X-Loop: help-debbugs@HIDDEN Subject: bug#60200: Incompatibilities between gcc-toolchain and R packages Resent-From: Lars-Dominik Braun <lars@HIDDEN> Original-Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> Resent-CC: bug-guix@HIDDEN Resent-Date: Mon, 19 Dec 2022 12:01:02 +0000 Resent-Message-ID: <handler.60200.B.167145122919994 <at> debbugs.gnu.org> Resent-Sender: help-debbugs@HIDDEN X-GNU-PR-Message: report 60200 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: 60200 <at> debbugs.gnu.org X-Debbugs-Original-To: bug-guix@HIDDEN Received: via spool by submit <at> debbugs.gnu.org id=B.167145122919994 (code B ref -1); Mon, 19 Dec 2022 12:01:02 +0000 Received: (at submit) by debbugs.gnu.org; 19 Dec 2022 12:00:29 +0000 Received: from localhost ([127.0.0.1]:38338 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <debbugs-submit-bounces <at> debbugs.gnu.org>) id 1p7Eom-0005CQ-FL for submit <at> debbugs.gnu.org; Mon, 19 Dec 2022 07:00:28 -0500 Received: from lists.gnu.org ([209.51.188.17]:45904) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from <lars@HIDDEN>) id 1p7Eok-0005CK-Id for submit <at> debbugs.gnu.org; Mon, 19 Dec 2022 07:00:27 -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 <lars@HIDDEN>) id 1p7Eoi-0002B0-Bx for bug-guix@HIDDEN; Mon, 19 Dec 2022 07:00:26 -0500 Received: from mout-p-102.mailbox.org ([80.241.56.152]) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_CHACHA20_POLY1305:256) (Exim 4.90_1) (envelope-from <lars@HIDDEN>) id 1p7Eof-0001DM-Gr for bug-guix@HIDDEN; Mon, 19 Dec 2022 07:00:23 -0500 Received: from smtp102.mailbox.org (smtp102.mailbox.org [IPv6:2001:67c:2050:b231:465::102]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange ECDHE (P-384) server-signature RSA-PSS (4096 bits) server-digest SHA256) (No client certificate requested) by mout-p-102.mailbox.org (Postfix) with ESMTPS id 4NbJDN1tJ2z9sqw for <bug-guix@HIDDEN>; Mon, 19 Dec 2022 13:00:04 +0100 (CET) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=6xq.net; s=MBO0001; t=1671451204; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type; bh=Cw7Ngt0BeLW1uCi/DST1K8dgA7JHcIN5i8JGlBSOav4=; b=1OdVOr+aMp3qRceYJgbEsOTuwLo+Rq7N83SRlY0WnIlAyJhQ517D9vHMNmj8NKE7xHTOjQ F91LMpVJhswp5s7ak6zlh+mzum/dMEHROCdRos0hwt9F5dLhf1EofevpBdBh+WcDcSOrBO 9fLjmvAXrgtgiVcBFec90W1GAhEB4Z936xbgfJMSIpK3yY1y/Pb/ia/BF2UwKu72McpXjd o7uHnRcz5UFZYDWbZRR1eYYgAeKDLTYEXdI3zi8ZNnDhJaVLR4h1wgiMuHSdfSEBW+OapJ F8SG8EuhaNB4aJNJlIz1Qkn2+FsVSZ1yM4cXRX0N6ZuHqSrwt2z/QZSA3txbLg== Date: Mon, 19 Dec 2022 13:00:02 +0100 From: Lars-Dominik Braun <lars@HIDDEN> Message-ID: <Y6BSQpbK7BgW5Idk@HIDDEN> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Disposition: inline X-Rspamd-Queue-Id: 4NbJDN1tJ2z9sqw Received-SPF: pass client-ip=80.241.56.152; envelope-from=lars@HIDDEN; helo=mout-p-102.mailbox.org 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, SPF_HELO_NONE=0.001, SPF_PASS=-0.001 autolearn=ham autolearn_force=no X-Spam_action: no action X-Spam-Score: -1.6 (-) X-BeenThere: debbugs-submit <at> debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: <debbugs-submit.debbugs.gnu.org> List-Unsubscribe: <https://debbugs.gnu.org/cgi-bin/mailman/options/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=unsubscribe> List-Archive: <https://debbugs.gnu.org/cgi-bin/mailman/private/debbugs-submit/> List-Post: <mailto:debbugs-submit <at> debbugs.gnu.org> List-Help: <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=help> List-Subscribe: <https://debbugs.gnu.org/cgi-bin/mailman/listinfo/debbugs-submit>, <mailto:debbugs-submit-request <at> debbugs.gnu.org?subject=subscribe> Errors-To: debbugs-submit-bounces <at> debbugs.gnu.org Sender: "Debbugs-submit" <debbugs-submit-bounces <at> debbugs.gnu.org> X-Spam-Score: -2.6 (--) Hi, I ran into issues with the package r-brms. Take the following reproducer as an example: $ guix shell r-brms r make sed gcc-toolchain bash -C --no-cwd --share=/tmp $ R > library(brms) > fit1 <- brm(count ~ zAge + zBase * Trt + (1|patient), data = epilepsy, family = poisson()) Compiling Stan program... Error in dyn.load(libLFile) : unable