From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp10.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id wDJRDD0znGNXLgAAbAwnHQ (envelope-from ) for ; Fri, 16 Dec 2022 09:58:37 +0100 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp10.migadu.com with LMTPS id UKJ/Cz0znGPoBwAAG6o9tA (envelope-from ) for ; Fri, 16 Dec 2022 09:58:37 +0100 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id B8ADF2AA4E for ; Fri, 16 Dec 2022 09:58:36 +0100 (CET) Received: from localhost ([::1] helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1p66Xn-0003KW-45; Fri, 16 Dec 2022 03:58:15 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p66Xl-0003KG-38 for guix-science@gnu.org; Fri, 16 Dec 2022 03:58:13 -0500 Received: from mail2-relais-roc.national.inria.fr ([192.134.164.83]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1p66Xi-0007D1-5w for guix-science@gnu.org; Fri, 16 Dec 2022 03:58:12 -0500 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=inria.fr; s=dc; h=from:to:cc:subject:references:date:in-reply-to: message-id:mime-version:content-transfer-encoding; bh=JqFdK0/vjCf+zSDeQqkKG3tFovWXyUPllNog8LqmsaA=; b=Qi6nntTOdnukNbwQHlxJ1eXWZCiHTY0/QZWDXymRxMua2CJ3kdjUmww3 +kr1XoWgcOMDfzsUqV2nBI7C+Ar4B1K09senasUvPgF3arbUfdaTZ6Kqv 5N3WduZ8Ie1WtLiieAEwZwIjbSxY3pUu+lcih+cm3/dnKXSKxYZ17u5XP M=; X-IronPort-AV: E=Sophos;i="5.96,249,1665439200"; d="scan'208";a="83785241" Received: from unknown (HELO ribbon) ([193.50.110.60]) by mail2-relais-roc.national.inria.fr with ESMTP/TLS/ECDHE-RSA-AES256-GCM-SHA384; 16 Dec 2022 09:58:07 +0100 From: =?utf-8?Q?Ludovic_Court=C3=A8s?= To: Lars-Dominik Braun Cc: Lars-Dominik Braun , Simon Tournier , guix-science@gnu.org, Simon Tournier Subject: Re: [PATCH] Add draft post "CRAN, a practical example for being reproducible at large scale using GNU Guix". References: <86y1rkitkk.fsf@gmail.com> <875yefwgtd.fsf@gnu.org> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: Sextidi 26 Frimaire an 231 de la =?utf-8?Q?R=C3=A9vo?= =?utf-8?Q?lution=2C?= jour du Pignon X-PGP-Key-ID: 0x090B11993D9AEBB5 X-PGP-Key: http://www.fdn.fr/~lcourtes/ludovic.asc X-PGP-Fingerprint: 3CE4 6455 8A84 FDC6 9DB4 0CFB 090B 1199 3D9A EBB5 X-OS: x86_64-pc-linux-gnu Date: Fri, 16 Dec 2022 09:58:05 +0100 In-Reply-To: (Lars-Dominik Braun's message of "Fri, 16 Dec 2022 09:00:36 +0100") Message-ID: <87tu1vk9nm.fsf@inria.fr> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/28.2 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Received-SPF: pass client-ip=192.134.164.83; envelope-from=ludovic.courtes@inria.fr; helo=mail2-relais-roc.national.inria.fr X-Spam_score_int: -27 X-Spam_score: -2.8 X-Spam_bar: -- X-Spam_report: (-2.8 / 5.0 requ) BAYES_00=-1.9, DKIM_SIGNED=0.1, DKIM_VALID=-0.1, DKIM_VALID_AU=-0.1, DKIM_VALID_EF=-0.1, RCVD_IN_DNSWL_LOW=-0.7, RCVD_IN_MSPIKE_H2=-0.001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-BeenThere: guix-science@gnu.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-science-bounces+larch=yhetil.org@gnu.org Sender: guix-science-bounces+larch=yhetil.org@gnu.org X-Migadu-Flow: FLOW_IN X-Migadu-Country: US ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=pass header.d=inria.fr header.s=dc header.b=Qi6nntTO; spf=pass (aspmx1.migadu.com: domain of "guix-science-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-science-bounces+larch=yhetil.org@gnu.org"; dmarc=pass (policy=none) header.from=inria.fr ARC-Seal: i=1; s=key1; d=yhetil.org; t=1671181116; a=rsa-sha256; cv=none; b=XQb1LTzYTGJEt3A2y65Oi1ZBuBM7yGbOAKNHywTved6NA42CO/WomQK4EjsDQdXg4atuVU YE7av9d6dNLl/bq+ZRGRoF4aU0DGQ0u06tlpR2rjnI8U92y1SDpWinS5vapmIIGPIVqnzK /uCR9e2PPrv11HhEcXp8VZtY+ypk7xDMo+nvLipxx9Ojx+MmFD4pV28mX0+kIl3/j/CGdz eJ5sebbgoo2Ul5dt7XAbHNHoip7Owv07NP14WvQhaYCCeMyrTAxnAn344NU9H5vLPMRB2J c1PFUI0dJdCiQj6M31CYY0jk9hBTyoYAgr0vTyI8r++CmrkVRYqFwZjerhZUhw== ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1671181116; h=from:from:sender:sender:reply-to:subject:subject:date:date: message-id:message-id:to:to:cc:cc:mime-version:mime-version: content-type:content-type: content-transfer-encoding:content-transfer-encoding: in-reply-to:in-reply-to:references:references:list-id:list-help: list-unsubscribe:list-subscribe:list-post:dkim-signature; bh=JqFdK0/vjCf+zSDeQqkKG3tFovWXyUPllNog8LqmsaA=; b=Gyy9LVN/xR3ubKUMeBtUKBJYFlL+wtNK8pBzAgsdEByKj7Iu4rs/EFIAzd72Oy59eJ/dUh 5vFoh5qnHEfxtplcmj9arcwoz5QREl+d07k+UvtRHGMSSUuRf9eN2iWE4te91y6z9UZbSx uZEJVx6haiu2ltLWGCn97kYPd0fw5HmbBAvM1EmVWjUx1BOtHJAWgjtwSP9auBbVKmKvQj fcj0cDLjE2HnnxmfLsMCLpRtISLbhbV+Im/ZeDUaOZMHbZQYsOf9kOTl2enQ+bFz+nG8Vw TaRqjyq8D1KZQyatPlYjg7ggpRvf3nyhoDTZWUi38iMr0r7b0Eu1O5inzxndAw== X-Migadu-Spam-Score: -9.34 X-Spam-Score: -9.34 X-Migadu-Queue-Id: B8ADF2AA4E Authentication-Results: aspmx1.migadu.com; dkim=pass header.d=inria.fr header.s=dc header.b=Qi6nntTO; spf=pass (aspmx1.migadu.com: domain of "guix-science-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="guix-science-bounces+larch=yhetil.org@gnu.org"; dmarc=pass (policy=none) header.from=inria.fr X-Migadu-Scanner: scn0.migadu.com X-TUID: YBrPqk/QnfJU Hello Lars, Lars-Dominik Braun skribis: >> As mentioned on #guix-hpc, I think it=E2=80=99d be interesting to add a >> reference to https://www.nature.com/articles/s41597-022-01143-6 to >> illustrate the rationale. I think it=E2=80=99s important because R user= s are >> likely to wonder why they=E2=80=99d bother with Guix in the first place. > from the article and the quotes in your patch I feel it=E2=80=99s not cle= ar > the execution failures are the result of mismatched dependencies. Sure, > if I put on my Guix glasses I would assume they are at least partially > responsible, but in =E2=80=9CLimitations of the Study=E2=80=9D they menti= on they did > not investigate causes for the failures. So arguing that code quality > in these open repositories is just terrible =E2=80=93 as we can see from = the > automated cleaning step doing wonders =E2=80=93 would be equally valid. O= r am > I missing something? The point I wanted to make is that, instead of going through the hacks they describe (R version guesswork, source =E2=80=9Ccleanup=E2=80=9D) and y= et being unable to run a large part of the code, we could have a tool that ensures *by construction* that one is going to be able to rerun the code. > You=E2=80=99re right that if the blog post would be published in a non-Gu= ix > context it would need a good reason to use Guix, but in this case I was > just describing a cool new toy for people already using Guix. Is that > mind-set acceptable for posts on hpc.guix.info or do we need a motivating > section? The way I see it, we=E2=80=99re trying to reach out to people who=E2=80=99r= e using R and are interested in reproducible research. Their first reaction might be =E2=80=9Cthis sounds nice, but is it really necessary?=E2=80=9D, or: =E2=80= =9Cisn=E2=80=99t renv/packrat already doing the job?=E2=80=9D Guix fans already know the answers. :-) Having said all that, you=E2=80=99re the author of the article, so let us k= now whether you want to publish it as-is or to modify it, and we=E2=80=99ll go = ahead (I=E2=80=99ll be on IRC today). I think it=E2=80=99s already an insightful= article! Thanks, Ludo=E2=80=99.