Package: ENVISIONQuery

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ENVISIONQuery_1.8.0.tar.gz

StartedAt: 2013-05-01 05:03:05 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:04:19 -0700 (Wed, 01 May 2013)

EllapsedTime: 73.9 seconds

RetCode: 0

Status:  OK

CheckDir: ENVISIONQuery.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/ENVISIONQuery.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'ENVISIONQuery/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ENVISIONQuery' 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'ENVISIONQuery' can be installed ... [6s/7s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'ENVISIONQuery/R/zzz.R':
  .onAttach calls:
    cat("This is ", pkgname, " ", desc$Version, " ", desc$Date, "\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
* 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' ... NOTE
The following files should probably not be installed:
  'ENVISIONQuery.lyx'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [9s/17s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
ENVISIONQuery 5.346   0.26  14.559
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/ENVISIONQuery.Rcheck/00check.log'
for details.

* installing *source* package 'ENVISIONQuery' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
This is  ENVISIONQuery   1.8.0   2011-07-17 
* DONE (ENVISIONQuery)

name	user	system	elapsed
ENVISIONQuery	5.346	0.260	14.559
getInputTypes	0.019	0.002	0.010
getService	0.027	0.001	0.014
getServiceClient	0.023	0.002	0.016
getServiceNames	0.011	0.001	0.012
getServiceOptions	0.021	0.000	0.022
getServices	0.010	0.001	0.011
getTool	0.086	0.002	0.089
getToolNames	0.008	0.000	0.015