Thanks Mike and Hervé for the answers! I’ll give it a go.
Best, Nico > On 4 Nov 2021, at 23:02, Mike Smith <grimbo...@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.git...@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@r-project.org mailing list > > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > > > -- > Hervé Pagès > > Bioconductor Core Team > hpages.on.git...@gmail.com > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
