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Package 239/251HostnameOS / ArchBUILDCHECKBUILD BIN
topGO 1.5.0
Adrian Alexa
Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/topGO
Last Changed Rev: 27716 / Revision: 29143
Last Changed Date: 2007-10-02 18:16:39 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  WARNINGS 
wilson2 Linux (openSUSE 10.3) / x86_64  OK [ WARNINGS ]
wellington Linux (openSUSE 10.3) / i686  OK  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  ERROR  skipped  skipped 
lemming Windows Server 2003 (32-bit) / x64  ERROR  skipped  skipped 
Package: topGO
Version: 1.5.0
Command: /home/biocbuild/bbs-2.2-bioc/R/bin/R CMD check topGO_1.5.0.tar.gz
StartedAt: 2007-12-11 05:05:22 -0700 (Tue, 11 Dec 2007)
EndedAt: 2007-12-11 05:09:20 -0700 (Tue, 11 Dec 2007)
EllapsedTime: 237.8 seconds
RetCode: 0
Status: WARNINGS
CheckDir: topGO.Rcheck
Warnings: 1

Command output

* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.2-bioc/meat/topGO.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-12-06 r43609)
* checking for file 'topGO/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'topGO' version '1.5.0'
* 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 name space can be loaded with stated dependencies ... 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
printDOT: no visible binding for global variable ‘.DOT.FILE.NAME’
showSigOfNodes: no visible binding for global variable ‘goDAG.r2l’
* checking Rd files ... WARNING
Rd files without 'description':
  getPvalues.Rd
These entries are required in an Rd file.

See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking data for non-ASCII characters ... OK
* creating topGO-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... NOTE
--- running texi2dvi on vignettes
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './topGO.tex' ...
LaTeX Warning: Citation `Chiaretti04' on page 1 undefined on input line 38.
LaTeX Warning: Citation `Alexa' on page 5 undefined on input line 421.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './topGO.tex' ...
LaTeX Warning: Citation `Chiaretti04' on page 1 undefined on input line 38.
LaTeX Warning: Citation `Alexa' on page 5 undefined on input line 421.
/usr/bin/texi2dvi: Running pdflatex --file-line-error </dev/null '\nonstopmode' '\input' './topGO.tex' ...
* creating topGO-manual.tex ... OK
* checking topGO-manual.tex ... OK

WARNING: There was 1 warning, see
  /loc/home/biocbuild/bbs-2.2-bioc/meat/topGO.Rcheck/00check.log
for details

topGO.Rcheck/00install.out:

/loc/home/biocbuild/bbs-2.2-bioc/meat/topGO.Rcheck
* Installing *source* package 'topGO' ...
** R
** data
** inst
** preparing package for lazy loading
Loading required package: graph
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

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

Loading required package: GO
Loading required package: AnnotationDbi
Loading required package: DBI
Loading required package: RSQLite
Loading required package: SparseM
Package SparseM (0.74) loaded.  To cite, see citation("SparseM")
Creating a new generic function for "print" in "topGO"
** help
Note: removing empty section \details
Note: removing empty section \value
Note: removing empty section \description
Note: removing empty section \seealso
Note: removing empty section \examples
Note: removing empty section \section{Methods}
 >>> Building/Updating help pages for package 'topGO'
     Formats: text html latex example 
  GOFisherTest                      text    html    latex
  GOKSTest                          text    html    latex
  GOdata                            text    html    latex   example
  annFUN.hgu                        text    html    latex   example
  buildGOgraph.topology             text    html    latex
  buildLevels                       text    html    latex   example
  classicCount-class                text    html    latex   example
  classicScore-class                text    html    latex   example
  elimCount-class                   text    html    latex   example
  elimScore-class                   text    html    latex   example
  getPvalues                        text    html    latex   example
  getSigGroups                      text    html    latex   example
  groupGOTerms                      text    html    latex
  groupStats-class                  text    html    latex   example
  inducedGraph                      text    html    latex   example
  mapGenes2GOgraph                  text    html    latex   example
  printGenes-methods                text    html    latex
  printGraph-methods                text    html    latex   example
  reverseArch                       text    html    latex   example
  topGO-package                     text    html    latex
  topGOdata-class                   text    html    latex   example
  topGOresult-class                 text    html    latex
  weightCount-class                 text    html    latex   example
  weightScore-class                 text    html    latex
** building package indices ...
* DONE (topGO)