[Bioc-sig-seq] read sequences from the web

[Thomas Girke]

Dear Biostrings Developers,

There seems to be a change (bug?) in the behavior of the read.XXStringSet functions
in the latest Biostrings version when pointing to files on the web. 

For instance: 

## This works under R-2.10.0
library(Biostrings)
read.AAStringSet("ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Halobacterium_sp/AE004437.faa", "fasta") 

## But the same command under R-2.10.1 returns the following error:
Error in .read.fasta.in.XStringSet(filepath, set.names, elementType, lkup) :
cannot open file 'ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Halobacterium_sp/AE004437.faa'

My session info for R-2.10.0 is:

R version 2.10.1 (2009-12-14) 
x86_64-unknown-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=C 
             LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] Biostrings_2.14.10 IRanges_1.4.9     

loaded via a namespace (and not attached):
[1] Biobase_2.6.1


Thanks in advance for your help.

Thomas