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HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework
https://github.com/HenrikBengtsson/aroma.seq
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Deprecated function Biostrings::fasta.info() - use fasta.seqlengths() instead #12

Closed HenrikBengtsson closed 9 years ago

HenrikBengtsson commented 9 years ago

When print():ing a FastaReferenceFile we now (R 3.2.0) get:

Warning message:
'Biostrings::fasta.info' is deprecated.
Use 'fasta.seqlengths' instead.
See help("Deprecated")
HenrikBengtsson commented 9 years ago

Seems as if that be replaced straight off;

> fasta.info(getPathname(fa))
gi|9626243|ref|NC_001416.1| Enterobacteria phage lambda, complete genome
                                                                   48502
Warning message:
'fasta.info' is deprecated.
Use 'fasta.seqlengths' instead.
See help("Deprecated")
> fasta.seqlengths(getPathname(fa))
gi|9626243|ref|NC_001416.1| Enterobacteria phage lambda, complete genome
                                                                   48502
HenrikBengtsson commented 9 years ago

Fixed in commit f735c1dd.