[Seqinr-forum] read.fasta error

[Beale, Mat]

Ooops, sorry for bothering people.  I had another enviromental function loaded called read.fasta that was messing things up.

________________________________
From: seqinr-forum-bounces at lists.r-forge.r-project.org <seqinr-forum-bounces at lists.r-forge.r-project.org> on behalf of Beale, Mat <mathew.beale at ucl.ac.uk>
Sent: 06 October 2016 15:09:42
To: seqinr-forum at lists.r-forge.r-project.org
Subject: [Seqinr-forum] read.fasta error


Hi All,


Has anyone noticed any strange behaviour with read.fasta since the update to v3.3.1?  I have a number of long-term scripts (running on various clusters and locally) that until recently all worked very nicely.  I revisited my scripts this week only to find error messages during the read.fasta stage:


wgsconsensus <-read.fasta(file=consensusfile,as.string=F, seqtype=c("DNA"),seqonly=F,set.attributes=F) # consensusfile is just the path to fasta


Error in read.fasta(file = consensusfile, as.string = F, seqtype = c("DNA"),  :
  unused arguments (as.string = F, seqtype = c("DNA"), seqonly = F, set.attributes = F)


I've encountered this on different platforms, running the latest (and older versions) of R, and with both new files and those I've run before.  Sequential removal of arguments hasn't been particularly informative, and running it without any arguments also doesn't help:


read.fasta(file=consensusfile)
Read 2 items
Error in seqs[[i]] : subscript out of bounds


Can anyone advise what is happening?  Have I just made a silly error?


Many thanks,


Mat

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