[BioC] Bug with R 1.9.0 beta (3/23) and PAMR?

[Liaw, Andy]

The error message is fairly clear.  Apparently the function uses the
function codes(), which is no longer available in R-1.9.0-to-be.  You should
contact the package maintainer for pamr and request update to the code.

Andy

> From: Tan, MinHan
> 
> Hi,
>  
> I hope this is the right place for this bug report:
>  
> I am running R.1.9.0 beta (3/23) and PAMR 1.12.1 [most 
> updated version]
> on a Win XP machine.
>  
> khan.data <- pamr.from.excel("summary-filter.txt", 75,
> sample.labels=TRUE)
> pamr.menu(khan.data)
>  
> I was running pamr.menu and ran into this error at pamr.cv 
> for my data.
>  
> Fold 1 :123456789101112131415161718192021222324252627282930
> Fold 2 :123456789101112131415161718192021222324252627282930
> Fold 3 :123456789101112131415161718192021222324252627282930
> Fold 4 :123456789101112131415161718192021222324252627282930
> Fold 5 :123456789101112131415161718192021222324252627282930
> Fold 6 :123456789101112131415161718192021222324252627282930
> Fold 7 :123456789101112131415161718192021222324252627282930
> Fold 8 :123456789101112131415161718192021222324252627282930
> Fold 9 :123456789101112131415161718192021222324252627282930
> Fold 10 :123456789101112131415161718192021222324252627282930
> Fold 11 :123456789101112131415161718192021222324252627282930
> Fold 12 :123456789101112131415161718192021222324252627282930
> Fold 13 :123456789101112131415161718192021222324252627282930
> Error: 'codes' is defunct.
>  
> (The bioconductor daily package update states that there should be no
> problems with the pamr package with this version of R)
>  
> This error does not occur with R 1.8.1, with the same data.
>  
> Selection: 2
> Fold 1 :123456789101112131415161718192021222324252627282930
> Fold 2 :123456789101112131415161718192021222324252627282930
> Fold 3 :123456789101112131415161718192021222324252627282930
> Fold 4 :123456789101112131415161718192021222324252627282930
> Fold 5 :123456789101112131415161718192021222324252627282930
> Fold 6 :123456789101112131415161718192021222324252627282930
> Fold 7 :123456789101112131415161718192021222324252627282930
> Fold 8 :123456789101112131415161718192021222324252627282930
> Fold 9 :123456789101112131415161718192021222324252627282930
> Fold 10 :123456789101112131415161718192021222324252627282930
> 
> Regards,
> Min-han Tan
> 
> This email message, including any attachments, is for the 
> so...{{dropped}}
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
>