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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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dump error #90

Open abrionne opened 8 months ago

abrionne commented 8 months ago

It's seems that bioMart have some difficulites to connect to Ensembl. Several people ask me why my package (ViSEAGO) no works with Ensembl from several days.

It's seems provide from collect() according the printed error.

library(biomaRt) listEnsembl() Error in collect(): ! Failed to collect lazy table. Caused by error in db_collect(): ! Arguments in ... must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name? Run rlang::last_trace() to see where the error occurred.

sessionInfo() R version 4.3.2 (2023-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Linux Mint 21.2

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale: [1] LC_CTYPE=fr_FR.UTF-8 LC_NUMERIC=C LC_TIME=fr_FR.UTF-8 LC_COLLATE=fr_FR.UTF-8 LC_MONETARY=fr_FR.UTF-8
[6] LC_MESSAGES=fr_FR.UTF-8 LC_PAPER=fr_FR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Paris tzcode source: system (glibc)

grimbough commented 8 months ago

This looks like the error reported in https://github.com/grimbough/biomaRt/issues/89 which is fixed by updating to the latest version of BiocFileCache.

abrionne commented 8 months ago

oh thank you!

sorry for the inconvenience

Aurélien