Package: pamr

Version: 1.33.0

Command: D:\biocbld\2.0d\R\bin\R.exe CMD check pamr_1.33.0.tar.gz

RetCode: 1

Time: 41.5 seconds

Status: ERROR

CheckDir: pamr.Rcheck

Warnings: NA

* checking for working latex ... OK
* using log directory 'D:/biocbld/2.0d/Rpacks/pamr.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'pamr/DESCRIPTION' ... OK
* this is package 'pamr' version '1.33.0'
* checking package dependencies ... WARNING
'library' or 'require' calls not declared from:
  cluster survival
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* checking if this is a source package ... OK
* checking whether package 'pamr' can be installed ... 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 syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating pamr-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'pamr-Ex.R' failed.
The error most likely occurred in:

> ### * pamr.cv
> 
> flush(stderr()); flush(stdout())
> 
> ### Name: pamr.cv
> ### Title: A function to cross-validate the nearest shrunken centroid
> ###   classifier
> ### Aliases: pamr.cv
> 
> 
> ### ** Examples
> 
> set.seed(120)
> x <- matrix(rnorm(1000*20),ncol=20)
> y <- sample(c(1:4),size=20,replace=TRUE)
> 
> mydata <- list(x=x,y=factor(y), geneid=as.character(1:nrow(x)), genenames=paste("g",as.character(1:nrow(x)),sep=""),)
the part of the args list of 'list' being evaluated was:
   (x = x, y = factor(y), geneid = as.character(1:nrow(x)), genenames = paste("g", as.character(1:nrow(x)), sep = ""), )
Error: element 5 is empty
Execution halted

installing R.css in D:/biocbld/2.0d/Rpacks/pamr.Rcheck


---------- Making package pamr ------------
  adding build stamp to DESCRIPTION
  installing NAMESPACE file and metadata
  making DLL ...
making cox_func.d from cox_func.c
gcc   -Id:/biocbld/2.0d/R/include  -Wall -O2 -std=gnu99   -c cox_func.c -o cox_func.o
g77 -O2 -Wall   -c knnimpute.f -o knnimpute.o
knnimpute.f: In subroutine `knnimp':
In file included from knnimpute.f:0:
knnimpute.f:6: warning: unused variable 'jj'
knnimpute.f: In subroutine `twomis':
knnimpute.f:132: warning: 'dold' might be used uninitialized in this function
windres --include-dir d:/biocbld/2.0d/R/include  -i pamr_res.rc -o pamr_res.o
gcc  -shared -s  -o pamr.dll pamr.def cox_func.o knnimpute.o pamr_res.o  -Ld:/biocbld/2.0d/R/bin   -lg2c -lR
  ... DLL made
  installing DLL
  installing R files
  installing inst files
  installing data files
  installing man source files
  installing indices
  not zipping data
  installing help
 >>> Building/Updating help pages for package 'pamr'
     Formats: text html latex example chm 
  khan                              text    html    latex           chm
  pamr.adaptthresh                  text    html    latex   example chm
  pamr.batchadjust                  text    html    latex   example chm
  pamr.confusion                    text    html    latex   example chm
  pamr.confusion.survival           text    html    latex   example chm
  pamr.cv                           text    html    latex   example chm
  pamr.decorrelate                  text    html    latex   example chm
  pamr.fdr                          text    html    latex   example chm
  pamr.from.excel                   text    html    latex           chm
  pamr.geneplot                     text    html    latex   example chm
  pamr.indeterminate                text    html    latex   example chm
  pamr.internal                     text    html    latex           chm
  pamr.knnimpute                    text    html    latex           chm
  pamr.listgenes                    text    html    latex   example chm
  pamr.makeclasses                  text    html    latex   example chm
  pamr.menu                         text    html    latex   example chm
  pamr.plotcen                      text    html    latex   example chm
  pamr.plotcv                       text    html    latex   example chm
  pamr.plotcvprob                   text    html    latex   example chm
  pamr.plotfdr                      text    html    latex   example chm
  pamr.plotstrata                   text    html    latex   example chm
  pamr.plotsurvival                 text    html    latex   example chm
  pamr.predict                      text    html    latex   example chm
  pamr.predictmany                  text    html    latex   example chm
  pamr.surv.to.class2               text    html    latex   example chm
  pamr.test.errors.surv.compute     text    html    latex   example chm
  pamr.to.excel                     text    html    latex           chm
  pamr.train                        text    html    latex   example chm
Microsoft HTML Help Compiler 4.74.8702

Compiling d:\biocbld\2.0d\Rpacks\pamr.Rcheck\00_pkg_src\pamr\chm\pamr.chm


Compile time: 0 minutes, 0 seconds
29	Topics
55	Local links
0	Internet links
1	Graphic


Created d:\biocbld\2.0d\Rpacks\pamr.Rcheck\00_pkg_src\pamr\chm\pamr.chm, 53,467 bytes
Compression decreased file by 54,269 bytes.
  adding MD5 sums

* DONE (pamr)