From: Ricardo Wurmus <rekado@elephly.net>
To: Lars-Dominik Braun <ldb@leibniz-psychology.org>
Cc: 38576@debbugs.gnu.org
Subject: [bug#38576] [PATCH] gnu: r-irkernel: Fix R kernel loading
Date: Thu, 12 Dec 2019 10:41:24 +0100 [thread overview]
Message-ID: <87wob13mpn.fsf@elephly.net> (raw)
In-Reply-To: <20191212074613.GA11713@zpidnp36>
Hi Lars-Dominik,
> * gnu/packages/cran.scm (r-irkernel): Absolute path to R binary
> [propagated-inputs]: Generate proper search paths by adding r-minimal
> ---
> gnu/packages/cran.scm | 8 ++++++++
> 1 file changed, 8 insertions(+)
>
> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
> index 765747ea3b..c54a076014 100644
> --- a/gnu/packages/cran.scm
> +++ b/gnu/packages/cran.scm
> @@ -12414,6 +12414,12 @@ running IRkernel session.")
> "--name" "ir"
> "--prefix" out
> (string-append out "/site-library/IRkernel/kernelspec"))
> + ;; Record the absolute file name of the 'R' executable in
> + ;; 'kernel.json'.
> + (substitute* (string-append out "/share/jupyter"
> + "/kernels/ir/kernel.json")
> + (("\\[\"R\",")
> + (string-append "[\"" (which "R") "\",")))
> #t))))))
> (inputs
> `(("jupyter" ,jupyter)))
This part looks fine to me, though I wonder if that’s what users of this
package would expect. Is there an expectation that the effective R is
defined by the environment? Or would that not work anyway?
> @@ -12423,6 +12429,8 @@ running IRkernel session.")
> ("r-evaluate" ,r-evaluate)
> ("r-irdisplay" ,r-irdisplay)
> ("r-jsonlite" ,r-jsonlite)
> + ;; sets R_LIBS_SITE, so R can actually find this package (IRkernel)
> + ("r-minimal" ,r-minimal)
> ("r-pbdzmq" ,r-pbdzmq)
> ("r-repr" ,r-repr)
> ("r-uuid" ,r-uuid)))
This doesn’t look right to me. It seems wrong for any R package to
propagate R itself. The R_LIBS_SITE variable is “attached” to
“r-minimal”, so when that is installed R will find the r-irkernel
package. Am I missing something?
--
Ricardo
next prev parent reply other threads:[~2019-12-12 9:42 UTC|newest]
Thread overview: 11+ messages / expand[flat|nested] mbox.gz Atom feed top
2019-12-12 7:46 [bug#38576] [PATCH] gnu: r-irkernel: Fix R kernel loading Lars-Dominik Braun
2019-12-12 9:41 ` Ricardo Wurmus [this message]
2019-12-12 10:04 ` Lars-Dominik Braun
2019-12-12 19:13 ` zimoun
2019-12-19 22:47 ` Ludovic Courtès
2020-01-02 7:35 ` Lars-Dominik Braun
2020-01-02 11:43 ` Ludovic Courtès
2020-01-03 15:12 ` bug#38576: " Ludovic Courtès
2020-01-06 18:14 ` [bug#38576] " zimoun
2020-01-07 21:02 ` Roel Janssen
2020-01-07 23:01 ` Ludovic Courtès
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