From unknown Sun Jun 22 07:49:18 2025 X-Loop: help-debbugs@gnu.org Subject: bug#49314: Stan package broken Resent-From: Kyle Andrews Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Thu, 01 Jul 2021 11:07:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 49314 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 49314@debbugs.gnu.org X-Debbugs-Original-To: bug-guix@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.162513760622632 (code B ref -1); Thu, 01 Jul 2021 11:07:02 +0000 Received: (at submit) by debbugs.gnu.org; 1 Jul 2021 11:06:46 +0000 Received: from localhost ([127.0.0.1]:59671 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lyuWs-0005sy-Hb for submit@debbugs.gnu.org; Thu, 01 Jul 2021 07:06:46 -0400 Received: from lists.gnu.org ([209.51.188.17]:59178) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lyuWr-0005sr-AJ for submit@debbugs.gnu.org; Thu, 01 Jul 2021 07:06:45 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:39008) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lyuWr-0007dF-2R for bug-guix@gnu.org; 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Thu, 01 Jul 2021 04:06:40 -0700 (PDT) User-agent: mu4e 1.4.15; emacs 27.2 From: Kyle Andrews 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-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 unknown Sun Jun 22 07:49:18 2025 X-Loop: help-debbugs@gnu.org Subject: bug#49314: Stan package broken Resent-From: Sarah Morgensen Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Fri, 23 Jul 2021 05:26:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 49314 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Kyle Andrews Cc: 49314@debbugs.gnu.org Received: via spool by 49314-submit@debbugs.gnu.org id=B49314.16270179484323 (code B ref 49314); Fri, 23 Jul 2021 05:26:01 +0000 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 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-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 unknown Sun Jun 22 07:49:18 2025 MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) X-Loop: help-debbugs@gnu.org From: help-debbugs@gnu.org (GNU bug Tracking System) To: Kyle Andrews Subject: bug#49314: closed (Re: bug#49314: Stan package broken) Message-ID: References: <8735f6a2x6.fsf@gmail.com> <878s2q1ef4.fsf@gmail.com> X-Gnu-PR-Message: they-closed 49314 X-Gnu-PR-Package: guix Reply-To: 49314@debbugs.gnu.org Date: Tue, 12 Jul 2022 13:15:02 +0000 Content-Type: multipart/mixed; boundary="----------=_1657631702-7271-1" This is a multi-part message in MIME format... ------------=_1657631702-7271-1 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="utf-8" Your bug report #49314: Stan package broken which was filed against the guix package, has been closed. The explanation is attached below, along with your original report. If you require more details, please reply to 49314@debbugs.gnu.org. --=20 49314: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D49314 GNU Bug Tracking System Contact help-debbugs@gnu.org with problems ------------=_1657631702-7271-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit 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 ------------=_1657631702-7271-1 Content-Type: message/rfc822 Content-Disposition: inline Content-Transfer-Encoding: 7bit Received: (at submit) by debbugs.gnu.org; 1 Jul 2021 11:06:46 +0000 Received: from localhost ([127.0.0.1]:59671 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lyuWs-0005sy-Hb for submit@debbugs.gnu.org; Thu, 01 Jul 2021 07:06:46 -0400 Received: from lists.gnu.org ([209.51.188.17]:59178) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1lyuWr-0005sr-AJ for submit@debbugs.gnu.org; Thu, 01 Jul 2021 07:06:45 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:39008) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1lyuWr-0007dF-2R for bug-guix@gnu.org; Thu, 01 Jul 2021 07:06:45 -0400 Received: from mail-io1-xd32.google.com ([2607:f8b0:4864:20::d32]:46880) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1lyuWp-0006Qu-GR for bug-guix@gnu.org; Thu, 01 Jul 2021 07:06:44 -0400 Received: by mail-io1-xd32.google.com with SMTP id f21so6941279ioh.13 for ; Thu, 01 Jul 2021 04:06:42 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=user-agent:from:to:subject:date:message-id:mime-version; bh=Da8+YONJf3z/r3AvWB4Cy7OR1+ol6Xs76q56kbcs0Lc=; b=VGgNTUH8MjJ82xnhAV/EoumZsXyTRlo650Yq6m6fwWoAB5PgAkkXNu6s3ykyhWkFvF JQOcRQMTfgwMtQ5RK9Gujo3qxPyUoy9hqtwHB2FW+fZrTCRj7MI6+lWMxZ6jK3ket4yI sr0ncRU8ajlVUYJeucn0YVQopBAJQh4FZf/EioCO/EhVvq1OkzVicy7CKTBppMDB2LHH 6mQclawTL1JfD1IdFUaNWD2PSTwpu8FUFmyw+wMYOU4BuxZUikwjaFuV+gVsxU5ro906 5kDAkZDsS88z8JK44ItpKEeRRUwZZL4TjNLnWuv1x/5usEYaM+Kpl81YscMWk0nWmM3S yHJw== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:user-agent:from:to:subject:date:message-id :mime-version; bh=Da8+YONJf3z/r3AvWB4Cy7OR1+ol6Xs76q56kbcs0Lc=; b=dmGgIzEfHD1KfMsyUybs8UzfY2EtN27wT5aYCrPWYLGpCr3xcLKa/AEvD4L6gRIS2n r77e5bOIYKr277nXzS4Hk/zrExE4S0EIdo4YW+7ieHJGljsDxYcYXJ19f16rcyjXeIow 9X6HmYuISijOtD7+wgHh9KNAHpgF4oAPNfdaU6V8zw4yLPWzWP8RfaJa8/ab2F5BvxLA X2XXGueismrMEY1sta8AOXpmM4v+xmRi2kqNZ/XsACRPbuf3hM09SYV5TLOMoEt9lh8W U3levXX2g9SobRYjpv+LPEE49GBxbZ9GbLVY9QgWjI/b3pQRiltZuanUoxp5u1rehk7O SCXA== X-Gm-Message-State: AOAM530qIWHTW6I8qys8KLOEYDR9ABH8KzOpuLRXSvRfVl9G9nIidUPQ bdRuAOKM1nvLrjBdflGZ7oSotK3YdaM= X-Google-Smtp-Source: ABdhPJyG/NxPNozK01A3JJ2xBAvLY8PyTyUCXpc2sz0PG/G4+m7FM8Gu6KWgxRm12i5v96n1d08r3w== X-Received: by 2002:a05:6638:279:: with SMTP id x25mr13503023jaq.33.1625137601497; 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 ------------=_1657631702-7271-1--