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

[Cook, Malcolm]

Hi Marc,

> A host argument has indeed been added to the devel branch.  

Great

> But more
> pertinent to your current issue is the fact that I am able to easily
> load your database using loadFeatures() or loadDB().  So I don't see
> anything wrong with the DB on this end.  We tested it in both Linux and
> Mac and are unable to recreate the problem.

Hmmm...

> This makes me think that there is something wrong with your current
> setup.  Your version of R could be a little more current, I don't really
> anticipate that this would cause a problem like this, but it might be
> worth updating to 2.14.1 anyhow.  And the only package I have that is
> more current than yours is XML, which should not matter here.  Are you
> sure that you have read permissions for your copy of this DB?

Yes.   I am sure.

FWIW: google finds a few others similarly afflicted , but only in very the recent past:
	5 days ago - http://lists.hexdump.org/pipermail/twitter-users-hexdump.org/2012-January/000027.html
	5 days ago - same problem in ggplot- https://groups.google.com/forum/?fromgroups#!topic/ggplot2/FciMhMfDZp4

But wait.  SUCCESS:
I just tried rebuilding from source, and, after the following I was able to load the database
	biocLite(c('RCurl','rtracklayer','GenomicFeatures','AnnotationDbi','Biobase','GenomicRanges','IRanges'), type='source')

HOORAY!

I guess we're not going to find the root cause this time.  
Like last time: http://permalink.gmane.org/gmane.science.biology.informatics.conductor/38404
That's OK.
If you have any suggestions for me to try something, fire away.

Other than that....

Thanks for your help sleuthing with me.  !!!

Cheers,

Malcolm



> 
> 
>    Marc
> 
> 
> On 02/03/2012 07:43 AM, Cook, Malcolm wrote:
> > 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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