Package: gaggle

Version: 1.1.0

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

RetCode: 1

Time: 39.8 seconds

Status: ERROR

CheckDir: gaggle.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory '/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
createObject.FindClass org/systemsbiology/gaggle/geese/rShell/RShellGoose failed
Exception in thread "main" java.lang.InternalError
	at java.util.zip.Inflater.init(Native Method)
	at java.util.zip.Inflater.(Inflater.java:75)
	at java.util.zip.ZipFile.getInflater(ZipFile.java:375)
	at java.util.zip.ZipFile.getInputStream(ZipFile.java:320)
	at java.util.zip.ZipFile.getInputStream(ZipFile.java:286)
	at java.util.jar.JarFile.hasClassPathAttribute(JarFile.java:462)
	at java.util.jar.JavaUtilJarAccessImpl.jarFileHasClassPathAttribute(JavaUtilJarAccessImpl.java:15)
	at sun.misc.URLClassPath$JarLoader.getClassPath(URLClassPath.java:809)
	at sun.misc.URLClassPath.getLoader(URLClassPath.java:293)
	at sun.misc.URLClassPath.getResource(URLClassPath.java:160)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:192)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
Error: package/namespace load failed for 'gaggle'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)), 
       call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'Generic functions and methods' of the 'Writing R Extensions'
manual.
* checking replacement functions ... WARNING
createObject.FindClass org/systemsbiology/gaggle/geese/rShell/RShellGoose failed
Exception in thread "main" java.lang.InternalError
	at java.util.zip.Inflater.init(Native Method)
	at java.util.zip.Inflater.(Inflater.java:75)
	at java.util.zip.ZipFile.getInflater(ZipFile.java:375)
	at java.util.zip.ZipFile.getInputStream(ZipFile.java:320)
	at java.util.zip.ZipFile.getInputStream(ZipFile.java:286)
	at java.util.jar.JarFile.hasClassPathAttribute(JarFile.java:462)
	at java.util.jar.JavaUtilJarAccessImpl.jarFileHasClassPathAttribute(JavaUtilJarAccessImpl.java:15)
	at sun.misc.URLClassPath$JarLoader.getClassPath(URLClassPath.java:809)
	at sun.misc.URLClassPath.getLoader(URLClassPath.java:293)
	at sun.misc.URLClassPath.getResource(URLClassPath.java:160)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:192)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
Error: package/namespace load failed for 'gaggle'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)), 
       call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
In R, the argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
createObject.FindClass org/systemsbiology/gaggle/geese/rShell/RShellGoose failed
Exception in thread "main" java.lang.InternalError
	at java.util.zip.Inflater.init(Native Method)
	at java.util.zip.Inflater.(Inflater.java:75)
	at java.util.zip.ZipFile.getInflater(ZipFile.java:375)
	at java.util.zip.ZipFile.getInputStream(ZipFile.java:320)
	at java.util.zip.ZipFile.getInputStream(ZipFile.java:286)
	at java.util.jar.JarFile.hasClassPathAttribute(JarFile.java:462)
	at java.util.jar.JavaUtilJarAccessImpl.jarFileHasClassPathAttribute(JavaUtilJarAccessImpl.java:15)
	at sun.misc.URLClassPath$JarLoader.getClassPath(URLClassPath.java:809)
	at sun.misc.URLClassPath.getLoader(URLClassPath.java:293)
	at sun.misc.URLClassPath.getResource(URLClassPath.java:160)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:192)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:188)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:268)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:251)
	at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:319)
Error: package/namespace load failed for 'gaggle'
Call sequence:
2: stop(gettextf("package/namespace load failed for '%s'", libraryPkgName(package)), 
       call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
See section 'System and foreign language interfaces' of the 'Writing R
Extensions' manual.
* checking Rd files ... OK
* checking for missing documentation entries ... ERROR
Error: package/namespace load failed for 'gaggle'

* 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)