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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:gaggle.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings gaggle_1.70.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/gaggle.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaggle/DESCRIPTION’ ... OK
* this is package ‘gaggle’ version ‘1.70.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'gaggle' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.18-bioc/meat/gaggle.Rcheck/00install.out’ for details.
* 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 startup messages can be suppressed ... NOTE

onLoad -- libname: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library pkgname: gaggle 
path to jar: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/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:  21 

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


It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library pkgname: gaggle 
path to jar: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/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:  21 

   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 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc/meat/gaggle.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL gaggle
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘gaggle’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

onLoad -- libname: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-gaggle/00new pkgname: gaggle 
path to jar: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/00LOCK-gaggle/00new/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:  21 

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

Warning: Package 'gaggle' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location

onLoad -- libname: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library pkgname: gaggle 
path to jar: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/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:  21 

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

Warning: Package 'gaggle' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (gaggle)