| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-01-02 09:00:54 -0500 (Mon, 02 Jan 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| palomino5 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" | 4165 |
| 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 | ||||
|
To the developers/maintainers of the topGO package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 2045/2158 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| topGO 2.51.0 (landing page) Adrian Alexa
| palomino5 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ||||||||
| Package: topGO |
| Version: 2.51.0 |
| Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:topGO.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings topGO_2.51.0.tar.gz |
| StartedAt: 2022-12-29 04:14:42 -0500 (Thu, 29 Dec 2022) |
| EndedAt: 2022-12-29 04:16:36 -0500 (Thu, 29 Dec 2022) |
| EllapsedTime: 114.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: topGO.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:topGO.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings topGO_2.51.0.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/topGO.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 10.4.0
GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'topGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topGO' version '2.51.0'
* 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 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 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 ... 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
* 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: 3 NOTEs
See
'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/topGO.Rcheck/00check.log'
for details.
topGO.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL topGO ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.17-bioc/R/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 | 0.03 | 0.00 | 0.03 | |
| annFUN | 0.60 | 0.11 | 0.74 | |
| classicCount-class | 0 | 0 | 0 | |
| classicExpr-class | 0 | 0 | 0 | |
| classicScore-class | 0.02 | 0.00 | 0.02 | |
| dagFunctions | 0 | 0 | 0 | |
| diagnosticMethods | 0.23 | 0.00 | 0.23 | |
| elimExpr-class | 0 | 0 | 0 | |
| elimScore-class | 0 | 0 | 0 | |
| geneList | 0 | 0 | 0 | |
| getPvalues | 2.82 | 0.09 | 2.97 | |
| getSigGroups | 1.79 | 0.06 | 1.86 | |
| groupGOTerms | 0.21 | 0.00 | 0.20 | |
| inducedGraph | 0.03 | 0.00 | 0.03 | |
| parentChild-class | 0 | 0 | 0 | |
| printGraph-methods | 0 | 0 | 0 | |
| topGOdata-class | 3.34 | 0.27 | 3.64 | |
| topGOresult-class | 0.03 | 0.00 | 0.03 | |