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Package 2/462HostnameOS / ArchBUILDCHECKBUILD BIN
a4Base 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/a4Base
Last Changed Rev: 54828 / Revision: 55359
Last Changed Date: 2011-04-14 10:39:51 -0700 (Thu, 14 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ ERROR ]
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  ERROR  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  ERROR  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  ERROR  OK 

Summary

Package: a4Base
Version: 1.1.1
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings a4Base_1.1.1.tar.gz
StartedAt: 2011-05-09 11:08:35 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 11:11:47 -0700 (Mon, 09 May 2011)
EllapsedTime: 192.5 seconds
RetCode: 1
Status:  ERROR 
CheckDir: a4Base.Rcheck
Warnings: NA

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/a4Base.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-18 r55504)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4Base/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4Base’ version ‘1.1.1’
* checking package name space information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  ‘gridSVG’ ‘JavaGD’
* checking if this is a source package ... OK
* checking whether package ‘a4Base’ can be installed ... OK
* checking installed package size ... 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 ... WARNING
‘library’ or ‘require’ call not declared from: ‘gridSVG’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotLogRatio: no visible global function definition for ‘JavaGD’
plotLogRatio: no visible global function definition for ‘grid.garnish’
plotLogRatio: no visible global function definition for
  ‘grid.hyperlink’
plotLogRatio: no visible global function definition for ‘grid.script’
plotLogRatio: no visible global function definition for ‘gridToSVG’
* 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 ... NOTE
‘library’ or ‘require’ call not declared from: ‘nlcv’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in ‘a4Base-Ex.R’ failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lassoReg
> ### Title: Multiple regression using the Lasso algorithm as implemented in
> ###   the glmnet package
> ### Aliases: lassoReg
> 
> ### ** Examples
> 
> if (require(ALL)){
+   data(ALL, package = "ALL")
+   ALL <- addGeneInfo(ALL)
+   ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
+ 
+   resultLasso <- lassoReg(object = ALL[1:100,], covariate = "age")
+   plot(resultLasso, label = TRUE,
+ 	   main = "Lasso coefficients in relation to degree of penalization.")
+   featResultLasso <- topTable(resultLasso, n = 15)
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "topTable", for signature "elnet"
Calls: topTable -> <Anonymous>
Execution halted

a4Base.Rcheck/00install.out:

* installing *source* package ‘a4Base’ ...
** 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: GO.db
Loading required package: DBI

Loading required package: KEGG.db

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

mpm version 1.0-17


Attaching package: ‘genefilter’

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

    area

Loading required package: Matrix
Loading required package: lattice

Attaching package: ‘Matrix’

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

    det

Loaded glmnet 1.6 

Attaching package: ‘a4Core’

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

    topTable

Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

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

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

mpm version 1.0-17

Loaded glmnet 1.6 

a4Base version 1.1.1


* DONE (a4Base)

a4Base.Rcheck/a4Base-Ex.timings:

nameusersystemelapsed
a4palette0.0120.0080.016
addQuantilesColors3.2400.1923.459
boxPlot3.2520.0963.352
combineTwoExpressionSet0.0000.0000.001
computeLogRatio19.138 0.19620.031
createExpressionSet0.0680.0000.067
filterVarInt3.2320.0283.258
heatmap.expressionSet0.0000.0040.001
histPvalue3.2800.0523.357
histpvalueplotter3.6400.1083.785