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
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