to load shared object '/tmp/RtmpKqzbYg/file3245e787c.so': /gnu/store/vqhamsanmlm8v6f90a635zc6gmhwlphp-gfortran-10.3.0-lib/lib/libstdc++.so.6: version `GLIBCXX_3.4.29' not found (required by /tmp/RtmpKqzbYg/file3245e787c.so) Error in sink(type = "output") : invalid connection The same code works well with gcc-toolchain@10 instead of gcc-toolchain (@12, which is the default). As we can see the generated shared library above depends on GCC 12, 10 and GFortran 10 at the same time: $ ldd /tmp/RtmpKqzbYg/file3245e787c.so | grep -e gcc -e fortran libstdc++.so.6 => /gnu/store/4zvswpr2h3b7dvqpvjcdam8vfhyjrmgl-gcc-12.2.0-lib/lib/libstdc++.so.6 (0x00007f69bd9fc000) libgcc_s.so.1 => /gnu/store/4zvswpr2h3b7dvqpvjcdam8vfhyjrmgl-gcc-12.2.0-lib/lib/libgcc_s.so.1 (0x00007f69bd898000) libgfortran.so.5 => /gnu/store/vqhamsanmlm8v6f90a635zc6gmhwlphp-gfortran-10.3.0-lib/lib/libgfortran.so.5 (0x00007f69bd3e6000) libquadmath.so.0 => /gnu/store/094bbaq6glba86h1d4cj16xhdi6fk2jl-gcc-10.3.0-lib/lib/libquadmath.so.0 (0x00007f69bd39b000) libgomp.so.1 => /gnu/store/094bbaq6glba86h1d4cj16xhdi6fk2jl-gcc-10.3.0-lib/lib/libgomp.so.1 (0x00007f69bccf9000) The command used to link that .so is revealed by strace to be (filenames are random and may differ between runs): ["g++", "-std=gnu++14", "-shared", "-L/gnu/store/145dmr8drw3yzrdhzbsksi05p599hrs6-r-minimal-4.2.2/lib/R/lib", "-L/usr/local/lib", "-o", "file3373276d0.so", "file3373276d0.o", "/gnu/store/5rdg6sv1nrg1ikqxcykvdh9g4yd2xjvy-r-rstan-2.21.7/site-library/rstan/lib//libStanServices.a", "-L/gnu/store/y7rvp47mz3hcnpvnqsx42qz5yvs10pnl-r-stanheaders-2.21.0-7/site-library/StanHeaders/lib/", "-lStanHeaders", "-L/gnu/store/01lhjrrkvrnsjd8xh4ssdn3bgxc422jl-r-rcppparallel-5.1.5/site-library/RcppParallel/lib/", "-ltbb", "-L/gnu/store/145dmr8drw3yzrdhzbsksi05p599hrs6-r-minimal-4.2.2/lib/R/lib", "-lR"] So it links against libStanServices.a, libStanHeaders(.a), libtbb(.so) and libR(.so) of which only libR has a reference to gfortran: $ ldd /gnu/store/145dmr8drw3yzrdhzbsksi05p599hrs6-r-minimal-4.2.2/lib/R/lib/libR.so | grep -i fortran libgfortran.so.5 => /gnu/store/vqhamsanmlm8v6f90a635zc6gmhwlphp-gfortran-10.3.0-lib/lib/libgfortran.so.5 (0x00007f5be49db000) That means every software linking against R is also incompatible with the current default gcc-toolchain (when using the command line or specifications; different story when writing package recipes). Possible solutions: - Make gcc-toolchain@10 the default and rename gcc-toolchain@12 to gcc-toolchain-next@12, like we do for Haskell and (sometimes) Python. - Update, both, the default GCC and GFortran to version 12. - Explicitly depend on the correct gcc-toolchain in packages that need a compiler. Cheers, Lars
Content-Disposition: inline Content-Transfer-Encoding: quoted-printable MIME-Version: 1.0 X-Mailer: MIME-tools 5.505 (Entity 5.505) Content-Type: text/plain; charset=utf-8 X-Loop: help-debbugs@HIDDEN From: help-debbugs@HIDDEN (GNU bug Tracking System) To: Lars-Dominik Braun <lars@HIDDEN> Subject: bug#60200: Acknowledgement (Incompatibilities between gcc-toolchain and R packages) Message-ID: <handler.60200.B.167145122919994.ack <at> debbugs.gnu.org> References: <Y6BSQpbK7BgW5Idk@HIDDEN> X-Gnu-PR-Message: ack 60200 X-Gnu-PR-Package: guix Reply-To: 60200 <at> debbugs.gnu.org Date: Mon, 19 Dec 2022 12:01:02 +0000 Thank you for filing a new bug report with debbugs.gnu.org. This is an automatically generated reply to let you know your message has been received. Your message is being forwarded to the package maintainers and other interested parties for their attention; they will reply in due course. Your message has been sent to the package maintainer(s): bug-guix@HIDDEN If you wish to submit further information on this problem, please send it to 60200 <at> debbugs.gnu.org. Please do not send mail to help-debbugs@HIDDEN unless you wish to report a problem with the Bug-tracking system. --=20 60200: https://debbugs.gnu.org/cgi/bugreport.cgi?bug=3D60200 GNU Bug Tracking System Contact help-debbugs@HIDDEN with problems
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