From debbugs-submit-bounces@debbugs.gnu.org Thu Dec 12 04:41:34 2019 Received: (at 38576) by debbugs.gnu.org; 12 Dec 2019 09:41:35 +0000 Received: from localhost ([127.0.0.1]:59055 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ifKyU-0001E0-Mu for submit@debbugs.gnu.org; Thu, 12 Dec 2019 04:41:34 -0500 Received: from sender4-of-o51.zoho.com ([136.143.188.51]:21132) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1ifKyT-0001Ds-6h for 38576@debbugs.gnu.org; Thu, 12 Dec 2019 04:41:33 -0500 ARC-Seal: i=1; a=rsa-sha256; t=1576143688; cv=none; d=zohomail.com; s=zohoarc; b=G/HNArxBp/XGR97zK+WUHRRboPkYooQgG0zGbzD0YJidb7F+IIPc+iLSu3LoI7BN3diM6Xtv81rztuEN2ytZhdkI/XYMZL7QgbrZ7JNeSXjbDfPm+KUHBfl0R+oEAJWCVb5M8jjoHR89O7D8kdTNwq8eS2s9n7oLXG4+RIG/m10= ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=zohomail.com; s=zohoarc; t=1576143688; h=Content-Type:Content-Transfer-Encoding:Cc:Date:From:In-Reply-To:MIME-Version:Message-ID:References:Subject:To; bh=4cA0M6/xISQEqAtb6vC9jnw10pQMMV7FjGOIiixQ2dM=; b=mbuQ6PkRG4nAEgheVHeik9tKg2akOX8bsxWR34BGN/N4/u8YJb6H+XloA+c5/Itl7I36lRb2KOEn6laPgnxoVoi2KKsklBUo1aWhsWaMMRewYShDequGnQnGTMq8GVIvfxPH+waV3ONDB+PRAUfHXOxbC9IeOxuv281ZZloaEa8= ARC-Authentication-Results: i=1; mx.zohomail.com; dkim=pass header.i=elephly.net; spf=pass smtp.mailfrom=rekado@elephly.net; dmarc=pass header.from= header.from= DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; t=1576143688; s=zoho; d=elephly.net; i=rekado@elephly.net; h=References:From:To:Cc:Subject:In-reply-to:Date:Message-ID:MIME-Version:Content-Type:Content-Transfer-Encoding; bh=4cA0M6/xISQEqAtb6vC9jnw10pQMMV7FjGOIiixQ2dM=; b=YZzkKHQ/C47IGvjRbMa0k00poPzj4gYJnWU0Ot5dxyRDUMRohEGiMb+awyR8XpM0 9X/na0GTZ2evbxkUWzjdxawRW/kslRtqLZ4rb0FaQYqU93WmREcg0+/XIk/S7b9Sh8G 6LpAdkhCN92otLN0U3kuUwLJKXj35EmZtX9cB0Vk= Received: from localhost (p54AD4459.dip0.t-ipconnect.de [84.173.68.89]) by mx.zohomail.com with SMTPS id 1576143687109709.435745777887; Thu, 12 Dec 2019 01:41:27 -0800 (PST) References: <20191212074613.GA11713@zpidnp36> User-agent: mu4e 1.2.0; emacs 26.3 From: Ricardo Wurmus To: Lars-Dominik Braun Subject: Re: [bug#38576] [PATCH] gnu: r-irkernel: Fix R kernel loading In-reply-to: <20191212074613.GA11713@zpidnp36> X-URL: https://elephly.net X-PGP-Key: https://elephly.net/rekado.pubkey X-PGP-Fingerprint: BCA6 89B6 3655 3801 C3C6 2150 197A 5888 235F ACAC Date: Thu, 12 Dec 2019 10:41:24 +0100 Message-ID: <87wob13mpn.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-ZohoMailClient: External X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 38576 Cc: 38576@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) 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/kernel= spec")) > + ;; 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=E2=80=99s 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 (IRkerne= l) > + ("r-minimal" ,r-minimal) > ("r-pbdzmq" ,r-pbdzmq) > ("r-repr" ,r-repr) > ("r-uuid" ,r-uuid))) This doesn=E2=80=99t look right to me. It seems wrong for any R package to propagate R itself. The R_LIBS_SITE variable is =E2=80=9Cattached=E2=80=9D= to =E2=80=9Cr-minimal=E2=80=9D, so when that is installed R will find the r-ir= kernel package. Am I missing something? -- Ricardo