From unknown Tue Jun 17 20:13:05 2025 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.509 (Entity 5.509) Content-Type: text/plain; charset=utf-8 From: bug#21909 <21909@debbugs.gnu.org> To: bug#21909 <21909@debbugs.gnu.org> Subject: Status: Segfault with eigen in R Reply-To: bug#21909 <21909@debbugs.gnu.org> Date: Wed, 18 Jun 2025 03:13:05 +0000 retitle 21909 Segfault with eigen in R reassign 21909 guix submitter 21909 Kyle Meyer severity 21909 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Fri Nov 13 11:06:39 2015 Received: (at submit) by debbugs.gnu.org; 13 Nov 2015 16:06:39 +0000 Received: from localhost ([127.0.0.1]:37360 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZxGs2-0008B4-QT for submit@debbugs.gnu.org; Fri, 13 Nov 2015 11:06:39 -0500 Received: from eggs.gnu.org ([208.118.235.92]:48853) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZxGfi-0007sX-Jt for submit@debbugs.gnu.org; Fri, 13 Nov 2015 10:53:54 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZxGfh-0006zs-BC for submit@debbugs.gnu.org; Fri, 13 Nov 2015 10:53:54 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.8 required=5.0 tests=BAYES_50,T_DKIM_INVALID autolearn=disabled version=3.3.2 Received: from lists.gnu.org ([2001:4830:134:3::11]:54618) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZxGfh-0006zj-86 for submit@debbugs.gnu.org; Fri, 13 Nov 2015 10:53:53 -0500 Received: from eggs.gnu.org ([2001:4830:134:3::10]:58840) by lists.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZxGfg-00005h-EJ for bug-guix@gnu.org; Fri, 13 Nov 2015 10:53:53 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZxGfc-0006wa-8v for bug-guix@gnu.org; Fri, 13 Nov 2015 10:53:52 -0500 Received: from mail-qk0-x235.google.com ([2607:f8b0:400d:c09::235]:34303) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZxGfc-0006wK-3M for bug-guix@gnu.org; Fri, 13 Nov 2015 10:53:48 -0500 Received: by qkfo3 with SMTP id o3so50935428qkf.1 for ; Fri, 13 Nov 2015 07:53:47 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=kyleam_com.20150623.gappssmtp.com; s=20150623; h=from:to:subject:date:message-id:user-agent:mime-version :content-type; bh=5wyKsTVCYufv4AmUlvu4e3SlG5+NdoKEcWXohldrzUg=; b=V7Pr9ZdxK1Kc3U4itZhfELcSdB6YWPCHie2kz22YUD4nLQTeMCsOVAiW8duvHL02ek hhuIm1vwZDd2gs6ajOquURmGWJjKp0J9fsWQvq8rGl/60aDzhHyjEnv2qd2Lbj2E7dqj GhfD0EhjaLeoiZLIEokeVkz98g0CDAFf+wqVwPpKpJGYCE1s8ijzGA7nE0UJkHMAs7zO v+VPbmS7TeqQzCEqnxT4acL/LBQJkDHdzrN2Tf08EbDz6ImIyMbWI/G6mx9tgWXU6ECB bQ1UhNL8N1WQwA2YOj36//mGpXnbbk/gNNV3clv78SDdoP0GMYmVFhpJ2t7jBHJ3dkFn /9Rg== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20130820; h=x-gm-message-state:from:to:subject:date:message-id:user-agent :mime-version:content-type; bh=5wyKsTVCYufv4AmUlvu4e3SlG5+NdoKEcWXohldrzUg=; b=GTypThNSYUQGsrZyQHd21wV9SsYOAdZmdTFoj+qo47nTzvawwGejF0afC+bmqtLs6T zYFVW/KJqBL4qM+bnWYnA8GY0g33BIf1zuvTtT520ptGMb+mYEx+OSsj1uLQDe4HuqcV MBWPr0nNa84qMbG4F8ZVX2R53KYqlH81gXEut08u/CtUX8s1yQ5tH+qph1A8RO6A2jxj GILfCozzghAshkWql9dQ9WcDHEhcoZLOln/Sy3DGXYbwBVvKVuuOJU2ax5EfNqQER56n OyvQ0z/n2dIQ9wFGjZeQu+t56zsP4Bp76q0CUdBPOmBPDKjCAoP32VJgJ9lgsqncviYV tnlg== X-Gm-Message-State: ALoCoQnyb3mjrtEsDZIowZb9YQrmqL6s6HMxfO3Ws6sjb5p1O0EB0ZfY0gwLN2SWtFrtBiB/v6qd X-Received: by 10.55.197.3 with SMTP id p3mr22296232qki.11.1447430027249; Fri, 13 Nov 2015 07:53:47 -0800 (PST) Received: from localhost (nat-130-132-173-5.central.yale.edu. [130.132.173.5]) by smtp.gmail.com with ESMTPSA id b22sm5424334qge.23.2015.11.13.07.53.46 for (version=TLSv1.2 cipher=ECDHE-RSA-AES128-GCM-SHA256 bits=128/128); Fri, 13 Nov 2015 07:53:46 -0800 (PST) From: Kyle Meyer To: Subject: Segfault with eigen in R X-Attribution: Kyle Date: Fri, 13 Nov 2015 10:53:42 -0500 Message-ID: <874mgpj3p5.fsf@kyleam.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.0.50 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: Error: Malformed IPv6 address (bad octet value). X-detected-operating-system: by eggs.gnu.org: Error: Malformed IPv6 address (bad octet value). X-Received-From: 2001:4830:134:3::11 X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: submit X-Mailman-Approved-At: Fri, 13 Nov 2015 11:06:29 -0500 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 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: -5.0 (-----) Hello, With R 3.2.2 built from r in statistics.scm (guix 0.9.0), I'm seeing a segfault when eigen is called with a matrix over some size. I can trigger the error with the following code [1]: > M <- 50 > N <- 500 > eigen(crossprod(matrix(rnorm(M * N), M, N))) *** caught segfault *** address 0xfb0, cause 'memory not mapped' Traceback: 1: eigen(crossprod(matrix(rnorm(M * N), M, N))) Can others reproduce this? Thanks. [1] This is a down-sized version of the snippet from an ATLAS bug report in 2011 for a similar error with R 2.14. http://sourceforge.net/p/math-atlas/support-requests/792/ -- Kyle From debbugs-submit-bounces@debbugs.gnu.org Fri Nov 13 15:26:44 2015 Received: (at 21909) by debbugs.gnu.org; 13 Nov 2015 20:26:44 +0000 Received: from localhost ([127.0.0.1]:37492 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZxKvk-0005xV-D8 for submit@debbugs.gnu.org; Fri, 13 Nov 2015 15:26:44 -0500 Received: from sender163-mail.zoho.com ([74.201.84.163]:24541) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZxKvh-0005xH-NL for 21909@debbugs.gnu.org; Fri, 13 Nov 2015 15:26:42 -0500 Received: from localhost (x4d07216c.dyn.telefonica.de [77.7.33.108]) by mx.zohomail.com with SMTPS id 1447446398115437.3022492556929; Fri, 13 Nov 2015 12:26:38 -0800 (PST) References: <874mgpj3p5.fsf@kyleam.com> User-agent: mu4e 0.9.13; emacs 24.5.1 From: Ricardo Wurmus To: Kyle Meyer Subject: Re: bug#21909: Segfault with eigen in R In-reply-to: <874mgpj3p5.fsf@kyleam.com> Date: Fri, 13 Nov 2015 21:26:34 +0100 Message-ID: <87pozd3ath.fsf@elephly.net> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 1.0 (+) X-Debbugs-Envelope-To: 21909 Cc: 21909@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 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 (+) Kyle Meyer writes: > With R 3.2.2 built from r in statistics.scm (guix 0.9.0), I'm seeing a > segfault when eigen is called with a matrix over some size. I can > trigger the error with the following code [1]: > > > M <- 50 > > N <- 500 > > eigen(crossprod(matrix(rnorm(M * N), M, N))) > > *** caught segfault *** > address 0xfb0, cause 'memory not mapped' > > Traceback: > 1: eigen(crossprod(matrix(rnorm(M * N), M, N))) > > Can others reproduce this? I can reproduce this running R 3.2.2 on GuixSD on a x86_64 machine. ~~ Ricardo From debbugs-submit-bounces@debbugs.gnu.org Wed Nov 18 19:37:43 2015 Received: (at 21909) by debbugs.gnu.org; 19 Nov 2015 00:37:43 +0000 Received: from localhost ([127.0.0.1]:43880 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZzDEN-0004sD-3I for submit@debbugs.gnu.org; Wed, 18 Nov 2015 19:37:43 -0500 Received: from pb-smtp0.int.icgroup.com ([208.72.237.35]:64441 helo=sasl.smtp.pobox.com) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZzDE1-0004rL-Rd for 21909@debbugs.gnu.org; Wed, 18 Nov 2015 19:37:41 -0500 Received: from sasl.smtp.pobox.com (unknown [127.0.0.1]) by pb-smtp0.pobox.com (Postfix) with ESMTP id 1C9BB2C8E8; Wed, 18 Nov 2015 19:37:20 -0500 (EST) DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=pobox.com; h=from:to:cc :subject:references:date:in-reply-to:message-id:mime-version :content-type; s=sasl; bh=oBjicXQs1LbGeIt2PDFP/kfvVWI=; b=PWZmNn XQdLMmoABio7FR57wGXgm/ag4Ep2tcNvwYyw3eiI4xNn/fBzFZUf3cRf4xbvMABJ JAYbC47IswYuVVIoG6AczAUiqrLDULDyEf8/GelRY0pty1f+UOJsVRJW/OEtg80R B6nqG0Hn2lKTzy0tgRUFIdfyeqkRNJgusxMho= Received: from pb-smtp0.int.icgroup.com (unknown [127.0.0.1]) by pb-smtp0.pobox.com (Postfix) with ESMTP id 148992C8E6; Wed, 18 Nov 2015 19:37:20 -0500 (EST) Received: from localhost (unknown [130.132.173.182]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pb-smtp0.pobox.com (Postfix) with ESMTPSA id A5A7F2C8E5; Wed, 18 Nov 2015 19:37:19 -0500 (EST) From: Kyle Meyer To: Ricardo Wurmus Subject: Re: bug#21909: Segfault with eigen in R References: <874mgpj3p5.fsf@kyleam.com> <87pozd3ath.fsf@elephly.net> X-Attribution: Kyle Date: Wed, 18 Nov 2015 19:37:12 -0500 In-Reply-To: <87pozd3ath.fsf@elephly.net> (Ricardo Wurmus's message of "Fri, 13 Nov 2015 21:26:34 +0100") Message-ID: <87twoisu2v.fsf@kyleam.