Recent problem with Ensembl: "object 'err_msg' not found"
Closed this issue · 3 comments
cemmeydan commented
Hi,
Very recently biomaRt started giving an unknown error. The code below has been functional for a very long time. None of the mirrors seem to be different either. Unless the server is having an extended outage I assume it might have to do with a change in how the Ensembl servers respond to requests?
human = useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "https://asia.ensembl.org")
mouse = useMart("ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = "https://asia.ensembl.org")
geneOrth_H2M = getLDS(attributes = c("hgnc_symbol"), mart = human, attributesL = c("mgi_symbol"), martL = mouse, uniqueRows = T)
Error in .createErrorMessage(error_code = status_code(res), host = host) :
object 'err_msg' not found
Traceback:
3. .createErrorMessage(error_code = status_code(res), host = host) at
utilityFunctions.R#196
2. .submitQueryXML(host = paste0(martHost(mart), sep), query = xmlQuery) at
biomaRt.R#799
1. getLDS(attributes = c("hgnc_symbol"), mart = human, attributesL = c("mgi_symbol"),
martL = mouse, uniqueRows = T)
yiolino commented
@cemmeydan
Hi,
I also encountered the same error.
Not the best solution, but I was able to get the getLDS function to work by specifying the archive host.
human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "https://dec2021.archive.ensembl.org/")
mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = "https://dec2021.archive.ensembl.org/")
cemmeydan commented
Thank you for the workaround, it does work with the archive.