Sara Aibar
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/FGNet |
| git_branch: RELEASE_3_13 |
| git_last_commit: 11b6029 |
| git_last_commit_date: 2021-05-19 12:01:32 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:04 -0400 (Fri, 15 Oct 2021).
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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? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 631/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| FGNet 3.26.0 (landing page) Sara Aibar
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: FGNet |
| Version: 3.26.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FGNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings FGNet_3.26.0.tar.gz |
| StartedAt: 2021-10-14 23:07:58 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 23:09:32 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 93.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: FGNet.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:FGNet.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings FGNet_3.26.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/FGNet.Rcheck'
* using R version 4.1.1 (2021-08-10)
* 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 '3.26.0'
* 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 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 ... OK
* 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotGoAncestors 6.69 1.22 7.91
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotGoAncestors 6.58 1.02 7.59
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.13-bioc/meat/FGNet.Rcheck/00check.log'
for details.
FGNet.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/FGNet_3.26.0.tar.gz && rm -rf FGNet.buildbin-libdir && mkdir FGNet.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=FGNet.buildbin-libdir FGNet_3.26.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL FGNet_3.26.0.zip && rm FGNet_3.26.0.tar.gz FGNet_3.26.0.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
76 1458k 76 1111k 0 0 1799k 0 --:--:-- --:--:-- --:--:-- 1798k
100 1458k 100 1458k 0 0 1998k 0 --:--:-- --:--:-- --:--:-- 1998k
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_gage html
fea_gtLinker html
fea_topGO html
format_david html
format_results html
functionalNetwork html
getTerms html
keywordsTerm html
plotGoAncestors 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_3.26.0.zip
* DONE (FGNet)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'FGNet' successfully unpacked and MD5 sums checked
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FGNet.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 -- Thu Oct 14 23:09:21 2021
***********************************************
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
1.09 0.12 1.20
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FGNet.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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 -- Thu Oct 14 23:09:22 2021
***********************************************
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
1.12 0.12 1.23
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FGNet.Rcheck/examples_i386/FGNet-Ex.timings
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FGNet.Rcheck/examples_x64/FGNet-Ex.timings
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