[BioC] FW: GenomicFeatures::makeTranscriptDbFromBiomart - Error in callSuper(...) : could not find function "initRefFields"

[Cook, Malcolm]

Hi Marc,

> I cannot say why your older annotation database is not working, but I
> suspect that it is just out of phase with recent changes introduced when
> you updated the code.  But the error you reported from when you tried to
> generate a new TxDb package is an unhappy message indeed.  It means that
> the data for cds ranges and total cds length (both from biomaRt) no
> longer agree with each other.  In other words, the data from the current
> drosophila ranges in biomaRt seems to disagree with itself, and so the
> code is refusing to make a package out of this data as a result.
> 
> So to try and get the 1st issue fixed I need more information.  I
> suspect that what has happened to your old DB is that is is missing some
> metadata that is required by the newer versions of GenomicFeatures.  Is
> there a place where you could put your DB so that I could DL it and have
> a look at it?

Sure - great - thanks - here it is:

	ftp://ftp.stowers-institute.org/pub/MEC/dmelanogaster_gene_ensembl.sqlite

> To get the 2nd issue fixed probably involves talking to ensembl about
> their CDS data for fly to see if we can resolve the discrepancy.

I would be happy to take this to them.

Can you recommend a best way to get a more diagnostic trace from the attempt at txdb creation so we can correctly report to ensembl team the errant transcript(s) ?

Finally, do you have any information on the progress of adding a 'host' option to makeTranscriptDbFromBiomart ?
If I install Bioc-dev should I expect to find this implemented?
And if I do, will a txdb so-created be backward compatible with current released GenomicFeatures (i.e. should I be able to load it)?

Thanks so much for you help,

Cheers,

Malcolm



> > 	txdb<-makeTranscriptDbFromBiomart(host='
> jun2011.archive.ensembl.org/biomart/martservice',biomart="ensembl",
> dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL)
> >
> > but I found that the `host` option is not (yet?) supported (in released).
> >
> > So, most urgently to me, is to find a workaround to my primary problem,
> namely, of getting past the missing 'initRefFields' when calling `loadFeatures`
> .
> >
> > Is there a fix/patch/workaround that can address this?
> >
> > Thanks,
> >
> > Malcolm Cook
> >
> >
> >
> >> sessionInfo()
> > R version 2.14.0 (2011-10-31)
> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> >
> > locale:
> > [1] C
> >
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
> >
> > other attached packages:
> > [1] GenomicFeatures_1.6.7 AnnotationDbi_1.16.11 Biobase_2.14.0
> > [4] GenomicRanges_1.6.6   IRanges_1.12.5
> >
> > loaded via a namespace (and not attached):
> >   [1] BSgenome_1.22.0    Biostrings_2.22.0  DBI_0.2-5          RCurl_1.9-5
> >   [5] RSQLite_0.11.1     XML_3.9-2          biomaRt_2.10.0     rtracklayer_1.14.4
> >   [9] tools_2.14.0       zlibbioc_1.0.0
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