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 |
* 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.
* 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)