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BioC 2.12: CHECK report for ENVISIONQuery on george2

This page was generated on 2013-10-09 09:37:42 -0700 (Wed, 09 Oct 2013).

Package 206/671HostnameOS / ArchBUILDCHECKBUILD BIN
ENVISIONQuery 1.8.1
Alex Lisovich , Roger Day
Snapshot Date: 2013-10-08 17:00:48 -0700 (Tue, 08 Oct 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/ENVISIONQuery
Last Changed Rev: 79643 / Revision: 81334
Last Changed Date: 2013-08-20 17:39:34 -0700 (Tue, 20 Aug 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 

Summary

Package: ENVISIONQuery
Version: 1.8.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings ENVISIONQuery_1.8.1.tar.gz
StartedAt: 2013-10-09 01:35:23 -0700 (Wed, 09 Oct 2013)
EndedAt: 2013-10-09 01:36:24 -0700 (Wed, 09 Oct 2013)
EllapsedTime: 61.5 seconds
RetCode: 0
Status:  OK 
CheckDir: ENVISIONQuery.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/ENVISIONQuery.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ENVISIONQuery/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ENVISIONQuery’ version ‘1.8.1’
* 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 ... 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/6s] 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 ... [4s/7s] OK
* 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
  ‘/home/biocbuild/bbs-2.12-bioc/meat/ENVISIONQuery.Rcheck/00check.log’
for details.

ENVISIONQuery.Rcheck/00install.out:

* 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   1.8.1   2013-08-20 
* DONE (ENVISIONQuery)

ENVISIONQuery.Rcheck/ENVISIONQuery-Ex.timings:

nameusersystemelapsed
ENVISIONQuery1.1920.1644.427
getInputTypes0.0120.0000.014
getService0.0200.0000.021
getServiceClient0.0200.0040.024
getServiceNames0.0080.0040.014
getServiceOptions0.0360.0200.117
getServices0.0120.0080.019
getTool0.0120.0120.026
getToolNames0.0120.0160.027