[R-pkg-devel] Package cannot connect to Ensembl

[Walter, Vonn]

Hi Everyone,

One of the functions in my DiNAMIC.Duo package on CRAN uses the biomaRt package to download gene position information from the Ensembl website.  Currently I use one of the Ensembl archives (ensemblHost=http://aug2020.archive.ensembl.org in the code below).  The archive is unavailable periodically, so the function includes the following code in an effort to ��fail gracefully,�� as is required by CRAN:

statusCode = curl::curl_fetch_memory(ensemblHost)$status_code
if (statusCode != 200)
{
stop(paste(ensemblHost, "currently not available"))
}

I recently received a notice from CRAN stating that that an error was received when checking examples with �Vrun-donttest.  Specifically, the following:

Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! SSL connect error [aug2020.archive.ensembl.org]:
OpenSSL/3.2.4: error:0A0000C6:SSL routines::packet length too long
Backtrace:
    �g
1. �|�wDiNAMIC.Duo::dataPrep(X = luadSubset, Y = NULL)
2.   �|�wbiomaRt::useMart(...)
3.     �|�wbiomaRt:::.useMart(...)
4.       �|�wbiomaRt:::.listMarts(...)
5.         �|�wbiomaRt:::bmRequest(...)
6.           �|�whttr2::req_perform(request)
7.             �|�whttr2:::handle_resp(req, resp, error_call = error_call)
8.               �|�wrlang::cnd_signal(resp)
Execution halted

Any suggestions on how to revise the existing code would be greatly appreciated.  Thanks in advance for your reply.

Best,

Vonn

Vonn Walter, PhD
Associate Professor
Department of Public Health Sciences
Department of Molecular and Precision Medicine
Co-Director
Biostatistics and Bioinformatics Shared Resource
Penn State Cancer Institute
Penn State College of Medicine
Pronouns:  he/him/his


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