BiomaRt Possible Ensembl SSL connectivity problems detected.
1
0
Entering edit mode
varga.luca • 0
@1e8cbbaa
Last seen 11 weeks ago
Hungary

Hi, I'm trying to use PureCN and I consistently get this error message:

Possible Ensembl SSL connectivity problems detected.
Please see the 'Connection Troubleshooting' section of the biomaRt vignette
vignette('accessing_ensembl', package = 'biomaRt')Error in curl::curl_fetch_memory(url, handle = handle) : 
  Peer certificate cannot be authenticated with given CA certificates: [uswest.ensembl.org] SSL certificate problem: certificate has expired

I've tried changing the mirror by adding these lines to the PureCN source code:

ensembl <- useEnsembl(biomart = "ensembl", 
                   dataset = "hsapiens_gene_ensembl", 
                   mirror = "www")

this doesn't work, it doesn't remove the warning message and all it does is it just keeps trying all mirrors and around half the time it returns this error and stops:

Error in bmRequest(request = request, verbose = verbose) : 
  Not Found (HTTP 404).
Calls: useEnsembl ... listMarts -> .listMarts -> bmRequest -> stop_for_status
Execution halted

It's a gamble if it works, I usually have 15 bam files I want to loop through and I keep having to redo about half of them. Is there a way to resolve this?

my session info:

 Session info 
 version  R version 4.0.2 (2020-06-22)
 os       Ubuntu 18.04.6 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  C.UTF-8
 ctype    C.UTF-8
 tz       Europe/Budapest
 date     2024-08-30
 rstudio  1.3.959 Middlemist Red (server)
 pandoc   NA

