[Bioc-devel] warning about read.DNAStringSet
hpages at fhcrc.org
Thu Apr 26 17:01:12 CEST 2012
On 04/26/2012 07:43 AM, Cabanski, Chris wrote:
> 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
> See ?Deprecated.
Yes read.DNAStringSet has been renamed readDNAStringSet in Biostrings
devel to be more consistent with the naming of other read* functions
Unfortunately the warning message reported by 'R CMD check' is
truncated. The full message is (with Biostrings 2.25.3):
> x <- read.DNAStringSet(filepath)
'read.DNAStringSet' is deprecated.
Use 'readDNAStringSet' instead.
Note that it tells the user what the new name is.
> 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 )
> A DNAStringSet instance of length 1
> width seq names
>  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?
Rsamtools is still using the old name. We'll change this.
> Christopher Cabanski
> PhD Candidate
> Department of Statistics and Operations Research
> University of North Carolina at Chapel Hill
> [[alternative HTML version deleted]]
> Bioc-devel at r-project.org mailing list
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