Question

biomaRt 'cache found' message

0

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Ni-Ar ▴ 10

@ni-ar-15663

Last seen 4.2 years ago

Spain/Barcelona

Hi Mike,

I love R package you're maintaining biomaRt! However there's a wee annoying thing. The message "Cache found", when getBM() finds the cache.

Is there a way to suppress this message? If not, it'd be great if the option verbose = F would silence that message as well.

Just a suggestion.

Best regards, Nicco

Biomart v 2.42.0

biomart suggestion cache message • 1.0k views

ADD COMMENT • link updated 4.2 years ago by Mike Smith ★ 6.5k • written 4.2 years ago by Ni-Ar ▴ 10

score 2 · Accepted Answer · 2020-02-10

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Mike Smith ★ 6.5k

@mike-smith

Last seen 5 hours ago

EMBL Heidelberg

I'll make this optional in a future version. Out of intrest, why is it annoying? Does it get in the way in your specific use case?

For now you can wrap the getBM() call in suppressMessages() which should stop it being printed.

ADD COMMENT • link 4.2 years ago Mike Smith ★ 6.5k

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Oh thanks! Okay, it's not super annoying... it's just that I was debugging some code that prints to stdout relevant info and has getBM() and getSequence() in a for loop. I had to scroll through the "Cache found" messages to find my problem.

My suggestion is more like to make the verbose = F option really stop any kind of printing. Anyway your suppressMessages() workaround works like a charm! Thanks!

ADD REPLY • link 4.2 years ago Ni-Ar ▴ 10

1

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Cool, thanks for the feedback. I included the message so I knew when the cache was being used during development. I thought it might be useful/interesting to a user, but I can also see it might be annoying. I'll make a verbose = FALSE option t=so it's more consistent with the rest of biomaRt.

ADD REPLY • link 4.2 years ago Mike Smith ★ 6.5k