Package: CMA

Version: 1.12.0

Command: rm -rf CMA.buildbin-libdir && mkdir CMA.buildbin-libdir && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=CMA.buildbin-libdir CMA_1.12.0.tar.gz >CMA-install.out 2>&1 && D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --library=CMA.buildbin-libdir --install="check:CMA-install.out" --force-multiarch --no-vignettes --timings CMA_1.12.0.tar.gz && mv CMA.buildbin-libdir/* CMA.Rcheck/ && rmdir CMA.buildbin-libdir

StartedAt: 2012-03-24 00:58:51 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:00:26 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 95.5 seconds

RetCode: 1

Status:  ERROR

CheckDir: CMA.Rcheck

Warnings: NA

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/CMA.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CMA' version '1.12.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'CMA' can be installed ... OK
* 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
* loading checks for arch 'i386'
** 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... 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
ROCinternal: no visible binding for global variable 'xlab'
ROCinternal: no visible binding for global variable 'ylab'
ROCinternal: no visible binding for global variable 'main'
ROCinternal: no visible binding for global variable 'lwd'
rfe: no visible binding for global variable 'cost'
* 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 ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
            old_size new_size compress
  golub.rda    443Kb    264Kb       xz
  khan.rda     943Kb    454Kb       xz
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... ERROR
Running examples in 'CMA-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gbmCMA
> ### Title: Tree-based Gradient Boosting
> ### Aliases: gbmCMA
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> ### load Golub AML/ALL data
> data(golub)
> ### extract class labels
> golubY <- golub[,1]
> ### extract gene expression
> golubX <- as.matrix(golub[,-1])
> ### select learningset
> ratio <- 2/3
> set.seed(111)
> learnind <- sample(length(golubY), size=floor(ratio*length(golubY)))
> ### run tree-based gradient boosting (no tuning)
> gbmresult <- gbmCMA(X=golubX, y=golubY, learnind=learnind, n.trees = 500)
Error in do.call(gbm.fit, args = ll) : object 'gbm.fit' not found
Calls: gbmCMA -> gbmCMA -> gbmCMA -> gbmCMA -> do.call
Execution halted

install for i386

* installing *source* package 'CMA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'CMA_vignette.rnw' 
** testing if installed package can be loaded

add DLL for x64

* installing *source* package 'CMA' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CMA' as CMA_1.12.0.zip

* DONE (CMA)