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R and R modules (and a Ruby twist)
From: |
Pjotr Prins |
Subject: |
R and R modules (and a Ruby twist) |
Date: |
Thu, 24 Sep 2015 10:37:32 +0200 |
User-agent: |
Mutt/1.5.21 (2010-09-15) |
When we add an R module, such as R-qtl, the R-build-system does not
provide R itself as a propagated input, i.e., the R interpreter is not
in the profile. In the R world this is kinda odd. Almost all modules
used from R. I.e. start up R and
library(qtl)
do something with R/qtl
Would have use people use that module in interactive mode. In the
current package install R is not included as a symlink and needs to be
separately installed.
Is this really a good idea?
Personally I think R should be in the path because that is the only
way a module is useful to 99% of users.
We can actually instruct users to install R separately (no different
from other packaging systems). Note that this opens its own can of
worms when the two are out of sync. I can imagine Guix modules having
different R's as dependencies.
It is one other thing I am trying to think through. With a standard R
distribution, every package is strictly aligned with the interpreter
(they get installed from inside R).
With Guix' rolling model of package updates modules may go out of sync
- even if they are correctly linked with an underlying R. So mixing
interpreters and modules/packages may potentially give problems.
The Ruby twist:
With Ruby we use the major version numbering of the interpreter to
share modules (named gems) - i.e. anything 2.2.x gets installed in the
profile under 2.2.0 - this is the default model in the Ruby world. I
am actually not completely happy with this model because it does not
isolate interpreters and the installed gems. Even though it `works' in
almost 100% of use cases. What happens now, for example, is that a
Ruby with ssl and and Ruby without ssl always share gems. This is
pretty evil. I would prefer incorporating the SHA value of the
interpreter in the Guix profile to host gems. That would guarantee
perfect isolation and is pretty easy to achieve.
Pj.
- [PATCH] Add python2-seqmagick., Ben Woodcroft, 2015/09/17
- Re: [PATCH] Add python2-seqmagick., Ricardo Wurmus, 2015/09/17
- Re: [PATCH] Add python2-seqmagick., Ben Woodcroft, 2015/09/19
- Re: [PATCH] Add python2-seqmagick., Pjotr Prins, 2015/09/21
- Re: [PATCH] Add python2-seqmagick., Ludovic Courtès, 2015/09/21
- Re: [PATCH] Add python2-seqmagick., Ben Woodcroft, 2015/09/21
- Re: [PATCH] Add python2-seqmagick., Pjotr Prins, 2015/09/24
- Re: [PATCH] Add python2-seqmagick., Ludovic Courtès, 2015/09/24
- R and R modules (and a Ruby twist),
Pjotr Prins <=
- Re: R and R modules (and a Ruby twist), Ricardo Wurmus, 2015/09/24
- Re: R and R modules (and a Ruby twist), Pjotr Prins, 2015/09/24
- Re: R and R modules (and a Ruby twist), Ricardo Wurmus, 2015/09/25
- Re: [PATCH] Add python2-seqmagick., Ricardo Wurmus, 2015/09/25
- Re: [PATCH] Add python2-seqmagick., Ben Woodcroft, 2015/09/25
- Re: [PATCH] Add python2-seqmagick., Ricardo Wurmus, 2015/09/28
Re: [PATCH] Add python2-seqmagick., Cyril Roelandt, 2015/09/21