Packages 
 package              * version   date (UTC) lib source
 AnnotationDbi          1.52.0    2020-10-27 [1] Bioconductor
 askpass                1.2.0     2023-09-03 [1] CRAN (R 4.0.2)
 Biobase              * 2.50.0    2020-10-27 [1] Bioconductor
 BiocFileCache          1.14.0    2020-10-27 [1] Bioconductor
 BiocGenerics         * 0.36.1    2021-04-16 [1] Bioconductor
 BiocManager          * 1.30.25   2024-08-28 [1] CRAN (R 4.0.2)
 BiocParallel         * 1.24.1    2020-11-06 [1] Bioconductor
 biomaRt              * 2.46.3    2024-08-26 [1] Bioconductor
 Biostrings           * 2.58.0    2020-10-27 [1] Bioconductor
 bit                    4.0.5     2022-11-15 [1] CRAN (R 4.0.2)
 bit64                  4.0.5     2020-08-30 [1] CRAN (R 4.0.2)
 bitops                 1.0-8     2024-07-29 [1] CRAN (R 4.0.2)
 blob                   1.2.4     2023-03-17 [1] CRAN (R 4.0.2)
 BSgenome               1.58.0    2020-10-27 [1] Bioconductor
 cachem                 1.1.0     2024-05-16 [1] CRAN (R 4.0.2)
 Cairo                  1.6-2     2023-11-28 [1] CRAN (R 4.0.2)
 circlize             * 0.4.16    2024-02-20 [1] CRAN (R 4.0.2)
 cli                    3.6.3     2024-06-21 [1] CRAN (R 4.0.2)
 clue                   0.3-65    2023-09-23 [1] CRAN (R 4.0.2)
 cluster                2.1.0     2019-06-19 [2] CRAN (R 4.0.2)
 colorspace             2.1-1     2024-07-26 [1] CRAN (R 4.0.2)
 ComplexHeatmap       * 2.6.2     2020-11-12 [1] Bioconductor
 crayon                 1.5.3     2024-06-20 [1] CRAN (R 4.0.2)
 curl                 * 5.2.2     2024-08-26 [1] CRAN (R 4.0.2)
 data.table             1.16.0    2024-08-27 [1] CRAN (R 4.0.2)
 DBI                    1.2.3     2024-06-02 [1] CRAN (R 4.0.2)
 dbplyr                 2.5.0     2024-03-19 [1] CRAN (R 4.0.2)
 DelayedArray           0.16.3    2021-03-24 [1] Bioconductor
 devtools             * 2.4.5     2022-10-11 [1] CRAN (R 4.0.2)
 digest                 0.6.37    2024-08-19 [1] CRAN (R 4.0.2)
 DNAcopy              * 1.64.0    2020-10-27 [1] Bioconductor
 dplyr                * 1.1.4     2023-11-17 [1] CRAN (R 4.0.2)
 ellipsis               0.3.2     2021-04-29 [1] CRAN (R 4.0.2)
 fansi                  1.0.6     2023-12-08 [1] CRAN (R 4.0.2)
 fastmap                1.2.0     2024-05-15 [1] CRAN (R 4.0.2)
 forcats              * 1.0.0     2023-01-29 [1] CRAN (R 4.0.2)
 formatR                1.14      2023-01-17 [1] CRAN (R 4.0.2)
 fs                   * 1.6.4     2024-04-25 [1] CRAN (R 4.0.2)
 futile.logger        * 1.4.3     2016-07-10 [1] CRAN (R 4.0.2)
 futile.options         1.0.1     2018-04-20 [1] CRAN (R 4.0.2)
 generics               0.1.3     2022-07-05 [1] CRAN (R 4.0.2)
 GenomeInfoDb         * 1.26.7    2021-04-08 [1] Bioconductor
 GenomeInfoDbData       1.2.4     2024-06-25 [1] Bioconductor
 GenomicAlignments      1.26.0    2020-10-27 [1] Bioconductor
 GenomicFeatures        1.42.3    2021-04-01 [1] Bioconductor
 GenomicRanges        * 1.42.0    2020-10-27 [1] Bioconductor
 getopt                 1.20.4    2023-10-01 [1] CRAN (R 4.0.2)
 GetoptLong             1.0.5     2020-12-15 [1] CRAN (R 4.0.2)
 ggplot2              * 3.5.1     2024-04-23 [1] CRAN (R 4.0.2)
 GlobalOptions          0.1.2     2020-06-10 [1] CRAN (R 4.0.2)
 glue                   1.7.0     2024-01-09 [1] CRAN (R 4.0.2)
 gridExtra              2.3       2017-09-09 [1] CRAN (R 4.0.2)
 gtable                 0.3.5     2024-04-22 [1] CRAN (R 4.0.2)
 hms                    1.1.3     2023-03-21 [1] CRAN (R 4.0.2)
 htmltools              0.5.8.1   2024-04-04 [1] CRAN (R 4.0.2)
 htmlwidgets            1.6.4     2023-12-06 [1] CRAN (R 4.0.2)
 httpuv                 1.6.15    2024-03-26 [1] CRAN (R 4.0.2)
 httr                   1.4.7     2023-08-15 [1] CRAN (R 4.0.2)
 IRanges              * 2.24.1    2020-12-12 [1] Bioconductor
 lambda.r               1.2.4     2019-09-18 [1] CRAN (R 4.0.2)
 later                  1.3.2     2023-12-06 [1] CRAN (R 4.0.2)
 lattice                0.20-41   2020-04-02 [2] CRAN (R 4.0.2)
 lifecycle              1.0.4     2023-11-07 [1] CRAN (R 4.0.2)
 lubridate            * 1.9.3     2023-09-27 [1] CRAN (R 4.0.2)
 maftools             * 2.6.05    2021-02-04 [1] Bioconductor
 magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.0.2)
 Matrix                 1.2-18    2019-11-27 [2] CRAN (R 4.0.2)
