Back to Multiple platform build/check report for BioC 3.18:   simplified   long
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This page was generated on 2023-11-02 11:40:41 -0400 (Thu, 02 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4729
palomino4Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4463
lconwaymacOS 12.6.5 Montereyx86_644.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" 4478
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.3.1 (2023-06-16) -- "Beagle Scouts" 4464
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

Package 708/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
FGNet 3.36.0  (landing page)
Sara Aibar
Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023)
git_url: https://git.bioconductor.org/packages/FGNet
git_branch: RELEASE_3_18
git_last_commit: caef61c
git_last_commit_date: 2023-10-24 09:56:31 -0400 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.6.5 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    WARNINGS  

CHECK results for FGNet on kunpeng2


To the developers/maintainers of the FGNet package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: FGNet
Version: 3.36.0
Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:FGNet.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings FGNet_3.36.0.tar.gz
StartedAt: 2023-11-02 10:30:03 -0000 (Thu, 02 Nov 2023)
EndedAt: 2023-11-02 10:31:51 -0000 (Thu, 02 Nov 2023)
EllapsedTime: 107.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: FGNet.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:FGNet.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings FGNet_3.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/FGNet.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘FGNet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘FGNet’ version ‘3.36.0’
* 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 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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plotGoAncestors 6.727  0.413   7.549
* 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-3.18-bioc/meat/FGNet.Rcheck/00check.log’
for details.



Installation output

FGNet.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL FGNet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.3.1/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)

Tests output

FGNet.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 -- Thu Nov  2 10:31:48 2023 
*********************************************** 
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 
  1.267   0.050   1.310 

Example timings

FGNet.Rcheck/FGNet-Ex.timings

nameusersystemelapsed
FGNet-package000
FGNet_GUI000
FGNet_report000
analyzeNetwork000
clustersDistance000
fea2incidMat000
fea_gage000
fea_gtLinker000
fea_topGO000
format_david0.5910.0460.683
format_results000
functionalNetwork0.0010.0000.001
getTerms000
keywordsTerm000
plotGoAncestors6.7270.4137.549