[Bioc-devel] SSL certificate error on nebbiolo2
Nicolas Delhomme
n|co|@@@de|homme @end|ng |rom umu@@e
Fri Nov 5 08:45:14 CET 2021
Thanks Mike and Hervé for the answers!
I’ll give it a go.
Best,
Nico
> On 4 Nov 2021, at 23:02, Mike Smith <grimbough using gmail.com> wrote:
>
> Hi Nico,
>
> Please try changing your calls to useMart() to useEnsembl(). That function has some checking that should detect this problem (it's real for all Ubuntu 20.04 users, plus various other Linux distros) and will try to apply the appropriate fix in the background. There's some further suggestions in the biomaRt vignette at if that doesn't work - https://bioconductor.org/packages/release/bioc/vignettes/biomaRt/inst/doc/accessing_ensembl.html#connection-troubleshooting
>
> The weird certificates that produce the issue are only on the Ensembl mirror sites, so it should not happen with the default arguments to useMart(), but if biomaRt finds it's taking > 10 seconds to get a response it will see if one of the mirrors is more responsive. That's why it might take a variable number of tries before reproducing the problem.
>
> Best,
> Mike
>
> On Thu, 4 Nov 2021 at 20:42, Hervé Pagès <hpages.on.github using gmail.com> wrote:
> Hi Nico,
>
> This looks like the usual flakiness of the Ensembl Mart service. I see
> these errors on the build report every day for various packages. The
> exact set of packages varies.
>
> I can reproduce on my laptop (Ubuntu 21.04):
>
> > library(biomaRt)
>
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
>
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
>
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
>
> Ensembl site unresponsive, trying uswest mirror
>
> Error in curl::curl_fetch_memory(url, handle = handle) :
>
> SSL certificate problem: unable to get local issuer certificate
>
>
> See my sessionInfo() below.
>
> Note that I had to try 3 times before getting the error.
>
> I can also reproduce this with the Docker container for RELEASE_3_14 but
> this time it took me 12 attempts:
>
> > library(biomaRt)
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_ensembl")
> > ensembl <- useMart(biomart = "ensembl", dataset =
> "dmelanogaster_gene_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
>
> See my sessionInfo() below.
>
> I'm not sure there's something we can do on our Linux builders about
> this, or if it would be a good idea at all to try to do something (the
> problem is real and can affect anybody using Ubuntu). Maybe discuss this
> with Mike Smith by opening an issue here
> https://github.com/grimbough/biomaRt
>
> Best,
> H.
>
>
> sessionInfo() for my laptop session:
>
>
> R version 4.1.1 (2021-08-10)
>
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> Running under: Ubuntu 21.04
>
>
>
> Matrix products: default
>
> BLAS: /home/hpages/R/R-4.1.1/lib/libRblas.so
>
> LAPACK: /home/hpages/R/R-4.1.1/lib/libRlapack.so
>
>
>
> locale:
>
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>
> [3] LC_TIME=en_GB 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] stats graphics grDevices utils datasets methods base
>
>
>
> other attached packages:
>
> [1] biomaRt_2.50.0
>
>
>
> loaded via a namespace (and not attached):
>
> [1] KEGGREST_1.34.0 progress_1.2.2 tidyselect_1.1.1
>
> [4] purrr_0.3.4 vctrs_0.3.8 generics_0.1.1
>
> [7] stats4_4.1.1 BiocFileCache_2.2.0 utf8_1.2.2
>
> [10] blob_1.2.2 XML_3.99-0.8 rlang_0.4.12
>
> [13] pillar_1.6.4 glue_1.4.2 DBI_1.1.1
>
> [16] rappdirs_0.3.3 BiocGenerics_0.40.0 bit64_4.0.5
>
> [19] dbplyr_2.1.1 GenomeInfoDbData_1.2.7 lifecycle_1.0.1
>
> [22] stringr_1.4.0 zlibbioc_1.40.0 Biostrings_2.62.0
>
> [25] memoise_2.0.0 Biobase_2.54.0 IRanges_2.28.0
>
> [28] fastmap_1.1.0 GenomeInfoDb_1.30.0 curl_4.3.2
>
> [31] AnnotationDbi_1.56.0 fansi_0.5.0 Rcpp_1.0.7
>
> [34] filelock_1.0.2 cachem_1.0.6 S4Vectors_0.32.0
>
> [37] XVector_0.34.0 bit_4.0.4 hms_1.1.1
>
> [40] png_0.1-7 digest_0.6.28 stringi_1.7.5
>
> [43] dplyr_1.0.7 tools_4.1.1 bitops_1.0-7
>
> [46] magrittr_2.0.1 RCurl_1.98-1.5 RSQLite_2.2.8
>
> [49] tibble_3.1.5 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_2.5.1 compiler_4.1.1
>
>
>
> sessionInfo() on my Docker session:
>
> R version 4.1.1 (2021-08-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 20.04.3 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_2.50.0 BiocManager_1.30.16
>
> loaded via a namespace (and not attached):
> [1] KEGGREST_1.34.0 progress_1.2.2 tidyselect_1.1.1
> [4] purrr_0.3.4 vctrs_0.3.8 generics_0.1.1
> [7] stats4_4.1.1 BiocFileCache_2.2.0 utf8_1.2.2
> [10] blob_1.2.2 XML_3.99-0.8 rlang_0.4.12
> [13] pillar_1.6.4 glue_1.4.2 DBI_1.1.1
> [16] rappdirs_0.3.3 BiocGenerics_0.40.0 bit64_4.0.5
> [19] dbplyr_2.1.1 GenomeInfoDbData_1.2.7 lifecycle_1.0.1
> [22] stringr_1.4.0 zlibbioc_1.40.0 Biostrings_2.62.0
> [25] memoise_2.0.0 Biobase_2.54.0 IRanges_2.28.0
> [28] fastmap_1.1.0 GenomeInfoDb_1.30.0 curl_4.3.2
> [31] AnnotationDbi_1.56.1 fansi_0.5.0 Rcpp_1.0.7
> [34] filelock_1.0.2 cachem_1.0.6 S4Vectors_0.32.0
> [37] XVector_0.34.0 bit_4.0.4 hms_1.1.1
> [40] png_0.1-7 digest_0.6.28 stringi_1.7.5
> [43] dplyr_1.0.7 tools_4.1.1 bitops_1.0-7
> [46] magrittr_2.0.1 RCurl_1.98-1.5 RSQLite_2.2.8
> [49] tibble_3.1.5 crayon_1.4.2 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_2.5.1 compiler_4.1.1
>
>
> On 03/11/2021 15:15, Nicolas Delhomme wrote:
> > Hej!
> >
> > The easyRNASeq package fails with the following error on nebbiolo2:
> >
> > easyRNASeq RUnit Tests - 20 test functions, 1 error, 0 failures
> > ERROR in test_getAnnotation_BiomaRt: Error in h(simpleError(msg, call)) :
> > error in evaluating the argument 'table' in selecting a method for function '%in%': SSL certificate problem: unable to get local issuer certificate
> >
> > Not exactly sure what I can do about that.
> >
> > Best,
> >
> > Nico
> > _______________________________________________
> > Bioc-devel using r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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