Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-10-19 13:20:15 -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 FGNet on nebbiolo1


To the developers/maintainers of the FGNet package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/FGNet.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 661/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FGNet 3.30.0  (landing page)
Sara Aibar
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/FGNet
git_branch: RELEASE_3_15
git_last_commit: 211573f
git_last_commit_date: 2022-04-26 11:16:52 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: FGNet
Version: 3.30.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:FGNet.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings FGNet_3.30.0.tar.gz
StartedAt: 2022-10-18 19:43:47 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 19:44:36 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 49.0 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: FGNet.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:FGNet.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings FGNet_3.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/FGNet.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 ‘FGNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FGNet’ version ‘3.30.0’
* 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 ‘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 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 ... 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plotGoAncestors 6.066   0.42   6.487
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/FGNet.Rcheck/00check.log’
for details.



Installation output

FGNet.Rcheck/00install.out

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


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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)

Tests output

FGNet.Rcheck/tests/runTests.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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 -- Tue Oct 18 19:44:32 2022 
*********************************************** 
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 
  0.859   0.095   0.937 

Example timings

FGNet.Rcheck/FGNet-Ex.timings

nameusersystemelapsed
FGNet-package0.0000.0000.001
FGNet_GUI0.0000.0000.001
FGNet_report0.0000.0010.001
analyzeNetwork0.0000.0010.000
clustersDistance000
fea2incidMat0.0000.0000.001
fea_gage0.0000.0000.001
fea_gtLinker000
fea_topGO000
format_david0.4260.0180.445
format_results000
functionalNetwork0.0000.0010.001
getTerms000
keywordsTerm000
plotGoAncestors6.0660.4206.487