Dear Valerie, thank you SO much for giving me hope that I will recover this structure. But I still couldn't figure out how to do it. I'm still with R 3.2.
#today, Dec 09 2016
R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04 LTS
attached base packages:
 stats4 parallel stats graphics grDevices utils datasets
 methods base
other attached packages:
 BiocInstaller_1.20.3 AnnotationHub_2.2.5 BSgenome_1.38.0
 rtracklayer_1.30.4 Biostrings_2.38.4 XVector_0.10.0
 GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 IRanges_2.4.8
 S4Vectors_0.8.11 BiocGenerics_0.16.1 RSQLite_1.0.0
update with biocLite()
Error: 20 package(s) out of date
I tried to do the following :
> hub = AnnotationHub()
# I got a list of 63 dates
>snapshotDate(hub) = "2016-07-20"
# I tried a few other dates, but I think that should be the right one
> query(hub, "communis")
AnnotationHub with 1 record
# snapshotDate(): 2016-07-20
# names(): AH10581
# $dataprovider: Inparanoid8
# $species: Ricinus communis
#That's the other only available thing on Ricinus communis, and it's not the one I want (AH48041 is the right one). There were 2 records originally, the other one was the OrgDb.
So I could not set AnnotationHub to a different date, and I still have the old versions of R/Bioconductor tha I hoped would make the trick. Please help me!!!
A comment: if you work with humans and have daily updates on data that is all very good, but this structure is the only one available with the correlation ENTREZID, Symbol, GO that I found anywhere for this species. Not nice when it's not available... Thank you in advance, Ana.