BioMart

Question

[Morris_Chair]

Hello everyone,

I'm running a script to get informations about the genelenght using Biomart and is retuning with an error :(

mart = biomaRt::useMart("ENSEMBL_MART_ENSEMBL", dataset = dataset, 
                    host = paste0(ens_build, ".archive.ensembl.org"), path = "/biomart/martservice", archive = FALSE)

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Protocol "sep2015https" not supported or disabled in libcurl
In addition: Warning message:
Ensembl will soon enforce the use of https.
Ensure the 'host' argument includes "https://"

I accept any advice to fix it

Thank you

Answer 1

[Mike Smith]

What is the value (or values) in ens_build? It looks like the host argument is being constructed incorrectly somewhere.

It might be easier to use the function useEnsembl() instead of useMart() and then use the version argument. e.g.

mart <- useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL", dataset = dataset, version = 80)

I also don't think there is a "September 2015" archive, if that's what you're trying to access. Version 80 in my example is from May 2015, which is the closest I can see. You can see a complete list of archives with listEnsemblArchives().

> listEnsemblArchives()
             name     date                                 url version current_release
1  Ensembl GRCh37 Feb 2014          https://grch37.ensembl.org  GRCh37                
2     Ensembl 108 Oct 2022 https://oct2022.archive.ensembl.org     108               *
3     Ensembl 107 Jul 2022 https://jul2022.archive.ensembl.org     107                
4     Ensembl 106 Apr 2022 https://apr2022.archive.ensembl.org     106                
5     Ensembl 105 Dec 2021 https://dec2021.archive.ensembl.org     105                
6     Ensembl 104 May 2021 https://may2021.archive.ensembl.org     104                
7     Ensembl 103 Feb 2021 https://feb2021.archive.ensembl.org     103                
8     Ensembl 102 Nov 2020 https://nov2020.archive.ensembl.org     102                
9     Ensembl 101 Aug 2020 https://aug2020.archive.ensembl.org     101                
10    Ensembl 100 Apr 2020 https://apr2020.archive.ensembl.org     100                
11     Ensembl 99 Jan 2020 https://jan2020.archive.ensembl.org      99                
12     Ensembl 98 Sep 2019 https://sep2019.archive.ensembl.org      98                
13     Ensembl 97 Jul 2019 https://jul2019.archive.ensembl.org      97                
14     Ensembl 96 Apr 2019 https://apr2019.archive.ensembl.org      96                
15     Ensembl 95 Jan 2019 https://jan2019.archive.ensembl.org      95                
16     Ensembl 94 Oct 2018 https://oct2018.archive.ensembl.org      94                
17     Ensembl 93 Jul 2018 https://jul2018.archive.ensembl.org      93                
18     Ensembl 92 Apr 2018 https://apr2018.archive.ensembl.org      92                
19     Ensembl 91 Dec 2017 https://dec2017.archive.ensembl.org      91                
20     Ensembl 80 May 2015 https://may2015.archive.ensembl.org      80                
21     Ensembl 77 Oct 2014 https://oct2014.archive.ensembl.org      77                
22     Ensembl 75 Feb 2014 https://feb2014.archive.ensembl.org      75                
23     Ensembl 54 May 2009 https://may2009.archive.ensembl.org      54

[Morris_Chair]

you were right, using your code it works fine :)

Thank you