Mac Builders Error - Githubissues

lgatto / pRoloc

A unifying bioinformatics framework for organelle proteomics

http://lgatto.github.io/pRoloc/

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Mac Builders Error #100

Closed LiNk-NY closed 7 years ago

LiNk-NY commented 7 years ago

Hi Laurent, @lgatto There are issues with the package on our Mac builders.

Please see: http://bioconductor.org/checkResults/devel/bioc-LATEST/pRoloc/

It seems like this is related to BioMart.

> getGOFromFeatures(fn, params = dunkley2006params)
Error in getBM(attributes = c(params@filter, attrs, "go_linkage_type"),  : 
  Query ERROR: caught BioMart::Exception::Usage: Attribute go_accession NOT FOUND
Calls: getGOFromFeatures -> getBM
Execution halted

Regards, Marcel

lgatto commented 7 years ago

That looks like a biomart issue. I recently had to make changes in my code because attribute names had changed, to address the consistent errors on all platforms. I don't understand why it only fails on Mac here. I am testing locally to see if I can reproduce this. If not, I don't see what I can do.

lgatto commented 7 years ago

Ok, seems to be another change in fucking biomart. I'm on it.

LiNk-NY commented 7 years ago

Thanks Laurent!

lgatto commented 7 years ago

Fixed with commit 0edf3425b97613267bae96a5069564f04864a6b2.