[BioC] GenomicFeatures::makeTranscriptDbFromBiomart - Error in callSuper(...) : could not find function "initRefFields"
MEC at stowers.org
Thu Feb 2 22:43:07 CET 2012
Hi Herve and Marc and Bioc fellow-travellers,
I am unhappy to report that....
It now happens that:
Error in callSuper(...) : could not find function "initRefFields"
... just after I updated installed Bioc packages today, using
At first glance it seems to be the same as reported earlier here:
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:
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?
R version 2.14.0 (2011-10-31)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 GenomicFeatures_1.6.7 AnnotationDbi_1.16.11 Biobase_2.14.0
 GenomicRanges_1.6.6 IRanges_1.12.5
loaded via a namespace (and not attached):
 BSgenome_1.22.0 Biostrings_2.22.0 DBI_0.2-5 RCurl_1.9-5
 RSQLite_0.11.1 XML_3.9-2 biomaRt_2.10.0 rtracklayer_1.14.4
 tools_2.14.0 zlibbioc_1.0.0
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