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grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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argument "httr_config" is missing, with no default in useMart() call for archival versions #50

Open lambdamoses opened 2 years ago

lambdamoses commented 2 years ago

I'm the maintainer of the Bioconductor package BUSpaRse, which uses biomaRt. Today, I got an error from the build of the devel version from a call of useMart() for archival version 99 of Ensembl: argument "httr_config" is missing, with no default. When I debugged and stepped into the useMart() call, I think the culprit is here:

https://github.com/grimbough/biomaRt/blob/605addfbe8b28e47f2ca21e93d0c2a395b1ba2af/R/biomaRt.R#L259

Here the function .listEnsemblArchives() has an argument httr_config, which does not have a default, and no argument is passed in the call of .listEnsemblArchives() in useMart():

https://github.com/grimbough/biomaRt/blob/605addfbe8b28e47f2ca21e93d0c2a395b1ba2af/R/ensembl.R#L45

hpages commented 2 years ago

Hi Mike @grimbough ,

FWIW this also affected Bioconductor packages customProDB, DominoEffect, metaseqR2, recoup, Sushi, and wiggleplotr on today's build report (Oct 18, 2021) e.g. https://bioconductor.org/checkResults/3.14/bioc-LATEST/Sushi/nebbiolo2-buildsrc.html

H.

pmoulos commented 2 years ago

Hi @grimbough, I can confirm this (I am the maintainer of metaseqR2 and recoup) and affects also the package sitadela. I can also confirm that the packages are building/checking OK with the older version of biomaRt. Thanks in advance.

pmoulos commented 2 years ago

Hi, metaseqR2, recoup and sitadela are building/checking ok. Thanks for your help. Maybe the issue can be closed.