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FredHutch / easybuild-life-sciences

Howto and implementation documentation
https://fredhutch.github.io/easybuild-life-sciences/
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Request for R package Breakaway #137

Closed scottsisco closed 5 years ago

scottsisco commented 5 years ago

Ticket: 167135

Message: Would it be possible to add breakaway (https://github.com/adw96/breakaway) to the R module? That would be very helpful, thanks,

Sam

scottsisco commented 5 years ago

Ticket 169454

Message: Hi,

I was hoping to use this package (https://github.com/adw96/breakaway) on rhino / gizmo, but I ran into some problems. I loaded the R module, but then it looks like phyloseq isn’t a part of that. When I try to install phyloseq (https://joey711.github.io/phyloseq/install.html) I run into this problem:

  /home/sminot/R/x86_64-pc-linux-gnu-library/3.4/rhdf5/libs/rhdf5.so: undefined symbol: ompi_mpi_cxx_op_intercept

Looks like maybe there’s a problem with openmpi? I can’t seem to get around this error. Any idea where I’m going wrong, or would it be possible to put either breakaway or phyloseq into the R module directly?

Thanks, Sam

bmcgough commented 5 years ago

We will add Breakaway to the next R module.

To compile mpi code, you need to use an mpi-aware compiler (actually, just a wrapper). By default you do not get this. Our easyconfigs specify this compiler for all required software package builds. The compiler is part of the OpenMPI package, so it should be available in your environment, provided you have the R environment module loaded when you are trying to install the package in question.

You can set the following, which should work for you:

CC=mpicc CXX=mpicxx

Exporting these into your environment before running R should work.

fizwit commented 5 years ago

ml R/3.5.2-foss-2016b-fh1

library(breakaway)