Open lambdamoses opened 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.
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.
Hi, metaseqR2, recoup and sitadela are building/checking ok. Thanks for your help. Maybe the issue can be closed.
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 theuseMart()
call, I think the culprit is here:https://github.com/grimbough/biomaRt/blob/605addfbe8b28e47f2ca21e93d0c2a395b1ba2af/R/biomaRt.R#L259
Here the function
.listEnsemblArchives()
has an argumenthttr_config
, which does not have a default, and no argument is passed in the call of.listEnsemblArchives()
inuseMart()
:https://github.com/grimbough/biomaRt/blob/605addfbe8b28e47f2ca21e93d0c2a395b1ba2af/R/ensembl.R#L45