Back to Multiple platform build/check report for BioC 3.11 |
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This page was generated on 2020-10-17 11:58:28 -0400 (Sat, 17 Oct 2020).
TO THE DEVELOPERS/MAINTAINERS OF THE FGNet PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 595/1905 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
FGNet 3.22.1 Sara Aibar
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | [ WARNINGS ] | OK |
Package: FGNet |
Version: 3.22.1 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FGNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FGNet_3.22.1.tar.gz |
StartedAt: 2020-10-17 01:08:05 -0400 (Sat, 17 Oct 2020) |
EndedAt: 2020-10-17 01:09:40 -0400 (Sat, 17 Oct 2020) |
EllapsedTime: 95.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: FGNet.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:FGNet.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings FGNet_3.22.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/FGNet.Rcheck’ * using R version 4.0.3 (2020-10-10) * using platform: x86_64-apple-darwin17.0 (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 ‘3.22.1’ * 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: ‘KEGG.db’ * 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_david : <anonymous>: no visible global function definition for ‘getIdTypes’ fea_david : <anonymous>: no visible global function definition for ‘getAllAnnotationCategoryNames’ fea_david: no visible global function definition for ‘postForm’ 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’ plotKegg: no visible global function definition for ‘columns’ plotKegg: no visible global function definition for ‘download_KEGGfile’ plotKegg: no visible global function definition for ‘parse_XMLfile’ plotKegg: no visible global function definition for ‘plot_profile’ 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’ tabDavid_fill: no visible binding for global variable ‘GtkShadowType’ 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 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 download_KEGGfile esset.grp evidenceScroll exprs gSignalConnect gage genesInTerm getAllAnnotationCategoryNames getIdTypes getSigGroups getURL groupGOTerms gtkEntryNew gtkFrameSetShadowType gtkLabelNew gtkVBox pangoFontDescriptionFromString parse_XMLfile plot_profile postForm rawResults reactomePATHID2NAME readList sigGenes 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 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 ‘/Users/biocbuild/bbs-3.11-bioc/meat/FGNet.Rcheck/00check.log’ for details.
FGNet.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL FGNet ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/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 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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 -- Sat Oct 17 01:09:31 2020 *********************************************** Number of test functions: 2 Number of errors: 0 Number of failures: 0 1 Test Suite : FGNet RUnit Tests - 2 test functions, 0 errors, 0 failures Number of test functions: 2 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 1.398 0.144 1.518
FGNet.Rcheck/FGNet-Ex.timings
name | user | system | elapsed | |
FGNet-package | 0.000 | 0.002 | 0.002 | |
FGNet_GUI | 0.000 | 0.001 | 0.001 | |
FGNet_report | 0.000 | 0.001 | 0.001 | |
analyzeNetwork | 0 | 0 | 0 | |
clustersDistance | 0 | 0 | 0 | |
fea2incidMat | 0.001 | 0.001 | 0.001 | |
fea_david | 4.566 | 0.214 | 4.817 | |
fea_gage | 0.000 | 0.000 | 0.001 | |
fea_gtLinker | 0.001 | 0.001 | 0.002 | |
fea_topGO | 0.000 | 0.001 | 0.001 | |
format_david | 0.950 | 0.116 | 1.082 | |
format_results | 0.001 | 0.000 | 0.001 | |
functionalNetwork | 0.002 | 0.001 | 0.002 | |
getTerms | 0 | 0 | 0 | |
keywordsTerm | 0 | 0 | 0 | |
plotGoAncestors | 4.267 | 0.537 | 4.808 | |
plotKegg | 0.226 | 0.008 | 0.235 | |