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BioC 3.6: CHECK report for gaggle on veracruz1

This page was generated on 2017-08-16 13:39:25 -0400 (Wed, 16 Aug 2017).

Package 497/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaggle 1.45.0
Christopher Bare
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gaggle
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: gaggle
Version: 1.45.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gaggle_1.45.0.tar.gz
StartedAt: 2017-08-16 03:19:29 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 03:20:10 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 40.9 seconds
RetCode: 0
Status:  OK 
CheckDir: gaggle.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings gaggle_1.45.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/gaggle.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaggle/DESCRIPTION’ ... OK
* this is package ‘gaggle’ version ‘1.45.0’
* 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 ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls to packages already attached by Depends:
  ‘RUnit’ ‘rJava’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RUnit’ ‘rJava’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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'.


onLoad -- libname: /Users/biocbuild/bbs-3.6-bioc/meat/gaggle.Rcheck pkgname: gaggle 
path to jar: /Users/biocbuild/bbs-3.6-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:  1.8.0_111 

   You are using the wrong version of Java.
   Please see http://gaggle.systemsbiology.org/docs/html/java

.broadcastAssociativeArray: no visible binding for global variable
  ‘goose’
.broadcastEnvironment: no visible binding for global variable ‘goose’
.broadcastGraph: no visible binding for global variable ‘goose’
.pkgVersion: no visible global function definition for ‘sessionInfo’
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’
Undefined global functions or variables:
  goose sessionInfo test.gaggle
Consider adding
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-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
** testing if installed package can be loaded

onLoad -- libname: /Users/biocbuild/bbs-3.6-bioc/meat/gaggle.Rcheck pkgname: gaggle 
path to jar: /Users/biocbuild/bbs-3.6-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:  1.8.0_111 

   You are using the wrong version of Java.
   Please see http://gaggle.systemsbiology.org/docs/html/java

* DONE (gaggle)

gaggle.Rcheck/gaggle-Ex.timings:

nameusersystemelapsed
newTuple0.020.000.02