biomaRt not working - lazy table error
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1
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Abhishek ▴ 10
@1d077953
Last seen 1 day ago
Canada

Hi everyone,

I am trying to annotate ensembl gene IDs. I have used the following code to load and select a biomaRt dataset:

ensembl <- useEnsembl(biomart="ensembl", dataset="mmusculus_gene_ensembl", mirror="www")  

This returns the error

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

This did not happen before and I have tried reinstall and reload biomaRt, dplyr, and tidyverse but none of that helps. I have also tried using other mirrors such as useast, uswest, and asia.

Because of this, getBM()... does not work either. Any help would be appreciated!

-shasabhi1

error lazy R biomaRt table • 4.3k views
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5
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Mike Smith ★ 6.4k
@mike-smith
Last seen 8 hours ago
EMBL Heidelberg

As James alluded to, this is actually an incompatibility between dbplyr and BiocFileCache, and biomaRt is an innocent bystander!

The problem in BiocFileCache should already have been fixed if you update to version 2.10.1 or greater (see BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR for more details).

This might necessitate updating to Bioconductor 3.18 if you aren't using that already. You can do that via:

BiocManager::install(version = "3.18")
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This was very helpful, thanks Mike!

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I tried install("BiocFileCache") and it installed version 2.6.1. And because I am using R version 4.2.2 so I couldn't upgrade BiocManager to 3.18.

I am afraid upgrading R may cause a rabbit hole of dependency issues with other packages in an ongoing project.

Would there be another solution?

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1
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You can try downgrading dbplyr instead. To install version 2.3.4 (I think that's the last working version) you can use:

install.packages('https://cran.r-project.org/src/contrib/Archive/dbplyr/dbplyr_2.3.4.tar.gz', repos = NULL)

However R will try very hard to upgrade again, asking you every time you install a new package, so you'll have to be vigilant that it doesn't get upgraded again with you reaslising.

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@james-w-macdonald-5106
Last seen 11 hours ago
United States
library(BiocManager)
install("BiocFileCache")

Then try again.

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None of the suggestions worked me :(

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1
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This doesn't give anyone much information to work with. I'd suggest creating a new post, and follow the posting guide by providing the code you're running, any error messages you're seeing, and the output of sessionInfo(). That way you're much more likely to get a helpful response.

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