Adrian Alexa
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/topGO |
| git_branch: RELEASE_3_20 |
| git_last_commit: fdfc42c |
| git_last_commit_date: 2024-10-29 09:27:28 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:08 -0500 (Mon, 23 Dec 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| 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 2168/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| topGO 2.58.0 (landing page) Adrian Alexa
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the topGO package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/topGO.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: topGO |
| Version: 2.58.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:topGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings topGO_2.58.0.tar.gz |
| StartedAt: 2024-12-21 12:11:12 -0500 (Sat, 21 Dec 2024) |
| EndedAt: 2024-12-21 12:13:45 -0500 (Sat, 21 Dec 2024) |
| EllapsedTime: 152.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: topGO.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:topGO.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings topGO_2.58.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/topGO.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘topGO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘topGO’ version ‘2.58.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
'BiocGenerics', 'graph', 'Biobase', 'GO.db', 'AnnotationDbi',
'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘topGO’ 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 whether startup messages can be suppressed ... NOTE
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘Rgraphviz’ ‘multtest’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: ‘globaltest:::globaltest’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GOplot: no visible global function definition for ‘getDefaultAttrs’
GOplot: no visible global function definition for ‘agopen’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
global function definition for ‘getNodeCenter’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
global function definition for ‘pieGlyph’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
global function definition for ‘getX’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
global function definition for ‘getY’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
global function definition for ‘getNodeLW’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
global function definition for ‘drawTxtLabel’
GOplot.counts : plotSigChart : buildDrawing : <anonymous>: no visible
global function definition for ‘txtLabel’
GOplot.counts : plotSigChart: no visible global function definition for
‘AgNode’
GOplot.counts : plotSigChart : <anonymous>: no visible global function
definition for ‘name’
GOplot.counts : plotSigChart : <anonymous>: no visible global function
definition for ‘getNodeCenter’
GOplot.counts : plotSigChart: no visible global function definition for
‘getNodeXY’
GOplot.counts : plotSigChart: no visible global function definition for
‘getY’
GOplot.counts: no visible global function definition for
‘getDefaultAttrs’
GOplot.counts: no visible global function definition for ‘agopen’
getPvalues: no visible global function definition for ‘mt.teststat’
getPvalues: no visible global function definition for ‘mt.rawp2adjp’
printDOT: no visible global function definition for ‘getDefaultAttrs’
printDOT: no visible global function definition for ‘toDot’
GOSumTest,classicScore: no visible binding for global variable
‘.PERMSUM.MAT’
GOSumTest,classicScore: no visible binding for global variable
‘.PERMSUM.LOOKUP’
initialize,classicExpr: no visible global function definition for
‘error’
scoresInTerm,topGOdata-missing: no visible global function definition
for ‘scoreInNode’
Undefined global functions or variables:
.PERMSUM.LOOKUP .PERMSUM.MAT AgNode agopen drawTxtLabel error
getDefaultAttrs getNodeCenter getNodeLW getNodeXY getX getY
mt.rawp2adjp mt.teststat name pieGlyph scoreInNode toDot txtLabel
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
topGOdata-class 5.107 0.308 5.54
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.20-bioc/meat/topGO.Rcheck/00check.log’
for details.
topGO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL topGO ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘topGO’ ... ** 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 groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package can be loaded from final location groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built. ** testing if installed package keeps a record of temporary installation path * DONE (topGO)
topGO.Rcheck/topGO-Ex.timings
| name | user | system | elapsed | |
| GOdata | 0.043 | 0.007 | 0.049 | |
| annFUN | 1.190 | 0.074 | 1.282 | |
| classicCount-class | 0 | 0 | 0 | |
| classicExpr-class | 0.002 | 0.001 | 0.002 | |
| classicScore-class | 0.003 | 0.000 | 0.003 | |
| dagFunctions | 0 | 0 | 0 | |
| diagnosticMethods | 0.267 | 0.012 | 0.278 | |
| elimExpr-class | 0.001 | 0.001 | 0.001 | |
| elimScore-class | 0 | 0 | 0 | |
| geneList | 0.003 | 0.003 | 0.005 | |
| getPvalues | 4.580 | 0.086 | 4.769 | |
| getSigGroups | 2.185 | 0.098 | 2.356 | |
| groupGOTerms | 0.249 | 0.002 | 0.253 | |
| inducedGraph | 0.076 | 0.007 | 0.084 | |
| parentChild-class | 0.002 | 0.001 | 0.002 | |
| printGraph-methods | 0.000 | 0.000 | 0.001 | |
| topGOdata-class | 5.107 | 0.308 | 5.540 | |
| topGOresult-class | 0.026 | 0.004 | 0.031 | |