Thanks Mike. I never heard about useEnsembl() before. That sounds like a
nice addition. There are a few packages maintained by the core team
(OrganismDbi, GenomicFeatures, etc...) where we still use useMart().
These packages are victims of the Ensembl Mart flakiness almost every
day on the build report :-/ Sounds like we should really give
useEnsembl() a try ;-)
I also see that the use of useMart() vs useEnsembl() is still about 80%
vs 20% across all Bioconductor software packages. I wonder if you would
consider advertising the latter a little bit e.g. by mentioning it in
the man page for useMart() and also maybe by emitting a note or warning
when people use useMart() to access the ensembl Mart. What do you think?
Cheers,
H.
On 04/11/2021 15:02, Mike Smith 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
<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
<mailto: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
<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
<http://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 <mailto:Bioc-devel@r-project.org>
mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>
--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com <mailto:hpages.on.git...@gmail.com>
_______________________________________________
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--
Hervé Pagès
Bioconductor Core Team
hpages.on.git...@gmail.com
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