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
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Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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