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

[Cook, Malcolm]

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.
> 
> 
> 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.con
> ductor/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/201111
> 08/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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> or
> 
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