Multiple platform build/check report for BioC 3.11 - CHECK report for FGNet on tokay2

Package: FGNet

Version: 3.22.1

Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FGNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings FGNet_3.22.1.tar.gz

StartedAt: 2020-10-17 04:02:39 -0400 (Sat, 17 Oct 2020)

EndedAt: 2020-10-17 04:04:35 -0400 (Sat, 17 Oct 2020)

EllapsedTime: 116.3 seconds

RetCode: 0

Status: WARNINGS

CheckDir: FGNet.Rcheck

Warnings: 1

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### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FGNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings FGNet_3.22.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/FGNet.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/FGNet.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/FGNet_3.22.1.tar.gz && rm -rf FGNet.buildbin-libdir && mkdir FGNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FGNet.buildbin-libdir FGNet_3.22.1.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL FGNet_3.22.1.zip && rm FGNet_3.22.1.tar.gz FGNet_3.22.1.zip
###
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 1464k  100 1464k    0     0  17.9M      0 --:--:-- --:--:-- --:--:-- 19.8M

install for i386

* installing *source* package 'FGNet' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'FGNet'
    finding HTML links ... done
    FGNet-package                           html  
    FGNet_GUI                               html  
    FGNet_report                            html  
    analyzeNetwork                          html  
    clustersDistance                        html  
    data                                    html  
    fea2incidMat                            html  
    fea_david                               html  
    fea_gage                                html  
    fea_gtLinker                            html  
    fea_topGO                               html  
    format_david                            html  
    format_results                          html  
    functionalNetwork                       html  
    getTerms                                html  
    keywordsTerm                            html  
    plotGoAncestors                         html  
    plotKegg                                html  
    readGeneTermSets                        html  
** 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

install for x64

* installing *source* package 'FGNet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'FGNet' as FGNet_3.22.1.zip
* DONE (FGNet)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'FGNet' successfully unpacked and MD5 sums checked


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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 04:04:23 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 
   1.48    0.09    1.54


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 04:04:26 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 
   1.46    0.15    1.81

name	user	system	elapsed
FGNet-package	0	0	0
FGNet_GUI	0	0	0
FGNet_report	0	0	0
analyzeNetwork	0	0	0
clustersDistance	0	0	0
fea2incidMat	0	0	0
fea_david	3.69	0.19	4.13
fea_gage	0	0	0
fea_gtLinker	0	0	0
fea_topGO	0	0	0
format_david	0.76	0.12	2.79
format_results	0	0	0
functionalNetwork	0	0	0
getTerms	0	0	0
keywordsTerm	0	0	0
plotGoAncestors	3.82	1.00	4.81
plotKegg	0.21	0.00	0.22

name	user	system	elapsed
FGNet-package	0	0	0
FGNet_GUI	0	0	0
FGNet_report	0	0	0
analyzeNetwork	0	0	0
clustersDistance	0	0	0
fea2incidMat	0	0	0
fea_david	4.18	0.08	4.26
fea_gage	0	0	0
fea_gtLinker	0	0	0
fea_topGO	0	0	0
format_david	0.89	0.05	0.99
format_results	0	0	0
functionalNetwork	0	0	0
getTerms	0	0	0
keywordsTerm	0	0	0
plotGoAncestors	3.46	0.75	4.35
plotKegg	0.14	0.02	0.15

CHECK report for FGNet on tokay2

Summary

Command output

Installation output

Tests output

Example timings