Issues with getBM function

[SM]

Hi, I'm having issues with the getBM function which worked fine as for yesterday.

mart = useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

  lookup <- getBM(attributes = c('entrezgene_id', 'ensembl_gene_id','gene_biotype','hgnc_symbol'),filters = 'ensembl_gene_id',values = ens.genes,uniqueRows = TRUE,mart = mart,)

This is the error I'm getting:

Error in str_extract_all(string = archives, pattern = "Ensembl [A-Za-z0-9 ]{2,6}|http[s]?://.*ensembl\\.org|[A-Z][a-z]{2} [0-9]{4}") : 

  lazy-load database '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/stringi/R/stringi.rdb' is corrupt

In addition: Warning messages:

1: In str_extract_all(string = archives, pattern = "Ensembl [A-Za-z0-9 ]{2,6}|http[s]?://.*ensembl\\.org|[A-Z][a-z]{2} [0-9]{4}") :

  restarting interrupted promise evaluation

2: In str_extract_all(string = archives, pattern = "Ensembl [A-Za-z0-9 ]{2,6}|http[s]?://.*ensembl\\.org|[A-Z][a-z]{2} [0-9]{4}") :

  internal error -3 in R_decompress1

Anyone else experience that?

Thanks,

[mchakiachvili]

Good morning, 

This doesn't seems to be related to the Biomart in itself, did you recently reinstalled a new R version? Or updated your system?

Marc

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Marc Chakiachvili

Ensembl Production Project Leader - Genomics Technology Infrastructure

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton

Cambridge CB10 1SD

United Kingdom