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.0.50 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Pobox-Relay-ID: B0F556F6-8E55-11E5-93A5-6BD26AB36C07-24757444!pb-smtp0.pobox.com X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 21909 Cc: 21909@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 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: -0.7 (/) Ricardo Wurmus writes: > Kyle Meyer writes: > >> With R 3.2.2 built from r in statistics.scm (guix 0.9.0), I'm seeing a >> segfault when eigen is called with a matrix over some size. I can >> trigger the error with the following code [1]: >> >> > M <- 50 >> > N <- 500 >> > eigen(crossprod(matrix(rnorm(M * N), M, N))) >> >> *** caught segfault *** >> address 0xfb0, cause 'memory not mapped' >> >> Traceback: >> 1: eigen(crossprod(matrix(rnorm(M * N), M, N))) >> >> Can others reproduce this? > > I can reproduce this running R 3.2.2 on GuixSD on a x86_64 machine. I haven't had any luck resolving this aside from just using R's internal BLAS by removing "--with-blas=openblas" and "--with-lapack" from the configure flags. -- Kyle From debbugs-submit-bounces@debbugs.gnu.org Thu Nov 19 04:39:24 2015 Received: (at 21909) by debbugs.gnu.org; 19 Nov 2015 09:39:24 +0000 Received: from localhost ([127.0.0.1]:44213 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZzLga-00073i-AO for submit@debbugs.gnu.org; Thu, 19 Nov 2015 04:39:24 -0500 Received: from eggs.gnu.org ([208.118.235.92]:55745) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZzLgY-00073a-5S for 21909@debbugs.gnu.org; Thu, 19 Nov 2015 04:39:22 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZzLgS-0000RN-JA for 21909@debbugs.gnu.org; Thu, 19 Nov 2015 04:39:21 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.1 required=5.0 tests=BAYES_05,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:49895) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZzLgS-0000RJ-G4; Thu, 19 Nov 2015 04:39:16 -0500 Received: from pluto.bordeaux.inria.fr ([193.50.110.57]:50588 helo=pluto) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1ZzLgR-0001wm-SQ; Thu, 19 Nov 2015 04:39:16 -0500 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Kyle Meyer Subject: Re: bug#21909: Segfault with eigen in R References: <874mgpj3p5.fsf@kyleam.com> <87pozd3ath.fsf@elephly.net> <87twoisu2v.fsf@kyleam.com> Date: Thu, 19 Nov 2015 10:39:12 +0100 In-Reply-To: <87twoisu2v.fsf@kyleam.com> (Kyle Meyer's message of "Wed, 18 Nov 2015 19:37:12 -0500") Message-ID: <87egfmfhvj.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/24.5 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: Error: Malformed IPv6 address (bad octet value). X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.6 (-----) X-Debbugs-Envelope-To: 21909 Cc: Ricardo Wurmus , 21909@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 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: -5.6 (-----) I can reproduce the bug with: guix environment --pure --ad-hoc r -- R and then typed =E2=80=9C1=E2=80=9D to get a core dump, which gives this: --8<---------------cut here---------------start------------->8--- Core was generated by `/gnu/store/zci2lb9jlc9hlck3x3hc04ab3y86fzf9-r-3.2.2/= lib/R/bin/exec/R'. Program terminated with signal SIGSEGV, Segmentation fault. #0 0x00007f34616450e0 in dgemv_t_SANDYBRIDGE () from /gnu/store/hw9p1zyn1n= h8pbm1cl69nm0i391lk6c7-openblas-0.2.15/lib/libopenblas.so.0 [Current thread is 1 (Thread 0x7f34651307c0 (LWP 3399))] (gdb) bt #0 0x00007f34616450e0 in dgemv_t_SANDYBRIDGE () from /gnu/store/hw9p1zyn1n= h8pbm1cl69nm0i391lk6c7-openblas-0.2.15/lib/libopenblas.so.0 #1 0x00000000000000a2 in ?? () [...] (gdb) disassemble Dump of assembler code for function dgemv_t_SANDYBRIDGE: [...] 0x00007f34616450cf <+207>: jle 0x7f3461645140 0x00007f34616450d1 <+209>: nopl 0x0(%rax,%rax,1) 0x00007f34616450d6 <+214>: nopw %cs:0x0(%rax,%rax,1) =3D> 0x00007f34616450e0 <+224>: movsd (%r9),%xmm0 [...] (gdb) p $r9=20=20=20=20=20=20=20=20 $1 =3D 4016 --8<---------------cut here---------------end--------------->8--- My CPU seems to be a Sandy Bridge: --8<---------------cut here---------------start------------->8--- $ cat /proc/cpuinfo | grep ^model | head -2 model : 42 model name : Intel(R) Core(TM) i5-2540M CPU @ 2.60GHz --8<---------------cut here---------------end--------------->8--- Might be useful to report it upstream? Thanks, Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Thu Nov 19 19:05:38 2015 Received: (at 21909) by debbugs.gnu.org; 20 Nov 2015 00:05:38 +0000 Received: from localhost ([127.0.0.1]:45332 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZzZCZ-0006Us-5y for submit@debbugs.gnu.org; Thu, 19 Nov 2015 19:05:37 -0500 Received: from pb-smtp0.int.icgroup.com ([208.72.237.35]:53255 helo=sasl.smtp.pobox.com) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZzZCX-0006Ui-7Z for 21909@debbugs.gnu.org; Thu, 19 Nov 2015 19:05:18 -0500 Received: from sasl.smtp.pobox.com (unknown [127.0.0.1]) by pb-smtp0.pobox.com (Postfix) with ESMTP id 8D1692B9B4; Thu, 19 Nov 2015 19:05:16 -0500 (EST) DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=pobox.com; h=from:to:cc :subject:references:date:in-reply-to:message-id:mime-version :content-type:content-transfer-encoding; s=sasl; bh=MR8rhcSTFwtd fFzV62NsDrsqbZ8=; b=SYNh80O2ZhTO1tf/EC52AEVNbcLRSRPtTCaU7d3BMEu9 iZsZZs02Yl9UF5tqPPE9q3Ck+SODkFtm82CMDgW+biigiOJE2dcZDeyhNDS2g6UN +0IZIv2nJKAAtZo+wxtCBVhngHqbBT6PqSsIuT/3cty02cafNDacATJe+Wm65mQ= Received: from pb-smtp0.int.icgroup.com (unknown [127.0.0.1]) by pb-smtp0.pobox.com (Postfix) with ESMTP id 8606D2B9B2; Thu, 19 Nov 2015 19:05:16 -0500 (EST) Received: from localhost (unknown [130.132.173.207]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pb-smtp0.pobox.com (Postfix) with ESMTPSA id 079942B9B1; Thu, 19 Nov 2015 19:05:16 -0500 (EST) From: Kyle Meyer To: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: Re: bug#21909: Segfault with eigen in R References: <874mgpj3p5.fsf@kyleam.com> <87pozd3ath.fsf@elephly.net> <87twoisu2v.fsf@kyleam.com> <87egfmfhvj.fsf@gnu.org> X-Attribution: Kyle Date: Thu, 19 Nov 2015 19:05:07 -0500 In-Reply-To: <87egfmfhvj.fsf@gnu.org> ("Ludovic =?utf-8?Q?Court=C3=A8s=22'?= =?utf-8?Q?s?= message of "Thu, 19 Nov 2015 10:39:12 +0100") Message-ID: <87twohr0wc.fsf@kyleam.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.0.50 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-Pobox-Relay-ID: 60C9F7B6-8F1A-11E5-AB29-6BD26AB36C07-24757444!pb-smtp0.pobox.com X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 21909 Cc: Ricardo Wurmus , 21909@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 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: -0.7 (/) ludo@gnu.org (Ludovic Court=C3=A8s) writes: > I can reproduce the bug with: > > guix environment --pure --ad-hoc r -- R [...] > Might be useful to report it upstream? Yes. In preparing to do so, I figured that I should reproduce the issue with a build outside of Guix. However, when I tried with a manual build on an Arch Linux system, the snippet ran fine. This was with gcc version 5.2.0, so I switched the gfortran input of openblas over to gfortran-5, which seems to fix the issue. While the issue should still be reported upstream, would it be OK to update the gfortran input to gfortran-5? -- Kyle From debbugs-submit-bounces@debbugs.gnu.org Fri Nov 20 04:58:57 2015 Received: (at 21909) by debbugs.gnu.org; 20 Nov 2015 09:58:57 +0000 Received: from localhost ([127.0.0.1]:45519 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZziT2-0008UV-Fw for submit@debbugs.gnu.org; Fri, 20 Nov 2015 04:58:56 -0500 Received: from eggs.gnu.org ([208.118.235.92]:35620) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1ZziT0-0008UK-HO for 21909@debbugs.gnu.org; Fri, 20 Nov 2015 04:58:54 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1ZziSv-0002vn-Fx for 21909@debbugs.gnu.org; Fri, 20 Nov 2015 04:58:54 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=0.2 required=5.0 tests=BAYES_50,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:49760) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1ZziSv-0002uq-Cu; Fri, 20 Nov 2015 04:58:49 -0500 Received: from reverse-83.fdn.fr ([80.67.176.83]:46968 helo=pluto) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1ZziSq-0003hJ-C8; Fri, 20 Nov 2015 04:58:44 -0500 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Kyle Meyer Subject: Re: bug#21909: Segfault with eigen in R References: <874mgpj3p5.fsf@kyleam.com> <87pozd3ath.fsf@elephly.net> <87twoisu2v.fsf@kyleam.com> <87egfmfhvj.fsf@gnu.org> <87twohr0wc.fsf@kyleam.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 30 Brumaire an 224 de la =?utf-8?Q?R=C3=A9volution?= X-PGP-Key-ID: 0x3D9AEBB5 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-unknown-linux-gnu Date: Fri, 20 Nov 2015 10:58:41 +0100 In-Reply-To: <87twohr0wc.fsf@kyleam.com> (Kyle Meyer's message of "Thu, 19 Nov 2015 19:05:07 -0500") Message-ID: <87wptdj8ku.