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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: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings a4Base_1.1.1.tar.gz
StartedAt: 2011-05-09 14:03:18 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:07:09 -0700 (Mon, 09 May 2011)
EllapsedTime: 231.1 seconds
RetCode: 1
Status:  ERROR  
CheckDir: a4Base.Rcheck
Warnings: NA

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/a4Base.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 ... WARNING
Found the following significant warnings:
  Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
  Warning: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2
See 'D:/biocbld/bbs-2.9-bioc/meat/a4Base.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
'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 ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
* checking foreign function calls ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
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 ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
All user-level objects in a package should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
* checking Rd \usage sections ... NOTE
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.
The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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
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 97-2004) files ENABLED.

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

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

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

mpm version 1.0-17

Loaded glmnet 1.6 
File type 'perl' not found or no open command associated with it.
File type 'perl' not found or no open command associated with it.

a4Base version 1.1.1

Warning messages:
1: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2 
2: running command 'C:\Windows\system32\cmd.exe /c ftype perl' had status 2 

* DONE (a4Base)

a4Base.Rcheck/a4Base-Ex.timings:

nameusersystemelapsed
a4palette0.010.000.02
addQuantilesColors3.360.093.59
boxPlot3.830.133.98
combineTwoExpressionSet000
computeLogRatio15.52 0.0315.91
createExpressionSet0.060.000.06
filterVarInt3.610.093.78
heatmap.expressionSet0.000.000.02
histPvalue3.710.134.28
histpvalueplotter4.020.074.88