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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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Update utilityFunctions.R #9

Closed manolisathan closed 5 years ago

manolisathan commented 5 years ago

increase the timeout session of curl from 300 seconds to 3000 for long queries

grimbough commented 5 years ago

Thanks for the pull request. Can I ask what query are you running that requires 50 minutes to complete? biomaRt is supposed to chunk queries into blocks of 500 values as the BioMart backend can be a bit unstable with really large/long queries. It would be unusual for one of these queries to require that length of time.

manolisathan commented 5 years ago

Hi,

I am queuing SNPs and have timeout even if querying one SNP. It’s ok I forked the project and made a local change and works for me so you can ignore my pull request it’s ok. Thanks for the reply. Best,

Manos

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7 Οκτ 2018, 5:23 μμ, ο χρήστης «Mike Smith notifications@github.com» έγραψε:

Thanks for the pull request. Can I ask what query are you running that requires 50 minutes to complete? biomaRt is supposed to chunk queries into blocks of 500 values as the BioMart backend can be a bit unstable with really large/long queries. It would be unusual for one of these queries to require that length of time.

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