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

[Cook, Malcolm]

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    
>