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Thu, 01 Jul 2021 04:06:41 -0700 (PDT) Received: from x1 ([2600:6c48:6d7f:e731::23a]) by smtp.gmail.com with ESMTPSA id y3sm9900275ioy.46.2021.07.01.04.06.39 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 01 Jul 2021 04:06:40 -0700 (PDT) User-agent: mu4e 1.4.15; emacs 27.2 From: Kyle Andrews To: bug-guix@gnu.org Subject: Stan package broken Date: Thu, 01 Jul 2021 07:06:39 -0400 Message-ID: <878s2q1ef4.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain Received-SPF: pass client-ip=2607:f8b0:4864:20::d32; envelope-from=kyle.c.andrews@gmail.com; helo=mail-io1-xd32.google.com X-Spam_score_int: -20 X-Spam_score: -2.1 X-Spam_bar: -- X-Spam_report: (-2.1 / 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, FREEMAIL_FROM=0.001, RCVD_IN_DNSWL_NONE=-0.0001, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.3 (-) X-Debbugs-Envelope-To: submit 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: -2.3 (--) 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 From debbugs-submit-bounces@debbugs.gnu.org Fri Jul 23 01:25:47 2021 Received: (at 49314) by debbugs.gnu.org; 23 Jul 2021 05:25:48 +0000 Received: from localhost ([127.0.0.1]:42123 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m6ngx-00017e-Mf for submit@debbugs.gnu.org; Fri, 23 Jul 2021 01:25:47 -0400 Received: from out0.migadu.com ([94.23.1.103]:62672) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1m6ngs-00017Q-0q for 49314@debbugs.gnu.org; Fri, 23 Jul 2021 01:25:46 -0400 X-Report-Abuse: Please report any abuse attempt to abuse@migadu.com and include these headers. DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=mgsn.dev; s=key1; t=1627017940; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc:mime-version:mime-version:content-type:content-type: in-reply-to:in-reply-to:references:references; bh=pefgMZtWPwQwr/zWJbdg1pmdexa0NdI4jbYYDsTlaZE=; b=NPe52ApQF6VSnFlNX6T4rEq5cXepTC2nI+/RSXY2+ePF/R9CaUSUh72IkeN3KwQtKlT/GD haqopngrdsle0j4pGuLWiuKaRA282HJ9dw2i2gLkBND2UKL9i2BVtXVlLX2tFBB0Z+Nt3g 01CU78hs5SXcWhL4KgbZ+BpvPrDk/Ms= From: Sarah Morgensen To: Kyle Andrews Subject: Re: bug#49314: Stan package broken References: <878s2q1ef4.fsf@gmail.com> Date: Thu, 22 Jul 2021 22:25:37 -0700 In-Reply-To: <878s2q1ef4.fsf@gmail.com> (Kyle Andrews's message of "Thu, 01 Jul 2021 07:06:39 -0400") Message-ID: <86lf5xr48e.fsf@mgsn.dev> MIME-Version: 1.0 Content-Type: text/plain X-Migadu-Flow: FLOW_OUT X-Migadu-Auth-User: iskarian@mgsn.dev X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 49314 Cc: 49314@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: -1.7 (-) Hello, Thanks for the bug report. Kyle Andrews writes: [...] > #+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) This kind of error typically occurs when something is compiled with a newer version of GCC/glibc and then linked with an older version. Do you happen to have a gcc or gcc-toolchain installed in your profile (and does removing it solve this issue)? > Error in sink(type = "output") : invalid connection > #+END_EXAMPLE > > I setup my environment with: > > : guix environment --ad-hoc r-rstan r-rstanarm r Alternatively, you could try guix environment --pure --ad-hoc r-rstan r-rstanarm r bash coreutils (Using --pure prevents packages from your profile being used.) -- Sarah From debbugs-submit-bounces@debbugs.gnu.org Tue Jul 12 09:14:38 2022 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 To: Kyle Andrews Subject: Re: bug#49314: Stan package broken 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-Spam-Score: -0.0 (/) X-Debbugs-Envelope-To: 49314-done Cc: 49314-done@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, 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 From unknown Fri Jun 20 20:11:01 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Wed, 10 Aug 2022 11:24:07 +0000 User-Agent: Fakemail v42.6.9 # This is a fake control message. # # The action: # bug archived. thanks # This fakemail brought to you by your local debbugs # administrator