(created using eb --new-pr)

I ran into this issue: IRkernel/IRkernel#388

At least two more people (@zao and eylenth) encountered this issue as well.

There are two options to run IRkernel on headless nodes: run an Xvfb so that the png device can still use the Xlib bitmaptype, or change the default bitmaptype to cairo. The latter makes most sense to me, since the cairo bitmaptype generally produces nicer plots to (e.g. can use TrueType fonts).

To do that, the kernelspec should read

{"argv": ["R", "--slave", "-e", "options(bitmapType='cairo'); IRkernel::main()", "--args", "{connection_file}"],
 "display_name":"R",
 "language":"R"
}

instead of

{"argv": ["R", "--slave", "-e", "IRkernel::main()", "--args", "{connection_file}"],
"display_name":"R",
"language":"R"
}

i.e. it should run the options(bitmapType='cairo') before starting the actual kernel.

Since running IRkernel on headless nodes is quite a common use case in the EasyBuild community, and since I've heard from @zao and eylenth that they hit the same issue, it makes sense to me to 'fix' this in the EasyConfig. I do that by adding

'sed -i \'s/"IRkernel::main()"/"options(bitmapType=\\x27cairo\\x27); IRkernel::main()"/g\' %s/kernels/ir/kernel.json' % local_kerneldir

To the postinstallcmds (which are already used to 'install' the kernelspec).

We can discuss if this also needs to be backported to older EasyConfigs, but I think the most important thing is that we adopt this in future versions.