EDIT: I tried updating biomaRt, which replaced it with version 2.38.0 (see my response to genomax). After restarting RStudio the error has vanished. Perhaps there was an issue with some dependency.
I'm trying to access biomart version 93 (human) because this happens to be the version that was used to build the reference GTF I've been using. This previous thread had the answer: BiomaRt: archive version of ensembl not working
Unfortunately the system seems to be broken. The listEnsemblArchives() function returns the error:
Error in getNodeSet(html, path = "//div[@class='plain-box float-right archive-box']")[] : subscript out of bounds In addition: Warning message: XML content does not seem to be XML: 'https://www.ensembl.org/info/website/archives/index.html?redirect=no'
Similarly, the following commands returns the identical error:
hg93 <- useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", version = "93") hg93 <- useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", version = "93") hg93 <- useMart("ensembl",host = "http://jul2018.archive.ensembl.org", dataset = "hsapiens_gene_ensembl")
The current version works fine. I normally use this format:
I'm not sure if there is any difference between useMart() and useEnsembl()
I experienced the same error today. And then I tried to open the wedsite:https://www.ensembl.org/info/website/archives/index.html,but it showed "The Ensembl web service you requested is temporarily unavailable". It might be the reason.
Works for me without an error.
As for your other question:
What version of R and biomaRt are you using?
I am on:
R version 3.5.1 (2018-07-02)
edit: I tried updating my biomart, which resulted in it being replace by biomaRt_2.38.0. I am on bioconductor version 3.8 because my university's compute cluster hasn't installed R 3.6 yet.
I'm not sure where 2.41.4 came from given that the latest version listed on https://bioconductor.org/packages/release/bioc/html/biomaRt.html is version 2.40.3
Anyway the error remains