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/24.5 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable X-detected-operating-system: by eggs.gnu.org: Error: Malformed IPv6 address (bad octet value). X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.6 (-----) X-Debbugs-Envelope-To: 21909 Cc: Ricardo Wurmus , 21909@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 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: -5.6 (-----) Kyle Meyer skribis: > ludo@gnu.org (Ludovic Court=C3=A8s) writes: > >> I can reproduce the bug with: >> >> guix environment --pure --ad-hoc r -- R > > [...] > >> Might be useful to report it upstream? > > Yes. In preparing to do so, I figured that I should reproduce the issue > with a build outside of Guix. However, when I tried with a manual build > on an Arch Linux system, the snippet ran fine. This was with gcc > version 5.2.0, so I switched the gfortran input of openblas over to > gfortran-5, which seems to fix the issue. Interesting. > While the issue should still be reported upstream, would it be OK to > update the gfortran input to gfortran-5? The problem is that this leads to an R linked against GCC 4.9=E2=80=99s lib= gcc_s and other run-time support libraries, and also against those of GCC 5.2, via OpenBLAS. I think we=E2=80=99d rather avoid it. An additional data point: --8<---------------cut here---------------start------------->8--- $ guix environment --pure --ad-hoc r valgrind -- R -d valgrind /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2.2/bin/R: line 8: uname: c= ommand not found =3D=3D3198=3D=3D Memcheck, a memory error detector =3D=3D3198=3D=3D Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward e= t al. =3D=3D3198=3D=3D Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyri= ght info =3D=3D3198=3D=3D Command: /gnu/store/jb11p396a277rndb52da20ygdksccji8-r-3.2= .2/lib/R/bin/exec/R =3D=3D3198=3D=3D=20 R version 3.2.2 (2015-08-14) -- "Fire Safety" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > M <- 50=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20= =20=20=20=20=20=20=20=20=20=20=20=20=20=20=20 > N <- 500=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20=20= =20=20=20=20=20=20=20=20=20=20=20=20=20=20=20 > eigen(crossprod(matrix(rnorm(M * N), M, N))) =3D=3D3198=3D=3D Invalid read of size 8 =3D=3D3198=3D=3D at 0x8E400E0: dgemv_t_SANDYBRIDGE (in /gnu/store/hw9p1z= yn1nh8pbm1cl69nm0i391lk6c7-openblas-0.2.15/lib/libopenblasp-r0.2.15.so) =3D=3D3198=3D=3D by 0x183AED48: dlatrd_ (in /gnu/store/jb11p396a277rndb5= 2da20ygdksccji8-r-3.2.2/lib/R/lib/libRlapack.so) =3D=3D3198=3D=3D by 0x18461F92: dsytrd_ (in /gnu/store/jb11p396a277rndb5= 2da20ygdksccji8-r-3.2.2/lib/R/lib/libRlapack.so) =3D=3D3198=3D=3D by 0x184B9540: dsyevr_ (in /gnu/store/jb11p396a277rndb5= 2da20ygdksccji8-r-3.2.2/lib/R/lib/libRlapack.so) =3D=3D3198=3D=3D by 0x1B742D5E: La_rs (in /gnu/store/jb11p396a277rndb52d= a20ygdksccji8-r-3.2.2/lib/R/modules/lapack.so) =3D=3D3198=3D=3D by 0x1B745B96: mod_do_lapack (in /gnu/store/jb11p396a27= 7rndb52da20ygdksccji8-r-3.2.2/lib/R/modules/lapack.so) =3D=3D3198=3D=3D by 0x4F35635: bcEval (in /gnu/store/jb11p396a277rndb52d= a20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) =3D=3D3198=3D=3D by 0x4F432DF: Rf_eval (in /gnu/store/jb11p396a277rndb52= da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) =3D=3D3198=3D=3D by 0x4F48F4B: Rf_applyClosure (in /gnu/store/jb11p396a2= 77rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) =3D=3D3198=3D=3D by 0x4F4345E: Rf_eval (in /gnu/store/jb11p396a277rndb52= da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) =3D=3D3198=3D=3D by 0x4F6B0D9: Rf_ReplIteration (in /gnu/store/jb11p396a= 277rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) =3D=3D3198=3D=3D by 0x4F6B430: R_ReplConsole (in /gnu/store/jb11p396a277= rndb52da20ygdksccji8-r-3.2.2/lib/R/lib/libR.so) =3D=3D3198=3D=3D Address 0xfb0 is not stack'd, malloc'd or (recently) free= 'd =3D=3D3198=3D=3D=20 *** caught segfault *** address 0xfb0, cause 'memory not mapped' --8<---------------cut here---------------end--------------->8--- Here this suggests an R issue more than an OpenBLAS problem. Ludo=E2=80=99. From debbugs-submit-bounces@debbugs.gnu.org Mon Nov 30 18:26:18 2015 Received: (at 21909) by debbugs.gnu.org; 30 Nov 2015 23:26:18 +0000 Received: from localhost ([127.0.0.1]:33397 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1a3Xpp-0001eh-Mc for submit@debbugs.gnu.org; Mon, 30 Nov 2015 18:26:17 -0500 Received: from pb-smtp0.int.icgroup.com ([208.72.237.35]:63305 helo=sasl.smtp.pobox.com) by debbugs.gnu.org with esmtp (Exim 4.80) (envelope-from ) id 1a3XpU-0001dz-7N for 21909@debbugs.gnu.org; Mon, 30 Nov 2015 18:26:15 -0500 Received: from sasl.smtp.pobox.com (unknown [127.0.0.1]) by pb-smtp0.pobox.com (Postfix) with ESMTP id A1BA42F96D; Mon, 30 Nov 2015 18:25:55 -0500 (EST) DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=pobox.com; h=from:to:cc :subject:references:date:in-reply-to:message-id:mime-version :content-type; s=sasl; bh=rb9WDO7/0+f/6i8k5fqj35Otqpk=; b=egqpFn kx97hHz3DkcgmNMw/2PJjbsiuuzD5zt5OijtWaHeHk2MlYJqZEuCmOpUmE4661Od 39EBNDAt2ZXqe3oHFtQsDOr2zAhpLmINOa3/cqJ9PyRH1dhRPTKcK4MvsTpd/8is Bg8YPCtTnV+3n4TeUd9ZFdZnIB6aBT7Hv8KjA= Received: from pb-smtp0.int.icgroup.com (unknown [127.0.0.1]) by pb-smtp0.pobox.com (Postfix) with ESMTP id 99F772F96C; Mon, 30 Nov 2015 18:25:55 -0500 (EST) Received: from localhost (unknown [130.132.173.5]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pb-smtp0.pobox.com (Postfix) with ESMTPSA id 47CED2F96B; Mon, 30 Nov 2015 18:25:55 -0500 (EST) From: Kyle Meyer To: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) Subject: Re: bug#21909: Segfault with eigen in R References: <874mgpj3p5.fsf@kyleam.com> <87pozd3ath.fsf@elephly.net> <87twoisu2v.fsf@kyleam.com> <87egfmfhvj.fsf@gnu.org> <87twohr0wc.fsf@kyleam.com> <87wptdj8ku.fsf@gnu.org> X-Attribution: Kyle Date: Mon, 30 Nov 2015 18:25:50 -0500 In-Reply-To: <87wptdj8ku.fsf@gnu.org> ("Ludovic =?utf-8?Q?Court=C3=A8s=22'?= =?utf-8?Q?s?= message of "Fri, 20 Nov 2015 10:58:41 +0100") Message-ID: <87r3j7qdc1.fsf@kyleam.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/25.0.50 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Pobox-Relay-ID: B4392460-97B9-11E5-B6F3-6BD26AB36C07-24757444!pb-smtp0.pobox.com X-Spam-Score: -0.7 (/) X-Debbugs-Envelope-To: 21909 Cc: Ricardo Wurmus , 21909@debbugs.gnu.org X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.15 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: -0.7 (/) I've opened an issue in the OpenBLAS repo [1]. https://github.com/xianyi/OpenBLAS/issues/703 I'm trying to answer their questions, but, as is apparent in that thread, I'm not really familiar with debugging these sorts of problems. Since others are able to reproduce the error, any help over there would be very appreciated. [1] The last post suggested it may be an R issue rather than an OpenBLAS one, but I wanted to be more sure of that before going to R developers, especially given their comment about the --with-lapack flag: "Please do bear in mind that using --with-lapack is 'definitely not recommended': it is provided only because it is necessary on some platforms and because some users want to experiment with claimed performance improvements. Reporting problems where it is used unnecessarily will simply irritate the R helpers." https://cran.r-project.org/doc/manuals/r-release/R-admin.html#LAPACK -- Kyle From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 02 05:41:03 2016 Received: (at 21909) by debbugs.gnu.org; 2 Mar 2016 10:41:03 +0000 Received: from localhost ([127.0.0.1]:57020 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84) (envelope-from ) id 1ab4DH-0002uL-ES for submit@debbugs.gnu.org; Wed, 02 Mar 2016 05:41:03 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:36098) by debbugs.gnu.org with esmtp (Exim 4.84) (envelope-from ) id 1ab4DF-0002tm-Dq for 21909@debbugs.gnu.org; Wed, 02 Mar 2016 05:41:02 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 2B2C538077A; Wed, 2 Mar 2016 11:41:00 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :in-reply-to:subject:subject:from:from:references:received :received:received; s=mdc; t=1456915254; x=1458729655; bh=wG00/a qlhCw7rYuLcGsiO1np+dgAijmAal9X/1C+uFI=; b=rphZXmYr1gI1FC9b3aBv5I wGpdktZeealXVvcupXGH7FenOsNLjZA/GgmiuYOeWMMOkX3A7YpMxrn6PxscMSI/ Yqrj0b8QwxAxXnYTiRuEbG9h+wc9QZrdAtH3GGfJhcDqW3YhzJ2weEzPOksuVqAM xGOtKfkY8OJTIglZLcIsU= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id IqmMTHc6Kt2j; Wed, 2 Mar 2016 11:40:54 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP; Wed, 2 Mar 2016 11:40:54 +0100 (CET) Received: from localhost (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.266.1; Wed, 2 Mar 2016 11:40:53 +0100 References: <874mgpj3p5.fsf@kyleam.com> <87pozd3ath.fsf@elephly.net> <87twoisu2v.fsf@kyleam.com> <87egfmfhvj.fsf@gnu.org> <87twohr0wc.fsf@kyleam.com> <87wptdj8ku.fsf@gnu.org> <87r3j7qdc1.fsf@kyleam.com> From: Ricardo Wurmus To: Kyle Meyer Subject: Re: bug#21909: Segfault with eigen in R In-Reply-To: <87r3j7qdc1.fsf@kyleam.com> Date: Wed, 2 Mar 2016 11:40:53 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4255-8.000.1202-22166.006 X-TM-AS-Result: No--3.946400-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 21909 Cc: Ludovic =?utf-8?Q?Court=C3=A8s?