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grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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Error in req_perform(useast) : Failed to perform HTTP request. #105

Closed satish1907 closed 3 weeks ago

satish1907 commented 1 month ago

Possible SSL connectivity problems detected. Please report this issue at https://github.com/grimbough/biomaRt/issues Error in req_perform(useast) : Failed to perform HTTP request. Caused by error in curl::curl_fetch_memory(): ! schannel: next InitializeSecurityContext failed: SEC_E_CERT_EXPIRED (0x80090328) - The received certificate has expired.

    biomart                version

1 genes Ensembl Genes 112 2 mouse_strains Mouse strains 112 3 snps Ensembl Variation 112 4 regulation Ensembl Regulation 112

satish1907 commented 1 month ago

Resolved now

splaisan commented 1 month ago

Hi! not resolved for me:

ubuntu 22 (uptodate) R 4.4.0 RStudio server 2023.12.1 Build 402 biomaRt 2.60.0

> ensembl <- useEnsembl(biomart = "genes")
Possible SSL connectivity problems detected.
Please report this issue at https://github.com/grimbough/biomaRt/issues
Error in req_perform(useast) : Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL peer certificate or SSH remote key was not OK: [useast.ensembl.org] SSL certificate problem: certificate has expired
splaisan commented 1 month ago

apparently, I had an older version of fastmap (1.1.1) that was not high enough but not triggering a warning with BiocManager::valid().

This fixed my issue after installing fastmap 1.2.0

remove.packages("fastmap")
BiocManager::install("fastmap")
grimbough commented 3 weeks ago

I think the original issue reported here was an SSL certificate issue that was resolved by the Ensembl team.

I'm not clear why updating fastmap would have any effect on this, as I don't think there's any link between it and biomaRt, but I'm glad the issue is resolved.