[Bioc-devel] Bioc-devel Digest, Vol 62, Issue 1

Marc Carlson mcarlson at fhcrc.org
Thu May 7 19:20:24 CEST 2009

Hi Kaiyu,

Since you have been somewhat coy about what exactly you did it is pretty
difficult to reproduce your problems.  For example, you never showed me
what the input for your function calls look like so I don't have any way
to know if you fed the right inputs to this code or not.  But now that
you have posted your sessionInfo() I can see that one problem is that
that many of your packages are very out of date.  The Category package
(to name just one example) should be version 2.10.0.  You do not want to
have bioconductor packages from several different releases installed
together like this.  To fix this, you should run update.packages() as
demonstrated on the bioconductor website.



ks280007 at ohio.edu wrote:
> Thanks Marc.
> I tried your code but still have the same problems. here are my sessionInfo()
> R version 2.9.0 (2009-04-17) 
> i386-pc-mingw32 
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
> attached base packages:
> [1] splines   tools     stats     graphics  grDevices utils     datasets 
> [8] methods   base     
> other attached packages:
>  [1] GO.db_2.2.5          ath1121501.db_2.2.11 GOstats_2.10.0      
>  [4] RSQLite_0.7-0        DBI_0.2-4            Category_2.6.0      
>  [7] genefilter_1.20.0    survival_2.35-4      annotate_1.18.0     
> [10] xtable_1.5-5         AnnotationDbi_1.6.0  graph_1.20.0        
> [13] Biobase_2.0.1       
> loaded via a namespace (and not attached):
> [1] cluster_1.11.13 RBGL_1.18.0    
> Please point out where the problems could be.
> Thanks
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