= , 21909@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: -5.0 (-----) Kyle Meyer writes: > I've opened an issue in the OpenBLAS repo [1]. > > https://github.com/xianyi/OpenBLAS/issues/703 > > I'm trying to answer their questions, but, as is apparent in that > thread, I'm not really familiar with debugging these sorts of problems. > Since others are able to reproduce the error, any help over there would > be very appreciated. > > [1] The last post suggested it may be an R issue rather than an OpenBLAS > one, but I wanted to be more sure of that before going to R > developers, especially given their comment about the --with-lapack > flag: > > "Please do bear in mind that using --with-lapack is 'definitely not > recommended': it is provided only because it is necessary on some > platforms and because some users want to experiment with claimed > performance improvements. Reporting problems where it is used > unnecessarily will simply irritate the R helpers." > > https://cran.r-project.org/doc/manuals/r-release/R-admin.html#LAPACK We have since removed OpenBLAS from the inputs of R and just use the internal BLAS instead. Without OpenBLAS I cannot reproduce this bug any more. ~~ Ricardo From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 02 05:42:17 2016 Received: (at control) by debbugs.gnu.org; 2 Mar 2016 10:42:18 +0000 Received: from localhost ([127.0.0.1]:57024 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84) (envelope-from ) id 1ab4ET-0002w7-PB for submit@debbugs.gnu.org; Wed, 02 Mar 2016 05:42:17 -0500 Received: from sinope.bbbm.mdc-berlin.de ([141.80.25.23]:51794) by debbugs.gnu.org with esmtp (Exim 4.84) (envelope-from ) id 1ab4ES-0002vz-3C for control@debbugs.gnu.org; Wed, 02 Mar 2016 05:42:16 -0500 Received: from localhost (localhost [127.0.0.1]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP id 326EE2806B7 for ; Wed, 2 Mar 2016 11:42:15 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:mime-version:message-id:date:date :subject:subject:from:from:received:received:received; s=mdc; t= 1456915328; x=1458729729; bh=e8N67Upj4XWvbLnafq2Ntx/RWtdNfCeuXa0 dHE3rtOo=; b=MlgqPuX5sPLE9qlyjsSXpHMH/IcdSqI8P06CvDtE/zT2etJjlnv NZ4RBm+w6EnUFtWgPXOP3MnvI6+Ro2kT2bgvwJB5ZUqY/gwSbZdxrQJTOLSEWo+w T5hMYiGcxc8iKYWZo7a1PNwPradiOVbIR6WgtpokEdSnEeH6VZD1SU9k= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from sinope.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (sinope.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id vYBKxzBt2yh4 for ; Wed, 2 Mar 2016 11:42:08 +0100 (CET) Received: from HTCAONE.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by sinope.bbbm.mdc-berlin.de (Postfix) with ESMTP for ; Wed, 2 Mar 2016 11:42:08 +0100 (CET) Received: from localhost (141.80.180.135) by HTCAONE.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.266.1; Wed, 2 Mar 2016 11:42:08 +0100 From: Ricardo Wurmus To: Subject: close Date: Wed, 2 Mar 2016 11:42:03 +0100 Message-ID: MIME-Version: 1.0 Content-Type: text/plain X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4255-8.000.1202-22166.006 X-TM-AS-Result: No--3.934900-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: control 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: -5.0 (-----) close 21909 thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Mar 02 16:10:06 2016 Received: (at 21909) by debbugs.gnu.org; 2 Mar 2016 21:10:06 +0000 Received: from localhost ([127.0.0.1]:58189 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84) (envelope-from ) id 1abE22-000163-LZ for submit@debbugs.gnu.org; Wed, 02 Mar 2016 16:10:06 -0500 Received: from eggs.gnu.org ([208.118.235.92]:51737) by debbugs.gnu.org with esmtp (Exim 4.84) (envelope-from ) id 1abE21-00015V-5i for 21909@debbugs.gnu.org; Wed, 02 Mar 2016 16:10:05 -0500 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.71) (envelope-from ) id 1abE1s-0001nB-U2 for 21909@debbugs.gnu.org; Wed, 02 Mar 2016 16:10:00 -0500 X-Spam-Checker-Version: SpamAssassin 3.3.2 (2011-06-06) on eggs.gnu.org X-Spam-Level: X-Spam-Status: No, score=-1.9 required=5.0 tests=BAYES_00,RP_MATCHES_RCVD autolearn=disabled version=3.3.2 Received: from fencepost.gnu.org ([2001:4830:134:3::e]:39381) by eggs.gnu.org with esmtp (Exim 4.71) (envelope-from ) id 1abE1s-0001n7-Qi; Wed, 02 Mar 2016 16:09:56 -0500 Received: from reverse-83.fdn.fr ([80.67.176.83]:43468 helo=pluto) by fencepost.gnu.org with esmtpsa (TLS1.2:RSA_AES_128_CBC_SHA1:128) (Exim 4.82) (envelope-from ) id 1abE1q-0005H0-8N; Wed, 02 Mar 2016 16:09:54 -0500 From: ludo@gnu.org (Ludovic =?utf-8?Q?Court=C3=A8s?