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Package 240/658HostnameOS / ArchBUILDCHECKBUILD BIN
gaggle 1.27.1
Christopher Bare
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gaggle
Last Changed Rev: 70685 / Revision: 74774
Last Changed Date: 2012-10-19 10:50:22 -0700 (Fri, 19 Oct 2012)
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 Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: gaggle
Version: 1.27.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch gaggle_1.27.1.tar.gz
StartedAt: 2013-03-25 02:33:13 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 02:34:15 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 62.0 seconds
RetCode: 0
Status:  OK 
CheckDir: gaggle.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/gaggle.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'gaggle/DESCRIPTION' ... OK
* this is package 'gaggle' version '1.27.1'
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'gaggle' can be installed ... [5s/5s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Non-standard license specification:
  GPL version 2 or newer
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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
File 'gaggle/R/gaggle.R':
  .onLoad calls:
    require("rJava")
    cat(paste("\nonLoad -- libname:", libname, "pkgname:", pkgname,     "\n"))
    cat("path to jar:", fullPathToGaggleJar, "\n")
    cat("      script: ", .scriptVersion(), "\n")
    cat("  os version: ", .jcall("java/lang/System", "S", "getProperty",     "os.name"), "\n")
    cat(" jvm version: ", jvmVersion, "\n")
    cat("\n   You are using the wrong version of Java.\n", "  Please see http://gaggle.systemsbiology.org/docs/html/java\n\n")

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

.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'
getTupleAsList: 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [3s/3s] 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
  '/Users/biocbuild/bbs-2.12-bioc/meat/gaggle.Rcheck/00check.log'
for details.

gaggle.Rcheck/00install.out:

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

onLoad -- libname: /Users/biocbuild/bbs-2.12-bioc/meat/gaggle.Rcheck pkgname: gaggle 
path to jar: /Users/biocbuild/bbs-2.12-bioc/meat/gaggle.Rcheck/gaggle/jars/gaggleRShell.jar 
      script:  gaggle.R $Revision: 4499 $   $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $ 
  os version:  Mac OS X 
 jvm version:  1.5.0_30 
* DONE (gaggle)

gaggle.Rcheck/gaggle-Ex.timings:

nameusersystemelapsed
newTuple0.0340.0100.061