Package: gaggle

Version: 1.18.0

Command: /home/biocbuild/bbs-2.7-bioc/R/bin/R CMD check --no-vignettes --timings gaggle_1.18.0.tar.gz

StartedAt: 2011-04-07 06:22:57 -0700 (Thu, 07 Apr 2011)

EndedAt: 2011-04-07 06:23:30 -0700 (Thu, 07 Apr 2011)

EllapsedTime: 32.5 seconds

RetCode: 0

Status:  OK

CheckDir: gaggle.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.7-bioc/meat/gaggle.Rcheck’
* using R version 2.12.2 (2011-02-25)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaggle/DESCRIPTION’ ... OK
* this is package ‘gaggle’ version ‘1.18.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘gaggle’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
.broadcastAssociativeArray: no visible binding for global variable
  ‘goose’
.broadcastEnvironment: no visible binding for global variable ‘goose’
.broadcastGraph: no visible binding for global variable ‘goose’
broadcast: no visible binding for global variable ‘goose’
connectToGaggle: no visible binding for global variable ‘goose’
disconnectFromGaggle: no visible binding for global variable ‘goose’
gaggleInit: no visible binding for '<<-' assignment to ‘goose’
gaggleInit: no visible binding for '<<-' assignment to ‘targetGoose’
gaggleInit: no visible binding for global variable ‘goose’
geese: no visible binding for global variable ‘goose’
getCluster: no visible binding for global variable ‘goose’
getMatrix: no visible binding for global variable ‘goose’
getNameList: no visible binding for global variable ‘goose’
getNetwork: no visible binding for global variable ‘goose’
getSpecies: no visible binding for global variable ‘goose’
getTargetGoose: no visible binding for global variable ‘goose’
getTuple: no visible binding for global variable ‘goose’
hideGoose: no visible binding for global variable ‘goose’
setSpecies: no visible binding for global variable ‘goose’
setTargetGoose: no visible binding for '<<-' assignment to
  ‘targetGoose’
setTargetGoose: no visible binding for global variable ‘goose’
showGoose: no visible binding for global variable ‘goose’
testGagglePackage: no visible global function definition for
  ‘test.gaggle’
* checking Rd files ... NOTE
prepare_Rd: connectToGaggle.Rd:9-10: Dropping empty section \arguments
prepare_Rd: disconnectFromGaggle.Rd:8-9: Dropping empty section \arguments
prepare_Rd: getCluster.Rd:8-9: Dropping empty section \arguments
prepare_Rd: getNameList.Rd:8-9: Dropping empty section \arguments
prepare_Rd: getTuple.Rd:6-7: Dropping empty section \arguments
* 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 examples ... NONE
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘gaggle’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

onLoad -- libname: /loc/home/biocbuild/bbs-2.7-bioc/meat/gaggle.Rcheck pkgname: gaggle 
path to jar: /loc/home/biocbuild/bbs-2.7-bioc/meat/gaggle.Rcheck/gaggle/jars/gaggleRShell.jar 
      script:  gaggle.R $Revision: 3504 $   $Date: 2008-09-22 10:45:45 -0700 (Mon, 22 Sep 2008) $ 
  os version:  Linux 
 jvm version:  1.6.0_24 

* DONE (gaggle)