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This page was generated on 2022-04-13 12:06:35 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for gaggle on tokay2


To the developers/maintainers of the gaggle package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gaggle.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 695/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaggle 1.62.0  (landing page)
Christopher Bare
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/gaggle
git_branch: RELEASE_3_14
git_last_commit: a13232a
git_last_commit_date: 2021-10-26 11:49:53 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: gaggle
Version: 1.62.0
Command: C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:gaggle.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings gaggle_1.62.0.tar.gz
StartedAt: 2022-04-12 19:54:40 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 19:57:34 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 174.0 seconds
RetCode: 0
Status:   OK  
CheckDir: gaggle.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:gaggle.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings gaggle_1.62.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/gaggle.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'gaggle/DESCRIPTION' ... OK
* this is package 'gaggle' version '1.62.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... 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 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: C:/Users/biocbuild/bbs-3.14-bioc/R/library pkgname: gaggle 
path to jar: C:/Users/biocbuild/bbs-3.14-bioc/R/library/gaggle/jars/gaggleRShell.jar 
      script:  gaggle.R $Revision: 4499 $   $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $ 
  os version:  Windows Server 2012 R2 
 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 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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/gaggle.Rcheck/00check.log'
for details.



Installation output

gaggle.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch gaggle
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
* installing *source* package 'gaggle' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'gaggle'
    finding HTML links ... done
    broadcast                               html  
    connectToGaggle                         html  
    disconnectFromGaggle                    html  
    gaggleInit                              html  
    geese                                   html  
    getCluster                              html  
    getJavaClassName                        html  
    getMatrix                               html  
    getNameList                             html  
    getNetwork                              html  
    getSpecies                              html  
    getTargetGoose                          html  
    getTuple                                html  
    hideGoose                               html  
    newTuple                                html  
    setSpecies                              html  
    setTargetGoose                          html  
    showGoose                               html  
    testGagglePackage                       html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location

onLoad -- libname: C:/Users/biocbuild/bbs-3.14-bioc/R/library/00LOCK-gaggle/00new pkgname: gaggle 
path to jar: C:/Users/biocbuild/bbs-3.14-bioc/R/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:  Windows Server 2012 R2 
 jvm version:  1.8.0_111 

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

** testing if installed package can be loaded from final location

onLoad -- libname: C:/Users/biocbuild/bbs-3.14-bioc/R/library pkgname: gaggle 
path to jar: C:/Users/biocbuild/bbs-3.14-bioc/R/library/gaggle/jars/gaggleRShell.jar 
      script:  gaggle.R $Revision: 4499 $   $Date: 2010-08-10 17:15:03 -0700 (Tue, 10 Aug 2010) $ 
  os version:  Windows Server 2012 R2 
 jvm version:  1.8.0_111 

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

** testing if installed package keeps a record of temporary installation path
* DONE (gaggle)
Making 'packages.html' ... done

Tests output


Example timings

gaggle.Rcheck/gaggle-Ex.timings

nameusersystemelapsed
newTuple0.030.000.03