From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp12.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms5.migadu.com with LMTPS id cAa2MkZ4zWI7aQAAbAwnHQ (envelope-from ) for ; Tue, 12 Jul 2022 15:33:58 +0200 Received: from aspmx1.migadu.com ([2001:41d0:2:bcc0::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp12.migadu.com with LMTPS id gPipMkZ4zWINLgEAauVa8A (envelope-from ) for ; Tue, 12 Jul 2022 15:33:58 +0200 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 9D3F48819 for ; Tue, 12 Jul 2022 15:33:58 +0200 (CEST) Received: from localhost ([::1]:37116 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1oBG1V-0008IR-KE for larch@yhetil.org; Tue, 12 Jul 2022 09:33:57 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:33554) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1oBFjD-0000Hm-4R for bug-guix@gnu.org; Tue, 12 Jul 2022 09:15:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:48040) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1oBFjC-000599-EI for bug-guix@gnu.org; Tue, 12 Jul 2022 09:15:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1oBFjC-0001u4-9h for bug-guix@gnu.org; Tue, 12 Jul 2022 09:15:02 -0400 Subject: bug#49314: Stan package broken Resent-From: Maxim Cournoyer Original-Sender: "Debbugs-submit" Resent-To: bug-guix@gnu.org Resent-Date: Tue, 12 Jul 2022 13:15:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: cc-closed 49314 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Kyle Andrews Cc: 49314-done@debbugs.gnu.org Mail-Followup-To: 49314@debbugs.gnu.org, maxim.cournoyer@gmail.com, kyle.c.andrews@gmail.com Received: via spool by 49314-done@debbugs.gnu.org id=D49314.16576316787200 (code D ref 49314); Tue, 12 Jul 2022 13:15:02 +0000 Received: (at 49314-done) by debbugs.gnu.org; 12 Jul 2022 13:14:38 +0000 Received: from localhost ([127.0.0.1]:41934 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oBFio-0001s4-Be for submit@debbugs.gnu.org; Tue, 12 Jul 2022 09:14:38 -0400 Received: from mail-qt1-f181.google.com ([209.85.160.181]:36432) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1oBFim-0001rs-S7 for 49314-done@debbugs.gnu.org; Tue, 12 Jul 2022 09:14:37 -0400 Received: by mail-qt1-f181.google.com with SMTP id 23so9261567qtt.3 for <49314-done@debbugs.gnu.org>; Tue, 12 Jul 2022 06:14:36 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=from:to:cc:subject:references:date:in-reply-to:message-id :user-agent:mime-version; bh=kO4sD3okq3OGmCTOvfodIylf0P0eMY8GP9zDZ3OaJXM=; b=MS79gvoXgOM2szUnQdJferCOt6Oe01V+Hn74yy0GolzObbff5pTlA/6x2UZDQNBC/C XvdXagWBIgow6wPlmonQ3dFSHZIrmfAMbC1MF4KuBZu1ajPba2M2cpx69K9cJ0/MlUdn pdFXch4gx47t9ejDQoJiaq8BxMLF1J1F1Hx8QNTngjn1B3heFwZMx5jnq2oOJKNnHu62 dOZuZ2ZtxfaFB8Ub4SPsBLa1RxxKMOFYJtLHb9GwVnsm0sDi6aIqiNB4ShONrTM49v3R O+UjWnJufR1sz8DtXIYoYaZdBgIYbJi5Gq9sEEls/q3kGPxlMaBtDeeHxUi7Aa8MoQQu aAQA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=x-gm-message-state:from:to:cc:subject:references:date:in-reply-to :message-id:user-agent:mime-version; bh=kO4sD3okq3OGmCTOvfodIylf0P0eMY8GP9zDZ3OaJXM=; b=VRvqX1VEHYWxiI7rZ/3nlysjhfmWHhGYlF8bzuUTYNmjB1vq0nR0jJfO9Ge+Jc86jk r4hCLHsvnNX3eVmBFlyr032ZQ7gpznBmtGDKwomvFndJuhHbNrzQVjq4WAhgLRh2VHdk FKrqAnCEfcMukG0m7NeqS0u2oTpyUcpgPbS1DE4CXfr/Ol+uqDX2JZ8UYURCvROoFec2 0C/35bwmUh7RIoGdtH+BfUcYfeQmHnr5cbBiUe39IhY/wmg3qA1Ud8IE1ys+WkGu4gQk eihH1IjzlXKP8CClgfP0x+VCKr4CVEJK5OEF0LgJAKcSageWjqH8vFAZb3HeOjoFYACV WoKw== X-Gm-Message-State: AJIora8apiCKjKNCa06z2r+k91PzlOpxqHEit6/uQCOn+dfv3p8kiJpz zLuBTlZw2bURX7pa6vgyfW5r3F7xT2T03y+D X-Google-Smtp-Source: AGRyM1uy4WFiztTzI6QfYSSqjC242yk1nuYIZzNTcSXvt7rSJS5IO887Jf0fMYyN9S7UlIqVgH1pwg== X-Received: by 2002:ac8:5c55:0:b0:31e:b3ec:1903 with SMTP