[Bioc-devel] warning about read.DNAStringSet

[Hervé Pagès]

Hi Chris,

On 04/26/2012 07:43 AM, Cabanski, Chris wrote:
> 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.

Yes read.DNAStringSet has been renamed readDNAStringSet in Biostrings
devel to be more consistent with the naming of other read* functions
in Bioconductor.

Unfortunately the warning message reported by 'R CMD check' is
truncated. The full message is (with Biostrings 2.25.3):

   > x <- read.DNAStringSet(filepath)
   Warning message:
   'read.DNAStringSet' is deprecated.
   Use 'readDNAStringSet' instead.
   See help("Deprecated")

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 )
>> 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?

Rsamtools is still using the old name. We'll change this.

Thanks!
H.

>
> Thanks,
> Chris
>
> --
> Christopher Cabanski
> PhD Candidate
> Department of Statistics and Operations Research
> University of North Carolina at Chapel Hill
>
>
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>
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-- 
Hervé Pagès

Program in Computational Biology
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