Package: gaggle

Version: 1.1.0

Command: D:\biocbld\1.9d\R\bin\R.exe CMD check gaggle_1.1.0.tar.gz

RetCode: 0

Time: 103.2 seconds

Status: WARNINGS

CheckDir: gaggle.Rcheck

Warnings: 5

* checking for working latex ... OK
* using log directory 'D:/biocbld/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 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: connect

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		2) You are using an out-of-date Gaggle Boss.

java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
tools::checkS3methods(package = "gaggle")
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: connect

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		2) You are using an out-of-date Gaggle Boss.

java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
tools::checkReplaceFuns(package = "gaggle")
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: connect

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		2) You are using an out-of-date Gaggle Boss.

java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
tools::checkFF(package = "gaggle")
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: connect

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		2) You are using an out-of-date Gaggle Boss.

java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
tools::undoc(package = "gaggle")
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: connect

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		2) You are using an out-of-date Gaggle Boss.

java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
tools::codoc(package = "gaggle")

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

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		2) You are using an out-of-date Gaggle Boss.

java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
tools::codocData(package = "gaggle")

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

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

java.lang.NullPointerException
	at org.systemsbiology.gaggle.geese.rShell.RShellGoose.getGeeseNames(RShellGoose.java:731)
tools::codocClasses(package = "gaggle")
* 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
  D:/biocbld/1.9d/Rpacks/gaggle.Rcheck/00check.log
for details

installing R.css in D:/biocbld/1.9d/Rpacks/gaggle.Rcheck


---------- Making package gaggle ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  installing R files
  installing inst files
  installing man source files
  installing indices
  installing help
 >>> Building/Updating help pages for package 'gaggle'
     Formats: text html latex example chm 
  broadcast                         text    html    latex           chm
  geese                             text    html    latex           chm
  getCluster                        text    html    latex           chm
  getHashMap                        text    html    latex           chm
  getMatrix                         text    html    latex           chm
  getNameList                       text    html    latex           chm
  getNetwork                        text    html    latex           chm
  getSpecies                        text    html    latex           chm
  getTargetGoose                    text    html    latex           chm
  hideGoose                         text    html    latex           chm
  setSpecies                        text    html    latex           chm
  setTargetGoose                    text    html    latex           chm
  showGoose                         text    html    latex           chm
  testGagglePackage                 text    html    latex           chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\1.9d\Rpacks\gaggle.Rcheck\00_pkg_src\gaggle\chm\gaggle.chm


Compile time: 0 minutes, 0 seconds
15	Topics
64	Local links
0	Internet links
1	Graphic


Created d:\biocbld\1.9d\Rpacks\gaggle.Rcheck\00_pkg_src\gaggle\chm\gaggle.chm, 23,303 bytes
Compression decreased file by 7,161 bytes.
  preparing package gaggle for lazy loading
  adding MD5 sums

* DONE (gaggle)