Adrian Alexa
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/topGO |
| Branch: RELEASE_3_7 |
| Last Commit: 78ce306 |
| Last Changed Date: 2018-04-30 10:35:06 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:33:08 -0400 (Wed, 17 Oct 2018).
| Package 1493/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| topGO 2.32.0 Adrian Alexa
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: topGO |
| Version: 2.32.0 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings topGO_2.32.0.tar.gz |
| StartedAt: 2018-10-17 05:13:51 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 05:16:46 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 174.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: topGO.Rcheck |
| Warnings: 0 |
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### Running command:
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### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:topGO.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings topGO_2.32.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/topGO.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'topGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topGO' version '2.32.0'
* 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
* 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 ... 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOdata-class 5.24 0.17 5.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
topGOdata-class 5.39 0.17 5.56
* 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
'C:/Users/biocbuild/bbs-3.7-bioc/meat/topGO.Rcheck/00check.log'
for details.
topGO.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/topGO_2.32.0.tar.gz && rm -rf topGO.buildbin-libdir && mkdir topGO.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=topGO.buildbin-libdir topGO_2.32.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL topGO_2.32.0.zip && rm topGO_2.32.0.tar.gz topGO_2.32.0.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
100 427k 100 427k 0 0 6154k 0 --:--:-- --:--:-- --:--:-- 6778k
install for i386
* installing *source* package 'topGO' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'topGO'
finding HTML links ... done
GOTests html
GOdata html
annFUN html
classicCount-class html
classicExpr-class html
classicScore-class html
dagFunctions html
diagnosticMethods html
elimCount-class html
elimExpr-class html
elimScore-class html
geneList html
getPvalues html
getSigGroups html
groupGOTerms html
groupStats-class html
inducedGraph html
parentChild-class html
printGraph-methods html
topGO-package html
topGOdata-class html
topGOresult-class html
weightCount-class html
** building package indices
** installing vignettes
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
In R CMD INSTALL
install for x64
* installing *source* package 'topGO' ...
** testing if installed package can be loaded
groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
* MD5 sums
packaged installation of 'topGO' as topGO_2.32.0.zip
* DONE (topGO)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'topGO' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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topGO.Rcheck/examples_i386/topGO-Ex.timings
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topGO.Rcheck/examples_x64/topGO-Ex.timings
|