Re: [Bioc-devel] SSL certificate error on nebbiolo2

[Hervé Pagès]

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 
 



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_MONET

Re: [Bioc-devel] SSL certificate error on nebbiolo2

[Nicolas Delhomme]

Thanks Mike and Hervé for the answers!

I’ll give it a go.

Best,

Nico

> On 4 Nov 2021, at 23:02, 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
>  
> 
> 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

Re: [Bioc-devel] SSL certificate error on nebbiolo2

[Mike Smith]

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   fansi_

Re: [Bioc-devel] SSL certificate error on nebbiolo2

[Hervé Pagès]

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   fansi_0.5.0Rcpp_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_1.0.7tools_4.1.1bitops_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-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=C
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_U

[Bioc-devel] SSL certificate error on nebbiolo2

[Nicolas Delhomme]

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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