I have used this code to query biomart database previously with no error.
mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = 'ensembl.org')mart Object of class 'Mart': Using the ENSEMBL_MART_ENSEMBL BioMart database Using the hsapiens_gene_ensembl dataset
mapping <- getBM(attributes = c("ensembl_gene_id", "ensembl_transcript_id"), mart = mart)
But now, I get two different errors:
mapping <- getBM(attributes = c("ensembl_gene_id","ensembl_transcript_id"), mart = mart)Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 3 elements
mapping <- biomaRt::getBM(attributes = c("ensembl_gene_id","ensembl_transcript_id"), mart = mart) No encoding supplied: defaulting to UTF-8. Error in biomaRt::getBM(mart = mart, attributes = c("ensembl_transcript_id", : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.
Is this related to the biomaRt connection issues that have been recently posted ?
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.6 (Final)
Matrix products: default
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 dplyr_0.7.4 biomaRt_2.34.1