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

[Nicolas Delhomme]

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