 MatrixGenerics       * 1.2.1     2021-01-30 [1] Bioconductor
 matrixStats          * 1.3.0     2024-04-11 [1] CRAN (R 4.0.2)
 memoise                2.0.1     2021-11-26 [1] CRAN (R 4.0.2)
 mime                   0.12      2021-09-28 [1] CRAN (R 4.0.2)
 miniUI                 0.1.1.1   2018-05-18 [1] CRAN (R 4.0.2)
 munsell                0.5.1     2024-04-01 [1] CRAN (R 4.0.2)
 openssl                2.2.1     2024-08-16 [1] CRAN (R 4.0.2)
 optparse             * 1.7.5     2024-04-16 [1] CRAN (R 4.0.2)
 pillar                 1.9.0     2023-03-22 [1] CRAN (R 4.0.2)
 pkgbuild               1.4.4     2024-03-17 [1] CRAN (R 4.0.2)
 pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.0.2)
 pkgload                1.4.0     2024-06-28 [1] CRAN (R 4.0.2)
 plyr                   1.8.9     2023-10-02 [1] CRAN (R 4.0.2)
 png                    0.1-8     2022-11-29 [1] CRAN (R 4.0.2)
 prettyunits            1.2.0     2023-09-24 [1] CRAN (R 4.0.2)
 profvis                0.3.8     2023-05-02 [1] CRAN (R 4.0.2)
 progress               1.2.3     2023-12-06 [1] CRAN (R 4.0.2)
 promises               1.3.0     2024-04-05 [1] CRAN (R 4.0.2)
 PureCN               * 1.20.0    2020-10-27 [1] Bioconductor
 purrr                * 1.0.2     2023-08-10 [1] CRAN (R 4.0.2)
 R6                     2.5.1     2021-08-19 [1] CRAN (R 4.0.2)
 rappdirs               0.3.3     2021-01-31 [1] CRAN (R 4.0.2)
 RColorBrewer         * 1.1-3     2022-04-03 [1] CRAN (R 4.0.2)
 Rcpp                   1.0.13    2024-07-17 [1] CRAN (R 4.0.2)
 RCurl                  1.98-1.16 2024-07-11 [1] CRAN (R 4.0.2)
 readr                * 2.1.5     2024-01-10 [1] CRAN (R 4.0.2)
 remotes                2.5.0     2024-03-17 [1] CRAN (R 4.0.2)
 reshape2               1.4.4     2020-04-09 [1] CRAN (R 4.0.2)
 rhdf5                  2.34.0    2020-10-27 [1] Bioconductor
 rhdf5filters           1.2.1     2021-05-03 [1] Bioconductor
 Rhdf5lib               1.12.1    2021-01-26 [1] Bioconductor
 rjson                  0.2.21    2022-01-09 [1] CRAN (R 4.0.2)
 rlang                  1.1.4     2024-06-04 [1] CRAN (R 4.0.2)
 Rsamtools            * 2.6.0     2020-10-27 [1] Bioconductor
 RSQLite                2.3.7     2024-05-27 [1] CRAN (R 4.0.2)
 rstudioapi             0.16.0    2024-03-24 [1] CRAN (R 4.0.2)
 rtracklayer            1.50.0    2020-10-27 [1] Bioconductor
 S4Vectors            * 0.28.1    2020-12-09 [1] Bioconductor
 scales                 1.3.0     2023-11-28 [1] CRAN (R 4.0.2)
 sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.0.2)
 shape                  1.4.6.1   2024-02-23 [1] CRAN (R 4.0.2)
 shiny                  1.9.1     2024-08-01 [1] CRAN (R 4.0.2)
 stringi                1.8.4     2024-05-06 [1] CRAN (R 4.0.2)
 stringr              * 1.5.1     2023-11-14 [1] CRAN (R 4.0.2)
 SummarizedExperiment * 1.20.0    2020-10-27 [1] Bioconductor
 survival               3.1-12    2020-04-10 [2] CRAN (R 4.0.2)
 tibble               * 3.2.1     2023-03-20 [1] CRAN (R 4.0.2)
 tidyr                * 1.3.1     2024-01-24 [1] CRAN (R 4.0.2)
 tidyselect             1.2.1     2024-03-11 [1] CRAN (R 4.0.2)
 tidyverse            * 2.0.0     2023-02-22 [1] CRAN (R 4.0.2)
 timechange             0.3.0     2024-01-18 [1] CRAN (R 4.0.2)
 tzdb                   0.4.0     2023-05-12 [1] CRAN (R 4.0.2)
 urlchecker             1.0.1     2021-11-30 [1] CRAN (R 4.0.2)
 usethis              * 3.0.0     2024-07-29 [1] CRAN (R 4.0.2)
 utf8                   1.2.4     2023-10-22 [1] CRAN (R 4.0.2)
 VariantAnnotation    * 1.36.0    2020-10-27 [1] Bioconductor
 vctrs                  0.6.5     2023-12-01 [1] CRAN (R 4.0.2)
 VGAM                   1.1-11    2024-05-15 [1] CRAN (R 4.0.2)
 vroom                * 1.6.5     2023-12-05 [1] CRAN (R 4.0.2)
 withr                  3.0.1     2024-07-31 [1] CRAN (R 4.0.2)
 XML                    3.99-0.17 2024-06-25 [1] CRAN (R 4.0.2)
 xml2                   1.3.6     2023-12-04 [1] CRAN (R 4.0.2)
 xtable                 1.8-4     2019-04-21 [1] CRAN (R 4.0.2)
 XVector              * 0.30.0    2020-10-27 [1] Bioconductor
 zlibbioc               1.36.0    2020-10-27 [1] Bioconductor
PureCN biomaRt • 741 views
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1
Entering edit mode
Mike Smith ★ 6.6k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg

You're running a pretty old version of R and Bioconductor (it's from October 2020). Unfortunately the uswest mirror of Ensembl has been retired - you can try visiting http://uswest.ensembl.org/ to find a message about this. Newer versions of the biomaRt package have removed references to that mirror, but I can't go back and change the older ones.

My primary suggestion would be to update R and Bioconductor to newer versions. If you want to keep version you currently have, then maybe try mirror = "useast". I'm not sure why mirror = www is failing. That mirror certainly exists, although it does seem to be slow to respond today when I visit it in a browser.
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Hi Mike, Thank you for the response. Updating the versions would be quite difficult as I'm working on a local server where I'm not the sole user of the programs, but it starts to seem it would be the only viable solution at this point.

I have tried all available mirrors, none of them seemed to work for some reason.

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I just found this workaround:

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

at this Stack Overflow link.

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Entering edit mode

Can this please be revisited and corrected ASAP? I'm encountering the same issue, using a slightly more modern version of R (4.1.0). It started happening right at November 1, which leads me to believe that Ensembl just needs to renew an SSL certificate on one of the servers (specifically, https://oct2022.archive.ensembl.org). Thanks!

Here's the call that is giving me trouble:

ensembl = useEnsembl(biomart="ensembl", dataset="hsapiens_gene_ensembl", version = "108")

And the error message thrown:

Possible SSL connectivity problems detected.
Please report this issue at https://github.com/grimbough/biomaRt/issues
Error in curl::curl_fetch_memory(url, handle = handle) :
SSL certificate problem: certificate has expired

And the R session:

> sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.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=C             
 [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] stats     graphics  grDevices utils     datasets  methods   base     
other attached packages:
[1] biomaRt_2.49.4
loaded via a namespace (and not attached):
 [1] KEGGREST_1.33.0        progress_1.2.2         tidyselect_1.1.1      
 [4] purrr_0.3.4            vctrs_0.3.8            generics_0.1.0        
 [7] stats4_4.1.0           BiocFileCache_2.1.1    utf8_1.2.1            
[10] blob_1.2.2             XML_3.99-0.7           rlang_0.4.11          
[13] pillar_1.6.1           glue_1.6.2             DBI_1.1.1             
[16] rappdirs_0.3.3         BiocGenerics_0.39.2    bit64_4.0.5           
[19] dbplyr_2.1.1           GenomeInfoDbData_1.2.6 lifecycle_1.0.0       
[22] stringr_1.4.0          zlibbioc_1.39.0        Biostrings_2.61.2     
[25] memoise_2.0.0          Biobase_2.53.0         IRanges_2.27.2        
[28] fastmap_1.1.0          GenomeInfoDb_1.29.5    curl_4.3.1            
[31] AnnotationDbi_1.55.1   fansi_0.4.2            Rcpp_1.0.7            
[34] filelock_1.0.2         cachem_1.0.5           S4Vectors_0.31.3      
[37] XVector_0.33.0         bit_4.0.4              hms_1.1.0             
[40] png_0.1-7              digest_0.6.27          stringi_1.6.2         
[43] dplyr_1.0.7            tools_4.1.0            bitops_1.0-7          
[46] magrittr_2.0.1         RCurl_1.98-1.4         RSQLite_2.2.8         
[49] tibble_3.1.2           crayon_1.4.1           pkgconfig_2.0.3       
[52] ellipsis_0.3.2         xml2_1.3.2             prettyunits_1.1.1     
[55] assertthat_0.2.1       httr_1.4.2             rstudioapi_0.13       
[58] R6_2.5.0               compiler_4.1.0
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