=) To: Ricardo Wurmus Subject: Re: bug#21909: Segfault with eigen in R References: <874mgpj3p5.fsf@kyleam.com> <87pozd3ath.fsf@elephly.net> <87twoisu2v.fsf@kyleam.com> <87egfmfhvj.fsf@gnu.org> <87twohr0wc.fsf@kyleam.com> <87wptdj8ku.fsf@gnu.org> <87r3j7qdc1.fsf@kyleam.com> X-URL: http://www.fdn.fr/~lcourtes/ X-Revolutionary-Date: 13 =?utf-8?Q?Vent=C3=B4se?= an 224 de la =?utf-8?Q?R?= =?utf-8?Q?=C3=A9volution?= X-PGP-Key-ID: 0x3D9AEBB5 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-unknown-linux-gnu Date: Wed, 02 Mar 2016 22:09:52 +0100 In-Reply-To: (Ricardo Wurmus's message of "Wed, 2 Mar 2016 11:40:53 +0100") Message-ID: <87egbsegdb.fsf@gnu.org> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/24.5 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-detected-operating-system: by eggs.gnu.org: GNU/Linux 2.2.x-3.x [generic] X-Received-From: 2001:4830:134:3::e X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 21909 Cc: Kyle Meyer , 21909@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: -5.0 (-----) Ricardo Wurmus skribis: > We have since removed OpenBLAS from the inputs of R and just use the > internal BLAS instead. Without OpenBLAS I cannot reproduce this bug > any more. Nice. So we can close? Ludo'. From debbugs-submit-bounces@debbugs.gnu.org Thu Mar 03 15:54:54 2016 Received: (at 21909) by debbugs.gnu.org; 3 Mar 2016 20:54:54 +0000 Received: from localhost ([127.0.0.1]:60528 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84) (envelope-from ) id 1abaGs-000206-LV for submit@debbugs.gnu.org; Thu, 03 Mar 2016 15:54:54 -0500 Received: from venus.bbbm.mdc-berlin.de ([141.80.25.30]:49227) by debbugs.gnu.org with esmtp (Exim 4.84) (envelope-from ) id 1abaGq-0001zx-Ia for 21909@debbugs.gnu.org; Thu, 03 Mar 2016 15:54:53 -0500 Received: from localhost (localhost [127.0.0.1]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP id 6452D380A04; Thu, 3 Mar 2016 21:54:51 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-transfer-encoding:content-type:content-type:mime-version :message-id:date:date:in-reply-to:subject:subject:from:from :user-agent:references:received:received:received; s=mdc; t= 1457038485; x=1458852886; bh=mieJHR+ceqgFe+36LW/RZ5xR1J1I6n6z4iq I06tew08=; b=PprMO6t1VKLKA67AtYbo1bQiV/xZcck71MRM+r5hVfRqiR95pAj Z5Y2dkkwaniHlOP8bTrN+Wi130oAV7kFotopODwP+tuGNIfCE+4moUSobP/pfOQt XukWl4T2LUBbTf999eALpN+NMPTV7F/ZAFpBA3/K4aE6zfw3lQz0o+SE= X-Virus-Scanned: amavisd-new at mdc-berlin.de Received: from venus.bbbm.mdc-berlin.de ([127.0.0.1]) by localhost (venus.bbbm.mdc-berlin.de [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id R83Tg7J1y3Aq; Thu, 3 Mar 2016 21:54:45 +0100 (CET) Received: from HTCATWO.mdc-berlin.net (puck.citx.mdc-berlin.de [141.80.36.101]) by venus.bbbm.mdc-berlin.de (Postfix) with ESMTP; Thu, 3 Mar 2016 21:54:45 +0100 (CET) Received: from localhost (141.80.180.135) by HTCATWO.mdc-berlin.net (141.80.180.125) with Microsoft SMTP Server (TLS) id 14.3.266.1; Thu, 3 Mar 2016 21:54:44 +0100 References: <874mgpj3p5.fsf@kyleam.com> <87pozd3ath.fsf@elephly.net> <87twoisu2v.fsf@kyleam.com> <87egfmfhvj.fsf@gnu.org> <87twohr0wc.fsf@kyleam.com> <87wptdj8ku.fsf@gnu.org> <87r3j7qdc1.fsf@kyleam.com> <87egbsegdb.fsf@gnu.org> User-agent: mu4e 0.9.13; emacs 24.5.1 From: Ricardo Wurmus To: Ludovic =?utf-8?Q?Court=C3=A8s?= Subject: Re: bug#21909: Segfault with eigen in R In-Reply-To: <87egbsegdb.fsf@gnu.org> Date: Thu, 3 Mar 2016 21:54:44 +0100 Message-ID: <87y49z9t9n.fsf@mdc-berlin.de> MIME-Version: 1.0 Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: 8bit X-Originating-IP: [141.80.180.135] X-TM-AS-Product-Ver: SMEX-11.0.0.4255-8.000.1202-22170.002 X-TM-AS-Result: No-1.637400-0.000000-31 X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-Spam-Score: -5.0 (-----) X-Debbugs-Envelope-To: 21909 Cc: Kyle Meyer , 21909@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: -5.0 (-----) Ludovic Courtès writes: > Ricardo Wurmus skribis: > >> We have since removed OpenBLAS from the inputs of R and just use the >> internal BLAS instead. Without OpenBLAS I cannot reproduce this bug >> any more. > > Nice. So we can close? I had already closed it in a subsequent email to control@debbugs.gnu.org. ~~ Ricardo From unknown Tue Jun 17 20:13:05 2025 Received: (at fakecontrol) by fakecontrolmessage; To: internal_control@debbugs.gnu.org From: Debbugs Internal Request Subject: Internal Control Message-Id: bug archived. Date: Fri, 01 Apr 2016 11:24:03 +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