Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 712/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
FGNet 3.40.0 (landing page) Sara Aibar
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. |
Package: FGNet |
Version: 3.40.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FGNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FGNet_3.40.0.tar.gz |
StartedAt: 2024-11-09 02:16:03 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 02:20:07 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 243.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: FGNet.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:FGNet.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings FGNet_3.40.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/FGNet.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.7 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘FGNet/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘FGNet’ version ‘3.40.0’ * 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 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 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 ‘/Users/biocbuild/bbs-3.20-bioc/meat/FGNet.Rcheck/00check.log’ for details.
FGNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL FGNet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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)
FGNet.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 -- Sat Nov 9 02:20:03 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 0.329 0.032 0.359
FGNet.Rcheck/FGNet-Ex.timings
name | user | system | elapsed | |
FGNet-package | 0.000 | 0.001 | 0.000 | |
FGNet_GUI | 0.000 | 0.000 | 0.001 | |
FGNet_report | 0.000 | 0.000 | 0.001 | |
analyzeNetwork | 0 | 0 | 0 | |
clustersDistance | 0 | 0 | 0 | |
fea2incidMat | 0 | 0 | 0 | |
fea_gage | 0 | 0 | 0 | |
fea_gtLinker | 0 | 0 | 0 | |
fea_topGO | 0 | 0 | 0 | |
format_david | 0.154 | 0.018 | 0.179 | |
format_results | 0.000 | 0.000 | 0.001 | |
functionalNetwork | 0.000 | 0.001 | 0.000 | |
getTerms | 0 | 0 | 0 | |
keywordsTerm | 0.000 | 0.000 | 0.001 | |
plotGoAncestors | 2.011 | 0.210 | 2.222 | |