id j21-20020ac85c55000000b0031eb3ec1903mr8512575qtj.524.1657631670854; Tue, 12 Jul 2022 06:14:30 -0700 (PDT) Received: from hurd (dsl-155-226.b2b2c.ca. [66.158.155.226]) by smtp.gmail.com with ESMTPSA id i14-20020a05620a248e00b006b555509398sm9401631qkn.136.2022.07.12.06.14.29 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Tue, 12 Jul 2022 06:14:30 -0700 (PDT) From: Maxim Cournoyer References: <878s2q1ef4.fsf@gmail.com> Date: Tue, 12 Jul 2022 09:14:29 -0400 In-Reply-To: <878s2q1ef4.fsf@gmail.com> (Kyle Andrews's message of "Thu, 01 Jul 2021 07:06:39 -0400") Message-ID: <8735f6a2x6.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/28.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Migadu-Flow: FLOW_IN X-Migadu-To: larch@yhetil.org X-Migadu-Country: US ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=yhetil.org; s=key1; t=1657632838; 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:resent-to:resent-from:resent-sender: resent-message-id:in-reply-to:in-reply-to:references:references: list-id:list-help:list-unsubscribe:list-subscribe:list-post: dkim-signature; bh=kO4sD3okq3OGmCTOvfodIylf0P0eMY8GP9zDZ3OaJXM=; b=ll9Vf+9cqViuuYs5EBp5NtdAZ1lWSzBN3WxEgRYuDVd9DHUgoSr2KZW10zItkGrms4xeK6 bgjQyT+I0g4HSRfddKDQVV3w8FMqVcAiFTN6MJ+nfl6M2QjadtBNTbidV1GvtAWh3w7M+u eEwYUtmX+jdV43TSIXu5vSM8+jICgjkUzLR9v37fXtJ7cT4aZvsafrzjAAghkEvT3QcZf6 ZEQ71XtqoM/iCk1d+AHtQ/VKeAns8xNX7ln8A7bkNj2pQ7qer3Zu0O5ifc+e6WzDuoDb1r ZQhwPA+yN2XXU/ufJaG2QB3Xb4FjRjL2jim4j4bDjzY1HW1DBoZhOQmBB/lCeg== ARC-Seal: i=1; s=key1; d=yhetil.org; t=1657632838; a=rsa-sha256; cv=none; b=QW6QN6AC+i0bOc+zCQn9o4yg2BrtwPyZtbvFNdk4v65DpdlqURVCwVhv5nuaVO8qPORPUS D88NLVa2ewbTpWs6I8JMzQbpwQQIAeGwes31piesgDHGCPOldmSc6XfA/We2/6KUu37y08 Ib/yCrvLukEsZf3U3ph7dP+EtUc2crM0gVF4JuWejVM0pixd0Q/EnqUp8RHrCtmUDHxJTZ 4QcNgJMvSjN4hAZ9U/Z/0LzxqN1JdZmrn5BCODB4YTPmJuVhCsUR7w88fgvL385cVDF8O/ RrdvHMxuXKannAigLrq8kCUx39Rr+u9Y2z14yyQSzQmH+ixyE60xEKgmpzUzww== ARC-Authentication-Results: i=1; aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=MS79gvoX; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Spam-Score: 6.05 Authentication-Results: aspmx1.migadu.com; dkim=fail ("headers rsa verify failed") header.d=gmail.com header.s=20210112 header.b=MS79gvoX; dmarc=fail reason="SPF not aligned (relaxed)" header.from=gmail.com (policy=none); spf=pass (aspmx1.migadu.com: domain of "bug-guix-bounces+larch=yhetil.org@gnu.org" designates 209.51.188.17 as permitted sender) smtp.mailfrom="bug-guix-bounces+larch=yhetil.org@gnu.org" X-Migadu-Queue-Id: 9D3F48819 X-Spam-Score: 6.05 X-Migadu-Scanner: scn1.migadu.com X-TUID: PuTYVLaaUY5k Hi, Kyle Andrews writes: > Hello, > > I tried to run a "Hello World" stan model using the r-rstan package. > > #+BEGIN_SRC R > stancode="data { > int N; > vector[N] x; > vector[N] y; > } > parameters { > real alpha; > real beta; > real sigma; > } > model { > y ~ normal(alpha + beta * x, sigma); > } > " > stan_lm = stan(model_code = stancode) > #+END_SRC > > > Running that code I get the error: > > #+BEGIN_EXAMPLE > Error in dyn.load(libLFile) : > unable to load shared object '/tmp/Rtmp1AXXXr/file1ffd36a95fa3.so': > /gnu/store/741057r2x06zwg6zcmqmdyv51spm6n9i-gfortran-7.5.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /tmp/Rtmp1AXXXr/file1ffd36a95fa3.so) > Error in sink(type = "output") : invalid connection > #+END_EXAMPLE > > I setup my environment with: > > : guix environment --ad-hoc r-rstan r-rstanarm r I've tried exercising some of the things shown at https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started in 'guix shell r-rstan r-rstanarm r-minimal' and it seems to work. I'm on Guix commit 17892c5. Closing. Thanks for the report! Maxim