From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp2 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id eAWSIpruf1/hcAAA0tVLHw (envelope-from ) for ; Fri, 09 Oct 2020 05:01:14 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp2 with LMTPS id sLFwHpruf1+1cAAAB5/wlQ (envelope-from ) for ; Fri, 09 Oct 2020 05:01:14 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id B100C9401D0 for ; Fri, 9 Oct 2020 05:01:12 +0000 (UTC) Received: from localhost ([::1]:42452 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1kQkWl-0007h3-4a for larch@yhetil.org; Fri, 09 Oct 2020 01:01:11 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:41010) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kQkWc-0007gv-Ld for bug-guix@gnu.org; Fri, 09 Oct 2020 01:01:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:50605) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kQkWc-0002pw-BU for bug-guix@gnu.org; Fri, 09 Oct 2020 01:01:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1kQkWc-0000XN-Ar for bug-guix@gnu.org; Fri, 09 Oct 2020 01:01:02 -0400 X-Loop: help-debbugs@gnu.org Subject: bug#43855: gnu: python-shapely fails to build Resent-From: Efraim Flashner Original-Sender: "Debbugs-submit" Resent-CC: bug-guix@gnu.org Resent-Date: Fri, 09 Oct 2020 05:01:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 43855 X-GNU-PR-Package: guix X-GNU-PR-Keywords: To: Malte Frank Gerdes Received: via spool by 43855-submit@debbugs.gnu.org id=B43855.160221961832297 (code B ref 43855); Fri, 09 Oct 2020 05:01:02 +0000 Received: (at 43855) by debbugs.gnu.org; 9 Oct 2020 05:00:18 +0000 Received: from localhost ([127.0.0.1]:33918 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQkVt-0008OM-Ty for submit@debbugs.gnu.org; Fri, 09 Oct 2020 01:00:18 -0400 Received: from flashner.co.il ([178.62.234.194]:41074) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQkVo-0008Bz-OV for 43855@debbugs.gnu.org; Fri, 09 Oct 2020 01:00:16 -0400 Received: from localhost (unknown [141.226.15.20]) by flashner.co.il (Postfix) with ESMTPSA id 65D564059A; Fri, 9 Oct 2020 05:00:05 +0000 (UTC) Date: Fri, 9 Oct 2020 07:59:32 +0300 From: Efraim Flashner Message-ID: <20201009045932.GB1157@E5400> References: <86h7r567u6.fsf@gmail.com> <20201008064427.GN21174@E5400> <87tuv4vs69.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="Clx92ZfkiYIKRjnr" Content-Disposition: inline In-Reply-To: <87tuv4vs69.fsf@gmail.com> X-PGP-Key-ID: 0x41AAE7DCCA3D8351 X-PGP-Key: https://flashner.co.il/~efraim/efraim_flashner.asc X-PGP-Fingerprint: A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 X-Spam-Score: -0.0 (/) X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-Spam-Score: -1.0 (-) X-BeenThere: bug-guix@gnu.org List-Id: Bug reports for GNU Guix List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Cc: 43855@debbugs.gnu.org Errors-To: bug-guix-bounces+larch=yhetil.org@gnu.org Sender: "bug-Guix" X-Scanner: scn0 Authentication-Results: aspmx1.migadu.com; dkim=none; dmarc=none; spf=pass (aspmx1.migadu.com: domain of bug-guix-bounces@gnu.org designates 209.51.188.17 as permitted sender) smtp.mailfrom=bug-guix-bounces@gnu.org X-Spam-Score: -2.61 X-TUID: DOhfYFO8yv/5 --Clx92ZfkiYIKRjnr Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Thu, Oct 08, 2020 at 02:05:50PM +0200, Malte Frank Gerdes wrote: > Efraim Flashner writes: >=20 > > It turns out this is due to a change in geos with 3.8 > > https://github.com/Toblerity/Shapely/issues/799 > > > > If I cherry-pick the patch to fix it then it passes the test suite. If I > > upgrade python-shapely to 1.7.1 the fix is already included but there's > > a new build error: > > > > gcc -pthread -shared > > -Wl,-rpath=3D/gnu/store/q9rm8h9imazsq2c4qiv2yjpvlvliywqb-python-3.8.2/l= ib > > build/temp.linux-x86_64-3.8/shapely/vectorized/_vectorized.o > > -L/gnu/store/pinvpk9w6izxcwci4ghiwgvykmgsfy2c-geos-3.8.1/lib > > -L/gnu/store/q9rm8h9imazsq2c4qiv2yjpvlvliywqb-python-3.8.2/lib -lgeos_c= -o > > /tmp/guix-build-python-shapely-1.7.1.drv-0/Shapely-1.7.1/shapely/vector= ized/_vectorized.cpython-38-x86_64-linux-gnu.so > > warning: no library file corresponding to > > '/gnu/store/603imkkh2bqs01z8ik0b2ndgpdz0jghk-python-numpy-1.17.3/lib/py= thon3.8/site-packages/numpy/core/include' > > found (skipping) > > warning: no library file corresponding to > > '/gnu/store/603imkkh2bqs01z8ik0b2ndgpdz0jghk-python-numpy-1.17.3/lib/py= thon3.8/site-packages/numpy/core/include' > > found (skipping) > > error: Could not find lib c or load any of its variants ['libc.musl-x86= _64.so.1']. > > command "python" "-c" "import setuptools, > > tokenize;__file__=3D'setup.py';f=3Dgetattr(tokenize, 'open', > > open)(__file__);code=3Df.read().replace('\\r\\n', > > '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed w= ith > > status 1 > > builder for `/gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely= -1.7.1.drv' failed with exit code 1 > > build of /gnu/store/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7= =2E1.drv failed > > View build log at '/var/log/guix/drvs/2y/z1ybl0156canhfz4vhay0g473c5nwv= -python-shapely-1.7.1.drv.bz2'. > > guix build: error: build of `/gnu/store/2yz1ybl0156canhfz4vhay0g473c5nw= v-python-shapely-1.7.1.drv' failed > > > > Do you want to take a stab at updating python-shapely to 1.7.1? >=20 > I can certainly try to fix this. I will look into it in the evening. > BTW: Are you using musl libc as your primary libc? If so, that's cool, > how did you do that? :) Ah, no. It comes from the code. I suppose it would be possible to tell Guix to use musl instead of glibc but I don't think the build system is set up for that. > > substitute* can take a list, so it would be simpler to write this as: > > substitute* '("shapely/geos.py" > > "shapely/_buildcfg.py") >=20 > One more thing i've learned :) >=20 > Malte --=20 Efraim Flashner =D7=90=D7=A4=D7=A8=D7=99=D7=9D = =D7=A4=D7=9C=D7=A9=D7=A0=D7=A8 GPG key =3D A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 Confidentiality cannot be guaranteed on emails sent or received unencrypted --Clx92ZfkiYIKRjnr Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAl9/7jQACgkQQarn3Mo9 g1FlcA//SH+DfFMzEfhSscQvVgnmk18hvEWCXYsS2sLANMfA9RKJE/xbqvmSHNTV g9OPNBkp8YBqVN/Qc9R3iO1nMobShkA8Ko2X9dSOVH5Fb+M9RhcbCBtjTVJtdT2A d9NXDXNflHemHlFbXjCnViZerwIu4ZcfWu0JATsaq2xYJMtY06tSguqHkw2aqcG7 Ycr3m8JoYwcTOPsbP7ahi365dzxP66CJ/c7kKJON/zW/5/rbvdgCzFoMA56FcgYs tPxUs5AS/nQqp662BKfXzJW73bfP7+agxFNN2i5UuyXql1kCOFAAl5H8tiyze+J2 zmLVBSiqzQ1sF5Pog8ki0Yedr/mgjVgi7klFFxpcMROKC2GHlfKJSy37vxdijIRQ w1Zwda2XKxXgsop538kGsOd9KKYqrbpm9ksSw11ex2ztXqb6gCj7XQjI++Up0GXv /cOsvmP6Q78gRp+c5YSms7JbDPnlM1b6rxfWCAveiBNemaeMjpJddVGDk1aLMLNk fF4QchB7ikRls6YpotO8XDfxrEE7PJSuqXHWKq2Yg8bQoxojsikY88EKrxebdRrx XObim5emtxRPJeg6sbeNXlNOtU2TJtb9m+NVO7Wkm+uFFSNSASJsYj3uX1BDEhA8 ery31vrexPGu5bRquQurwTuUzVtTd0HrCQMxaDzWMiGuA23fOpE= =KS2a -----END PGP SIGNATURE----- --Clx92ZfkiYIKRjnr--