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BioC 3.0: CHECK report for rols on oaxaca

This page was generated on 2015-04-10 10:06:06 -0700 (Fri, 10 Apr 2015).

Package 768/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rols 1.8.0
Laurent Gatto
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/rols
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ OK ] OK 

Summary

Package: rols
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch rols_1.8.0.tar.gz
StartedAt: 2015-04-10 03:00:02 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 03:02:08 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 125.9 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/rols.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.8.0’
* 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 ... [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 ... [12s/62s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
allIds        6.404  0.024   8.564
CVParam-class 1.182  0.016  21.990
isIdObsolete  0.284  0.003   9.450
termMetadata  0.167  0.001   5.305
term          0.159  0.002   8.326
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-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 1.182 0.01621.990
allIds6.4040.0248.564
childrenRelations0.0760.0010.393
isIdObsolete0.2840.0039.450
olsQuery0.3290.0032.153
olsVersion0.0150.0010.329
ontologies0.030.000.03
ontologyLoadDate0.1040.0020.735
ontologyNames0.0220.0010.022
parents0.0800.0010.396
rootId0.2220.0021.157
term0.1590.0028.326
termMetadata0.1670.0015.305