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Package 139/208OSArchBUILDCHECKBUILD BIN

pamr

1.33.0

Rob TIbshirani
Linux (SUSE 9.2) x86_64 OK [ ERROR ]
Linux (SUSE 10.1) x86_64 OK  ERROR 
Linux (SUSE 9.2) i686 OK  ERROR 
Solaris 2.9 sparc OK  ERROR 
Windows Server 2003 x86_64 OK  ERROR  OK 
Windows Server 2003 NA OK  ERROR  OK 
Mac OS X (10.4.6) i686 OK  ERROR 
Package: pamr
Version: 1.33.0
Command: /loc/biocbuild/2.0d/R/bin/R CMD check pamr_1.33.0.tar.gz
RetCode: 1
Time: 40.8 seconds
Status: ERROR
CheckDir: pamr.Rcheck
Warnings: NA

Command output

* checking for working latex ... OK
* using log directory '/loc/biocbuild/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 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 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

pamr.Rcheck/00install.out:

* Installing *source* package 'pamr' ...
** libs
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include  -I/usr/local/include    -fpic  -g -O2 -Wall -c cox_func.c -o cox_func.o
g77   -fpic  -g -O2 -Wall -c knnimpute.f -o knnimpute.o
knnimpute.f: In subroutine `knnimp':
knnimpute.f:6: warning: unused variable `jj'
knnimpute.f: In subroutine `twomis':
knnimpute.f:132: warning: `dold' might be used uninitialized in this function
gcc -std=gnu99 -shared -L/usr/local/lib64 -o pamr.so cox_func.o knnimpute.o  -lg2c -lm -lgcc_s 
** R
** data
** inst
** help
 >>> Building/Updating help pages for package 'pamr'
     Formats: text html latex example 
  khan                              text    html    latex
  pamr.adaptthresh                  text    html    latex   example
  pamr.batchadjust                  text    html    latex   example
  pamr.confusion                    text    html    latex   example
  pamr.confusion.survival           text    html    latex   example
  pamr.cv                           text    html    latex   example
  pamr.decorrelate                  text    html    latex   example
  pamr.fdr                          text    html    latex   example
  pamr.from.excel                   text    html    latex
  pamr.geneplot                     text    html    latex   example
  pamr.indeterminate                text    html    latex   example
  pamr.internal                     text    html    latex
  pamr.knnimpute                    text    html    latex
  pamr.listgenes                    text    html    latex   example
  pamr.makeclasses                  text    html    latex   example
  pamr.menu                         text    html    latex   example
  pamr.plotcen                      text    html    latex   example
  pamr.plotcv                       text    html    latex   example
  pamr.plotcvprob                   text    html    latex   example
  pamr.plotfdr                      text    html    latex   example
  pamr.plotstrata                   text    html    latex   example
  pamr.plotsurvival                 text    html    latex   example
  pamr.predict                      text    html    latex   example
  pamr.predictmany                  text    html    latex   example
  pamr.surv.to.class2               text    html    latex   example
  pamr.test.errors.surv.compute     text    html    latex   example
  pamr.to.excel                     text    html    latex
  pamr.train                        text    html    latex   example
** building package indices ...
* DONE (pamr)