Hi,

I just discovered that the development version of the ReQON package is reporting a warning.

* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'read.DNAStringSet' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.

I am not using this function directly, so I am trying to figure out where this function is being called.  In the vignette, I read in a fasta file using various functions from Rsamtools.  It seems that scanFa is reporting a DNAStringSet:

> seqs <- scanFa( ref_f )
> seqs
  A DNAStringSet instance of length 1
     width seq                                              names
[1] 115991 AAAGTCAAAACATTTATTATGCA...GGGCTCTGGTTGAGAAAATACG seq1

I then extract the sequence information using toString().  Can anyone suggest a way to extract the sequence from a fasta file without calling read.DNAStringSet?  Is this an issue with Rsamtools?

Thanks,
Chris

--
Christopher Cabanski
PhD Candidate
Department of Statistics and Operations Research
University of North Carolina at Chapel Hill


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