004  20.471
termMetadata  0.189  0.002   8.285
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-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:

nameusersystemelapsed
CVParam-class 2.205 0.01721.483
allIds 9.104 0.03411.763
childrenRelations0.6860.0021.033
isIdObsolete 0.712 0.00420.471
olsQuery0.3520.0031.930
olsVersion0.3880.0020.710
ontologies0.020.000.02
ontologyLoadDate0.0850.0010.739
ontologyNames0.0230.0000.024
parents0.0590.0010.391
rootId0.1900.0021.815
term 0.785 0.00412.230
termMetadata0.1890.0028.285