SSL certificate problem: unable to get local issuer certificate

[kbrulois]

Hello,

I'm getting the following error when trying to use the useEnsembl function:

mouse = useEnsembl("ensembl", dataset = "mmusculus_gene_ensembl", host = "http://www.ensembl.org", mirEnsembl site unresponsive, trying uswest mirror

Error in curl::curl_fetch_memory(url, handle = handle) : SSL certificate problem: unable to get local issuer certificate sessionInfo() R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /share/software/user/open/openblas/0.2.19/lib/libopenblasp-r0.2.19.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base

other attached packages: [1] httr_1.4.2 biomaRt_2.44.1
[3] org.Mm.eg.db_3.11.4 AnnotationDbi_1.50.3
[5] stringr_1.4.0 data.table_1.13.0
[7] magrittr_1.5 batchtools_0.9.13
[9] doParallel_1.0.15 iterators_1.0.12
[11] foreach_1.5.0 phateR_1.0.4
[13] Matrix_1.2-18 scran_1.16.0
[15] SingleCellExperiment_1.10.1 SummarizedExperiment_1.18.2 [17] DelayedArray_0.14.1 matrixStats_0.57.0
[19] Biobase_2.48.0 GenomicRanges_1.40.0
[21] GenomeInfoDb_1.24.2 IRanges_2.22.2
[23] S4Vectors_0.26.1 BiocGenerics_0.34.0
[25] ggplot2_3.3.2 BiocParallel_1.22.0

loaded via a namespace (and not attached): [1] bitops_1.0-6 bit64_4.0.5
[3] progress_1.2.2 tools_4.0.2
[5] backports_1.1.10 R6_2.4.1
[7] irlba_2.3.3 vipor_0.4.5
[9] DBI_1.1.0 colorspace_1.4-1
[11] withr_2.3.0 tidyselect_1.1.0
[13] gridExtra_2.3 prettyunits_1.1.1
[15] curl_4.3 bit_4.0.4
[17] compiler_4.0.2 BiocNeighbors_1.6.0
[19] scales_1.1.1 checkmate_2.0.0
[21] askpass_1.1 rappdirs_0.3.1
[23] digest_0.6.25 XVector_0.28.0
[25] scater_1.16.2 pkgconfig_2.0.3
[27] umap_0.2.6.0 dbplyr_1.4.4
[29] limma_3.44.3 rlang_0.4.8
[31] RSQLite_2.2.0 DelayedMatrixStats_1.10.1 [33] generics_0.0.2 jsonlite_1.7.1
[35] gtools_3.8.2 dplyr_1.0.2
[37] zip_2.1.1 RCurl_1.98-1.2
[39] BiocSingular_1.4.0 GenomeInfoDbData_1.2.3
[41] Rcpp_1.0.5 ggbeeswarm_0.6.0
[43] munsell_0.5.0 reticulate_1.16
[45] viridis_0.5.1 lifecycle_0.2.0
[47] stringi_1.5.3 edgeR_3.30.3
[49] debugme_1.1.0 zlibbioc_1.34.0
[51] BiocFileCache_1.12.1 grid_4.0.2
[53] blob_1.2.1 dqrng_0.2.1
[55] crayon_1.3.4 lattice_0.20-41
[57] hms_0.5.3 locfit_1.5-9.4
[59] pillar_1.4.6 igraph_1.2.6
[61] base64url_1.4 codetools_0.2-16
[63] XML_3.99-0.5 glue_1.4.2
[65] vctrs_0.3.4 openssl_1.4.3
[67] gtable_0.3.0 purrr_0.3.4
[69] assertthat_0.2.1 openxlsx_4.2.2
[71] rsvd_1.0.3 RSpectra_0.16-0
[73] viridisLite_0.3.0 tibble_3.0.3
[75] beeswarm_0.2.3 memoise_1.1.0
[77] statmod_1.4.34 ellipsis_0.3.1
[79] brew_1.0-6

[lldelisle]

Hi, I also got:

> ensembl <- useMart("ensembl")
Ensembl site unresponsive, trying asia mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: unable to get local issuer certificate

[lldelisle]

For me it went back to normal.

[grimbough]

Thank you both for the reports. This seems to be happening intermittently for some of the Ensembl mirror sites.

If it happens again you can try running the following in your R sesssion:

httr::set_config(httr::config(ssl_verifypeer = FALSE))

I think you'll need to run it once each time you restart R, but it should persist for the duration of your R session. I'll try to come up with a strategy for detecting this in biomaRt and using it automatically.

[jennylsmith]

I've also been getting the same error, and this solved it! Thanks!

Ensembl site unresponsive, trying asia mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: unable to get local issuer certificate

[grimbough]

This setting should now be applied automatically when biomaRt is loaded.