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Re: [rb-general] Paper preprint: Reproducible genomics analysis pipeline
From: |
Ricardo Wurmus |
Subject: |
Re: [rb-general] Paper preprint: Reproducible genomics analysis pipelines with GNU Guix |
Date: |
Fri, 11 May 2018 10:19:54 +0200 |
User-agent: |
mu4e 1.0; emacs 25.3.1 |
Ludovic Courtès <address@hidden> writes:
> Perhaps we could add to Autoconf-Archive (if it doesn’t have such things
> already) macros to deal with the R and Python stuff you had to deal
> with? And then publish a simple template that people could use as a
> starting point.
I submitted my macros for R packages (and they have been accepted), but
I actually don’t really like them because they are not as useful as it
may seem. While they do check for R packages in the environment at
configure time, nothing is done to record the environment necessary to
access these packages.
That’s a general problem for software that depends on search path
environment variables. I can’t just record the location of each
individual R package that was detected and use that to set up the
environment at runtime. The R packages have other runtime dependencies
that would also need to be recorded.
It’s not ideal.
--
Ricardo