Received: (at submit) by debbugs.gnu.org; 19 Dec 2022 12:00:29 +0000 From debbugs-submit-bounces <at> debbugs.gnu.org Mon Dec 19 07:00:28 2022 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> To: bug-guix@HIDDEN Subject: Incompatibilities between gcc-toolchain and R packages 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-Debbugs-Envelope-To: submit 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
Lars-Dominik Braun <lars@HIDDEN>
:bug-guix@HIDDEN
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