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Package 419/436HostnameOS / ArchBUILDCHECKBUILD BIN
topGO 2.3.1
Adrian Alexa
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/topGO
Last Changed Rev: 50445 / Revision: 53255
Last Changed Date: 2010-10-25 14:29:23 -0700 (Mon, 25 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK [ OK ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: topGO
Version: 2.3.1
Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings topGO_2.3.1.tar.gz
StartedAt: 2011-02-24 23:07:46 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 23:09:32 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 105.9 seconds
RetCode: 0
Status:  OK 
CheckDir: topGO.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/topGO.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘topGO/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘topGO’ version ‘2.3.1’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘topGO’ can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated 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
GOSumTest,classicScore: no visible binding for global variable
  ‘.PERMSUM.MAT’
GOSumTest,classicScore: no visible binding for global variable
  ‘.PERMSUM.LOOKUP’
* 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 data for non-ASCII characters ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

topGO.Rcheck/00install.out:

* installing *source* package ‘topGO’ ...
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: AnnotationDbi
Loading required package: DBI
Package SparseM (0.86) loaded.
	   To cite, see citation("SparseM")


Attaching package: 'SparseM'

The following object(s) are masked from 'package:base':

    backsolve

Creating a new generic function for "print" in "topGO"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

* DONE (topGO)

topGO.Rcheck/topGO-Ex.timings:

nameusersystemelapsed
GOdata0.2040.0040.208
annFUN1.5520.0481.661
classicCount-class0.0000.0000.001
classicExpr-class0.0040.0000.001
classicScore-class0.0080.0000.006
dagFunctions000
diagnosticMethods0.4720.0080.479
elimExpr-class0.0040.0000.001
elimScore-class0.0000.0000.001
geneList0.0040.0000.004
getPvalues4.3400.1164.572
getSigGroups5.8160.0205.839
groupGOTerms0.4410.0040.443
inducedGraph0.0720.0000.073
parentChild-class0.0000.0000.002
printGraph-methods000
topGOdata-class6.0600.0406.101
topGOresult-class0.0320.0040.037