[BioC] Fwd: [Bioc-devel] Changes in the %in% function for DNAStringSet?

[Nicolas Delhomme]

Hi all,

Any thoughts on that?

Cheers,

Nico

Begin forwarded message:

> From: Nicolas Delhomme <delhomme at embl.de>
> Date: May 1, 2012 2:28:29 PM GMT+02:00
> To: bioc-devel at r-project.org
> Subject: [Bioc-devel] Changes in the %in% function for DNAStringSet?
> 
> Hi all,
> 
> In R 2.15.0, Bioc 2.10, the following works:
> 
> library(Biostrings)
> c("TTGCGA","ATGGCT","ACACTG") %in% DNAStringSet(c("TTGCGA","ATGRCT","ACASTG"))
> [1]  TRUE FALSE FALSE
>> sessionInfo()R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] Biostrings_2.24.1  IRanges_1.14.2     BiocGenerics_0.2.0
> 
> loaded via a namespace (and not attached):
> [1] stats4_2.15.0
> 
> 
> While in Bioc 2.11 it fails:
> 
> Error in match(x, table, nomatch = 0L) : 
>  'match' requires vector arguments
>> sessionInfo()
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
> 
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] Biostrings_2.25.3  IRanges_1.15.7     BiocGenerics_0.3.0
> 
> loaded via a namespace (and not attached):
> [1] stats4_2.15.0
> 
> 
> 
> I'd just like to know if that is that a change of API or not. If yes, I'd need to adapt my code that currently fails building.
> 
> Cheers,
> 
> Nico
> 
> ---------------------------------------------------------------
> Nicolas Delhomme
> 
> Genome Biology Computational Support
> 
> European Molecular Biology Laboratory
> 
> Tel: +49 6221 387 8310
> Email: nicolas.delhomme at embl.de
> Meyerhofstrasse 1 - Postfach 10.2209
> 69102 Heidelberg, Germany
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany