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

[Marc Carlson]

Hi Malcolm,

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?

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.


   Marc



On 02/02/2012 01:58 PM, Cook, Malcolm wrote:
> Hi Herve and Marc and Bioc fellow-travellers,
>
> I am unhappy to report that....
>
> It now happens that:
>
> 	>  txdb<-loadFeatures('dmelanogaster_gene_ensembl.sqlite')
> 	Error in callSuper(...) : could not find function "initRefFields"
>
> ... just after I updated installed Bioc packages today, using
>
> 	source("http://bioconductor.org/biocLite.R")
> 	old.packages(repos=biocinstallRepos())
>
> At first glance it seems to be the same as reported earlier here:
>
> 	http://permalink.gmane.org/gmane.science.biology.informatics.conductor/38404
>
> However, trying the same workaround, namely, re-updating from source
>
> 	>  biocLite(c('GenomicFeatures'), type='source')
>
> and starting a new session, fails to fix... the error still occurs.
>
> As a potential workaround, I tried re-building the txdb from ensembl, but this is now failing (possibly due to new schema/data at Ensembl?), yielding the following error:
>
> 	txdb<-makeTranscriptDbFromBiomart(biomart="ensembl", dataset="dmelanogaster_gene_ensembl",circ_seqs=NULL)
> 	Download and preprocess the 'transcripts' data frame ... OK
> 	Download and preprocess the 'chrominfo' data frame ... OK
> 	Download and preprocess the 'splicings' data frame ... Error in .extractCdsRangesFromBiomartTable(bm_table) :
>    	BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute from BioMart
>
> So, I looked for the hoped-for further workaround, of being able to specify an (archive) 'host' to makeTranscriptDbFromBiomart, (as discussed:https://stat.ethz.ch/pipermail/bioconductor/attachments/20111108/a5ece78c/attachment.pl)_ which I would expect to call as
>
> 	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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