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Package 1/462HostnameOS / ArchBUILDCHECKBUILD BIN
a4 1.1.1
Tobias Verbeke
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/a4
Last Changed Rev: 54827 / Revision: 55359
Last Changed Date: 2011-04-14 10:35:57 -0700 (Thu, 14 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  ERROR  skipped 
liverpool Windows Server 2003 R2 (32-bit) / x64  ERROR  skipped  skipped 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64 [ ERROR ] skipped  skipped 
pelham Mac OS X Leopard (10.5.8) / i386  ERROR  skipped  skipped 

Summary

Package: a4
Version: 1.1.1
Command: chmod a+r a4 -R && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data a4
StartedAt: 2011-05-09 13:59:45 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:01:14 -0700 (Mon, 09 May 2011)
EllapsedTime: 88.6 seconds
RetCode: 1
Status:  ERROR  
PackageFile: None
PackageFileSize: NA

Command output

* checking for file 'a4/DESCRIPTION' ... OK
* preparing 'a4':
* checking DESCRIPTION meta-information ... OK
* installing the package to re-build vignettes
* creating vignettes ... ERROR
Loading required package: a4Base
Loading required package: grid
Loading required package: Biobase

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: annaffy
Loading required package: GO.db
Loading required package: DBI

Loading required package: KEGG.db

Loading required package: mpm
Loading required package: MASS
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

mpm version 1.0-17

Loading required package: genefilter

Attaching package: 'genefilter'

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

    area

Loading required package: limma
Loading required package: multtest
Loading required package: glmnet
Loading required package: Matrix
Loading required package: lattice

Attaching package: 'Matrix'

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

    det

Loading required package: a4Preproc
Loading required package: a4Core

Attaching package: 'a4Core'

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

    topTable

Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
File type 'perl' not found or no open command associated with it.
Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
gdata: read.xls support for 'XLS' (Excel
gdata: 97-2004) files ENABLED.

gdata: Unable to load perl libaries needed
gdata: by read.xls()
gdata: to support 'XLSX' (Excel 2007+)
gdata: files.

gdata: Run the function
gdata: 'installXLSXsupport()'
gdata: to automatically download and install
gdata: the perl
gdata: libaries needed to support Excel XLS
gdata: and XLSX formats.

Attaching package: 'gdata'

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

    combine

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

    nobs

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

    object.size

Loading required package: caTools
Loading required package: bitops

Attaching package: 'gplots'

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

    wapply

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

    lowess


a4Base version 1.1.1

Loading required package: a4Classif
Loading required package: MLInterfaces
Loading required package: rpart
Loading required package: rda
Loading required package: annotate
Loading required package: cluster
Loading required package: ROCR
Loading required package: pamr
Loading required package: survival
Loading required package: splines
Loading required package: varSelRF
Loading required package: randomForest
randomForest 4.6-2
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    combine

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

    combine

Loading required package: a4Reporting

Attaching package: 'a4'

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

    .onAttach

Loading required package: ALL
Loading required package: nlcv
Loading required package: RColorBrewer
Loading required package: xtable

Attaching package: 'xtable'

The following object(s) are masked from 'package:a4Reporting':

    xtable

Loading required package: ipred
Loading required package: mlbench
Loading required package: nnet
Loading required package: class

Attaching package: 'ipred'

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

    cv


nlcv version 0.2-0

Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db



Error: processing vignette 'a4vignette.Rnw' failed with diagnostics:
 chunk 25 (label = lasso) 
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "topTable", for signature "lognet"
Execution halted