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 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-8LC_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_1.34.0progress_1.2.2 tidyselect_1.1.1
>
> [4] purrr_0.3.4vctrs_0.3.8generics_0.1.1
>
> [7] stats4_4.1.1 BiocFileCache_2.2.0utf8_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_0.40.0bit64_4.0.5
>
> [19] dbplyr_2.1.1 GenomeInfoDbData_1.2.7 lifecycle_1.0.1
>
> [22] stringr_1.4.0 zlibbioc_1.40.0Biostrings_2.62.0
>
> [25] memoise_2.0.0 Biobase_2.54.0 IRanges_2.28.0
>
> [28] fastmap_1.1.0 GenomeInfoDb_1.30.0curl_4.3.2
>
> [31] AnnotationDbi_1.56.0
