Package: gaggle

Version: 1.1.0

Command: /loc/biocbuild/1.9d/R/bin/R CMD check gaggle_1.1.0.tar.gz

RetCode: 0

Time: 72.3 seconds

Status: WARNINGS

CheckDir: gaggle.Rcheck

Warnings: 5

* checking for working latex ... OK
* using log directory '/extra/loc/biocbuild/1.9d/Rpacks/gaggle.Rcheck'
* using R version 2.4.0 Under development (unstable) (2006-06-04 r38279)
* checking for file 'gaggle/DESCRIPTION' ... OK
* this is package 'gaggle' version '1.1.0'
* 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for library.dynam ... OK
* checking S3 generic/method consistency ... WARNING


	Failed to connect to Gaggle Boss  at rmi://localhost/gaggle:
		Connection refused to host: localhost; nested exception is: 
	java.net.ConnectException: Connection refused

	Possible causes: 
		1) You forgot to start a Gaggle Boss.
		2) You are using an out-of-date Gaggle Boss.

Exception in thread "main" java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING


	Failed to connect to Gaggle Boss  at rmi://localhost/gaggle:
		Connection refused to host: localhost; nested exception is: 
	java.net.ConnectException: Connection refused

	Possible causes: 
		1) You forgot to start a Gaggle Boss.
		2) You are using an out-of-date Gaggle Boss.

Exception in thread "main" java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING


	Failed to connect to Gaggle Boss  at rmi://localhost/gaggle:
		Connection refused to host: localhost; nested exception is: 
	java.net.ConnectException: Connection refused

	Possible causes: 
		1) You forgot to start a Gaggle Boss.
		2) You are using an out-of-date Gaggle Boss.

Exception in thread "main" java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... OK
* checking for missing documentation entries ... WARNING


	Failed to connect to Gaggle Boss  at rmi://localhost/gaggle:
		Connection refused to host: localhost; nested exception is: 
	java.net.ConnectException: Connection refused

	Possible causes: 
		1) You forgot to start a Gaggle Boss.
		2) You are using an out-of-date Gaggle Boss.

Exception in thread "main" java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING


	Failed to connect to Gaggle Boss  at rmi://localhost/gaggle:
		Connection refused to host: localhost; nested exception is: 
	java.net.ConnectException: Connection refused

	Possible causes: 
		1) You forgot to start a Gaggle Boss.
		2) You are using an out-of-date Gaggle Boss.

Exception in thread "main" java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)


	Failed to connect to Gaggle Boss  at rmi://localhost/gaggle:
		Connection refused to host: localhost; nested exception is: 
	java.net.ConnectException: Connection refused

	Possible causes: 
		1) You forgot to start a Gaggle Boss.
		2) You are using an out-of-date Gaggle Boss.

Exception in thread "main" java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)


	Failed to connect to Gaggle Boss  at rmi://localhost/gaggle:
		Connection refused to host: localhost; nested exception is: 
	java.net.ConnectException: Connection refused

	Possible causes: 
		1) You forgot to start a Gaggle Boss.
		2) You are using an out-of-date Gaggle Boss.

Exception in thread "main" java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
* checking Rd \usage sections ... OK
* creating gaggle-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating gaggle-manual.tex ... OK
* checking gaggle-manual.tex ... OK

WARNING: There were 5 warnings, see
  /extra/loc/biocbuild/1.9d/Rpacks/gaggle.Rcheck/00check.log
for details

* Installing *source* package 'gaggle' ...
** R
** inst
** preparing package for lazy loading
Loading required package: rJava
Loading required package: graph
Loading required package: Ruuid
Loading required package: Ruuid
** help
 >>> Building/Updating help pages for package 'gaggle'
     Formats: text html latex example 
  broadcast                         text    html    latex
  geese                             text    html    latex
  getCluster                        text    html    latex
  getHashMap                        text    html    latex
  getMatrix                         text    html    latex
  getNameList                       text    html    latex
  getNetwork                        text    html    latex
  getSpecies                        text    html    latex
  getTargetGoose                    text    html    latex
  hideGoose                         text    html    latex
  setSpecies                        text    html    latex
  setTargetGoose                    text    html    latex
  showGoose                         text    html    latex
  testGagglePackage                 text    html    latex
** building package indices ...
* DONE (gaggle)