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/201 11108/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 >