Question: System dependent biomaRt curl ssl error "wrong version number"
0
gravatar for Anthony Castanza
5 weeks ago by
University of California, San Diego
Anthony Castanza0 wrote:

When specifying the current version of Ensembl (97) to the biomaRt package in the same way that you would specify the archive version I’m getting the following error message and the script fails.

I should note that this does not occur on my work computer which has a slightly older version of R installed via conda, but does happen on my personal computer which has the latest version of R installed directly from CRAN.

Any guidance for resolving this error would be greatly appreciated, the code (with the version swapped for a user prompt) is going in a script that will be user-facing, so having it fail under unknown circumstances is a bit of a problem.

   > species <- "hsapiens_gene_ensembl"
   > ensemblversion <- "97"
   > ensmart <- useEnsembl(biomart = "ensembl", dataset = species, version = ensemblversion)

Note: requested houst was redirected from
http://jul2019.archive.ensembl.org to https://www.ensembl.org:80/biomart/martservice
This often occurs when connecting to the archive URL for the current Ensembl release
You can check the current version number using listEnsemblArchives()
Error in curl::curl_fetch_memory(url, handle = handle) :
    error:1400410B:SSL routines:CONNECT_CT_SRVR_HELLO:wrong version number

I initially reached out to ENSEMBL about the error and they believe that it is a biomaRt error and not on their end.

Thanks for any assistance

biomart • 84 views
ADD COMMENTlink modified 4 weeks ago by Mike Smith3.9k • written 5 weeks ago by Anthony Castanza0

Can you provide the output of sessionInfo() so we can see which version of biomaRt you are using?

There's definitely something odd going on as it's specify https and port 80 which is probably incompatible, and will be due to a bug in trying to match up the 'current version' URL with the fact this is automatically redirected to www

ADD REPLYlink written 5 weeks ago by Mike Smith3.9k

Here's that output:

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.40.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1           AnnotationDbi_1.46.0 magrittr_1.5         hms_0.5.0            BiocGenerics_0.30.0  progress_1.2.2       IRanges_2.18.1       bit_1.1-14          
 [9] R6_2.4.0             rlang_0.4.0          httr_1.4.0           stringr_1.4.0        blob_1.2.0           tools_3.6.1          parallel_3.6.1       Biobase_2.44.0      
[17] DBI_1.0.0            assertthat_0.2.1     bit64_0.9-7          digest_0.6.20        tibble_2.1.3         crayon_1.3.4         BiocManager_1.30.4   vctrs_0.2.0         
[25] S4Vectors_0.22.0     bitops_1.0-6         curl_3.3             RCurl_1.95-4.12      zeallot_0.1.0        memoise_1.1.0        RSQLite_2.1.1        stringi_1.4.3       
[33] compiler_3.6.1       pillar_1.4.2         prettyunits_1.0.2    backports_1.1.4      stats4_3.6.1         XML_3.98-1.20        pkgconfig_2.0.2
ADD REPLYlink written 5 weeks ago by Anthony Castanza0
Answer: System dependent biomaRt curl ssl error "wrong version number"
1
gravatar for Mike Smith
4 weeks ago by
Mike Smith3.9k
EMBL Heidelberg / de.NBI
Mike Smith3.9k wrote:

This should now be fixed in biomaRt version 2.40.3. It will take a few days to propagate through to the Bioconductor repository.

> library(biomaRt)
> Biobase::package.version("biomaRt")
[1] "2.40.3"

> species <- "hsapiens_gene_ensembl"
> ensemblversion <- "97"
> ensmart <- useEnsembl(biomart = "ensembl", dataset = species, version = ensemblversion)
> ensmart
Object of class 'Mart':
  Using the ENSEMBL_MART_ENSEMBL BioMart database
  Using the hsapiens_gene_ensembl dataset
ADD COMMENTlink written 4 weeks ago by Mike Smith3.9k

Thanks! I'll test it once I get the update and confirm the fix.

Edit: The new version does, in fact, fix this error.

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by Anthony Castanza0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 217 users visited in the last hour