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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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Missing R package 'copynumber' when running amber and cobalt: #621

Closed AndreasSandJespersen closed 3 weeks ago

AndreasSandJespersen commented 4 weeks ago

Hi there,

I'm having some issues running amber and cobalt. This is an issue with my java installation. Although I have a copynumber available in my version of R, java is not using this version of R it seems. It is however loading some version as it is able to load the dplyr package. To be clear I'm working on an HPC where I load these tools individually, so there's not much reason to think that my version of R has much to do with my version of java. I've tried looking online for help with this, but haven't had much success. I understand this isn't really an issue with either of your tools, but I was wondering if you could point me in the right direction. The java version I'm using is jdk/21.0.1.

Thanks, Andreas

hongwingl commented 4 weeks ago

Amber and Cobalt uses RScript on the PATH to run R. Are you able to make sure the correct RScript is on the PATH variable?

AndreasSandJespersen commented 3 weeks ago

Hi thanks for your quick reply

And thanks for the clarification. I had a second version of R loaded in a seperate module (gridss), which did not have copynumber installed. I.e. there were two Rscripts on the PATH variable.