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This page was generated on 2022-10-19 13:20:17 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 nebbiolo1


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 716/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gaggle 1.64.0  (landing page)
Christopher Bare
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/gaggle
git_branch: RELEASE_3_15
git_last_commit: a3d5c88
git_last_commit_date: 2022-04-26 10:58:30 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: gaggle
Version: 1.64.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:gaggle.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings gaggle_1.64.0.tar.gz
StartedAt: 2022-10-18 19:48:41 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:49:11 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 29.3 seconds
RetCode: 0
Status:   OK  
CheckDir: gaggle.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:gaggle.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings gaggle_1.64.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/gaggle.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaggle/DESCRIPTION’ ... OK
* this is package ‘gaggle’ version ‘1.64.0’
* 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 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: /home/biocbuild/bbs-3.15-bioc/R/library pkgname: gaggle 
path to jar: /home/biocbuild/bbs-3.15-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:  Linux 
 jvm version:  11.0.16 

   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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/gaggle.Rcheck/00check.log’
for details.



Installation output

gaggle.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL gaggle
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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: /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-gaggle/00new pkgname: gaggle 
path to jar: /home/biocbuild/bbs-3.15-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:  Linux 
 jvm version:  11.0.16 

   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: /home/biocbuild/bbs-3.15-bioc/R/library pkgname: gaggle 
path to jar: /home/biocbuild/bbs-3.15-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:  Linux 
 jvm version:  11.0.16 

   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)

Tests output


Example timings

gaggle.Rcheck/gaggle-Ex.timings

nameusersystemelapsed
newTuple0.0180.0040.014