[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [PATCH] Add draft post "CRAN, a practical example for being reproduc

From: Ludovic Courtès
Subject: Re: [PATCH] Add draft post "CRAN, a practical example for being reproducible at large scale using GNU Guix".
Date: Tue, 13 Dec 2022 14:53:34 +0100
User-agent: Gnus/5.13 (Gnus v5.13) Emacs/28.2 (gnu/linux)


Lars-Dominik Braun <> skribis:

>> Applied, thanks.  It is under drafts/ [1].  Last round proofread before
>> publishing.  On Friday?
> Friday sounds good. I’m attching minor changes to the synax highlighting.

We missed one Friday but there are plenty coming up.  :-)

As mentioned on #guix-hpc, I think it’d be interesting to add a
reference to to
illustrate the rationale.  I think it’s important because R users are
likely to wonder why they’d bother with Guix in the first place.

Here’s a proposal in that direction; feel free to take it, tear it down,
change it, or whatever.


diff --git a/drafts/ b/drafts/
index c691163..28f6108 100644
--- a/drafts/
+++ b/drafts/
@@ -60,6 +60,42 @@ pre-built substitutes to speed up installation times. 
 reproducing environments would include fewer steps if the package
 recipes were available to anyone by default.
+## Why deploy R software with Guix anyway?
+At this point, perhaps you're wondering: R is stable, and tools such as
+[Packrat]( let me save and restore
+the exact R package versions I need.  While this might seem “good
+enough”, we can already tell this approach [has a number of
+one of which being that it cannot handle dependencies not written in
+R—such as R itself.
+A [study published in *Nature Scientific Data* in February
+2022]( gives empirical
+insight into this:
+> _[We] retrieve and analyze more than 2000 replication datasets with
+> over 9000 unique R files published from 2010 to 2020. Second, we
+> execute the code in a clean runtime environment to assess its ease of
+> reuse. […] We find that 74% of R files failed to complete without
+> error in the initial execution, while 56% failed when code cleaning
+> was applied, showing that many errors can be prevented with good
+> coding practices._
+Three fourth of those R packages fail to run out of the box—this is
+huge.  How did the authors re-execute this code?
+> _We re-executed R code from each of the replication packages using
+> three R software versions, R 3.2, R 3.6, and R 4.0, in a clean
+> environment._
+Despite this guesswork, coupled with automatic “source cleaning”, the
+authors found that most packages still fail to run.
+The motivation to deploy R software with Guix becomes clear: it’s the
+ability to automatically redeploy the same software environment, at
+different points in time, on different machines.
 ## Introducing guix-cran
 GNU Guix provides a mechanism called “channels”,

reply via email to

[Prev in Thread] Current Thread [Next in Thread]