a4Classif 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/a4Classif | | Last Changed Rev: 54829 / Revision: 55359 | | Last Changed Date: 2011-04-14 10:40:06 -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 |
* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/a4Classif.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 'a4Classif/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Classif' version '1.1.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'a4Classif' 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/a4Classif.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
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See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
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See section 'Generic functions and methods' of the 'Writing R
Extensions' manual.
* checking replacement functions ... WARNING
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See the chapter 'System and foreign language interfaces' of the
'Writing R Extensions' manual.
* checking R code for possible problems ... NOTE
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* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
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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
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The \usage entries for S3 methods should use the \method markup and not
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See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... ERROR
Running examples in 'a4Classif-Ex.R' failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lassoClass
> ### Title: Classify using the Lasso
> ### Aliases: lassoClass
> ### Keywords: models
>
> ### ** Examples
>
> if (require(ALL)){
+ data(ALL, package = "ALL")
+ ALL <- addGeneInfo(ALL)
+ ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
+
+ resultLasso <- lassoClass(object = ALL, groups = "BTtype")
+ 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 "lognet"
Calls: topTable -> <Anonymous>
Execution halted
* installing *source* package 'a4Classif' ...
** R
** inst
** preparing package for lazy loading
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: glmnet
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Attaching package: 'Matrix'
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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()'
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Attaching package: 'gdata'
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Loading required package: survival
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Loading required package: randomForest
randomForest 4.6-2
Type rfNews() to see new features/changes/bug fixes.
Attaching package: 'randomForest'
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** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Loaded glmnet 1.6
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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 (a4Classif)