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### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:FGNet.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings FGNet_3.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/FGNet.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘FGNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FGNet’ version ‘3.40.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘FGNet’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 ... WARNING
'::' or ':::' import not declared from: ‘RGtk2’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildGeneSets: no visible global function definition for ‘columns’
buildGeneSets: no visible binding for global variable ‘GO.db’
buildGeneSets: no visible binding for global variable
  ‘reactomePATHID2NAME’
fea_gage: no visible global function definition for ‘exprs’
fea_gage: no visible global function definition for ‘gage’
fea_gage: no visible global function definition for ‘esset.grp’
fea_gtLinker_getResults: no visible global function definition for
  ‘url.exists’
fea_topGO: no visible global function definition for ‘groupGOTerms’
fea_topGO: no visible binding for global variable ‘annFUN.gene2GO’
fea_topGO: no visible global function definition for ‘getSigGroups’
fea_topGO: no visible global function definition for ‘GenTable’
fea_topGO : <anonymous>: no visible global function definition for
  ‘genesInTerm’
fea_topGO : <anonymous>: no visible global function definition for
  ‘sigGenes’
formatResultsFile: no visible binding for global variable ‘rawResults’
format_david: no visible global function definition for ‘getURL’
plotGoAncestors : <anonymous>: no visible binding for global variable
  ‘GOTERM’
processFile: no visible binding for '<<-' assignment to ‘rawResults’
processFile: no visible binding for global variable ‘rawResults’
refList: no visible global function definition for ‘columns’
submitQuery: no visible global function definition for ‘readList’
tabFEA_fill: no visible binding for global variable ‘GtkShadowType’
tabFEA_fill: no visible global function definition for ‘gtkVBox’
tabFEA_fill: no visible global function definition for
  ‘pangoFontDescriptionFromString’
tabFEA_fill: no visible global function definition for
  ‘gtkFrameSetShadowType’
tabFEA_fill: no visible global function definition for ‘gtkEntryNew’
tabFEA_fill: no visible global function definition for ‘newDavidVars’
tabFEA_fill: no visible global function definition for ‘tabDavid_fill’
tabFEA_fill: no visible binding for '<<-' assignment to ‘rawResults’
tabFEA_fill: no visible global function definition for ‘gtkLabelNew’
tabGTL_fill: no visible binding for global variable ‘GtkShadowType’
tabGage_fill: no visible binding for global variable ‘GtkShadowType’
tabHelp_fill: no visible binding for global variable ‘GtkShadowType’
tabNetwork_common_fill: no visible binding for global variable
  ‘GtkShadowType’
tabNetwork_common_fill: no visible global function definition for
  ‘pangoFontDescriptionFromString’
tabNetwork_common_fill: no visible global function definition for
  ‘gSignalConnect’
tabNetwork_fill: no visible global function definition for
  ‘gtkLabelNew’
tabOther_fill: no visible binding for global variable ‘GtkShadowType’
tabOther_fill : <anonymous>: no visible binding for global variable
  ‘GtkShadowType’
tabPlotNetwork_fill: no visible binding for global variable
  ‘GtkShadowType’
tabSubNetwork_fill: no visible binding for global variable
  ‘GtkShadowType’
tabTopGo_fill: no visible binding for global variable ‘GtkShadowType’
tabTopGo_fill: no visible binding for global variable ‘evidenceScroll’
viewFile: no visible binding for global variable ‘rawResults’
Undefined global functions or variables:
  GO.db GOTERM GenTable GtkShadowType annFUN.gene2GO columns esset.grp
  evidenceScroll exprs gSignalConnect gage genesInTerm getSigGroups
  getURL groupGOTerms gtkEntryNew gtkFrameSetShadowType gtkLabelNew
  gtkVBox newDavidVars pangoFontDescriptionFromString rawResults
  reactomePATHID2NAME readList sigGenes tabDavid_fill url.exists
* checking Rd files ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/FGNet.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL FGNet
###
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘FGNet’ ...
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (FGNet)

R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("FGNet")


RUNIT TEST PROTOCOL -- Thu Dec 19 23:45:07 2024 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
FGNet RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  0.797   0.075   0.861