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

[Marc Carlson]

Hi Malcolm,

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

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?


   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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