[BioC] makeTranscriptDbFromGFF finished successfully or not?

Jing [guest] guest at bioconductor.org
Thu Dec 5 14:27:29 CET 2013

I have finished makeTranscriptDbFromGFF step, but I am not sure whether it fished successfully? could you help me check?

 -- output of sessionInfo(): 

> txdb <- makeTranscriptDbFromGFF("D:/R-package/RtmpE7FyTD/downloaded_packages/tmp.out",format="gff3",exonRankAttributeName=NA,dataSource="gff file for test", species="test")
extracting transcript information
Extracting gene IDs
extracting transcript information
Processing splicing information for gff3 file.
Deducing exon rank from relative coordinates provided
Prepare the 'metadata' data frame ... metadata: OK
Now generating chrominfo from available sequence names. No chromosome length information is available.
Warning messages:
1: In as.data.frame(data, stringsAsFactors = FALSE) :
  Arguments in '...' ignored
2: In .deduceExonRankings(exs, format = "gff") :
  Infering Exon Rankings.  If this is not what you expected, then please be sure that you have provided a valid attribute for exonRankAttributeName
3: In matchCircularity(chroms, circ_seqs) :
  None of the strings in your circ_seqs argument match your seqnames.

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