From unknown Sat Jun 21 03:23:43 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#43855 <43855@debbugs.gnu.org> To: bug#43855 <43855@debbugs.gnu.org> Subject: Status: gnu: python-shapely fails to build Reply-To: bug#43855 <43855@debbugs.gnu.org> Date: Sat, 21 Jun 2025 10:23:43 +0000 retitle 43855 gnu: python-shapely fails to build reassign 43855 guix submitter 43855 Malte Frank Gerdes severity 43855 normal thanks From debbugs-submit-bounces@debbugs.gnu.org Wed Oct 07 17:32:08 2020 Received: (at submit) by debbugs.gnu.org; 7 Oct 2020 21:32:08 +0000 Received: from localhost ([127.0.0.1]:58269 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQH2e-0004kk-Jm for submit@debbugs.gnu.org; Wed, 07 Oct 2020 17:32:08 -0400 Received: from lists.gnu.org ([209.51.188.17]:56030) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQH2d-0004kd-Hu for submit@debbugs.gnu.org; Wed, 07 Oct 2020 17:32:07 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:53764) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1kQH2d-0005e0-AP for bug-guix@gnu.org; Wed, 07 Oct 2020 17:32:07 -0400 Received: from mail-ej1-x62c.google.com ([2a00:1450:4864:20::62c]:33781) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1kQH2a-0000jR-DU for bug-guix@gnu.org; Wed, 07 Oct 2020 17:32:06 -0400 Received: by mail-ej1-x62c.google.com with SMTP id c22so5085730ejx.0 for ; Wed, 07 Oct 2020 14:32:03 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:date:message-id:user-agent:mime-version; bh=R5uL50riCc1j1YiqDNZiYLG3XZtYHcf9jYW2mYv9ePM=; b=pKmpkbRckuouB1jj5eVxkgPl1xm7mAastTKicNzRwUxm/mBl/GzUAqpWi550kfYyE9 rcfLIPxvT/86AtcsFXHN/7eJFvLDU98FhjaAp5IKCbSkT+gDVlg3fPXwnstcv5ado5b7 Vg8tfqgCBrYXdHkGJJ/TjNa6JrLeBVReiNRtql9ugahOeG0mNe3o2Y4pE6g8wzWx0h4S i3gj0sFotF6Sd3KM4ciaGAYSstVltejyB9S3Un25tlxihC4YcFzQTAGzQ7dim1U8rD0T Ua6B5ogQ7wJwyR35xARPu1JWB4zoLVncAHNoS3l9QYqaBKgenVsL8Hm+ym5GRbGggpn3 JaOQ== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:date:message-id:user-agent :mime-version; bh=R5uL50riCc1j1YiqDNZiYLG3XZtYHcf9jYW2mYv9ePM=; b=qdM+bIF1HjkFgAUZmaMyUZ1LYz15VCT4aF3U/5SV6GcamYEvF7MSAMQAiGbDdJeN5j B62FoQPB892b1WDOEmAc4O2/PiuqnHcTHCUQiBDoJhN0ff/aQczh9rh19+6U1kGkFwo4 WClZwOJOv5XQQojUz9xL2yPPEMl3nPiD89tZxYyJPtwYDE5F+ul5r2mKEBUaYvKxXzRJ AO/cM/L02kCN3FCUFwySa0DwbF95RC48wwRwiNDexsoThFnOkmuvI1iaA5QS9CFShFQS Gn8uyrnbDHs27btic2WDdLQ8207wpC3WOHgtO1WdYMaUvqZssL4KeO5uC9iRuA+qXL5v sa3w== X-Gm-Message-State: AOAM5318yRSSDRj3/DwPSmsmiL15NIlndBm11+MOqAe/vHWvU05+xVJ7 09NLaOPP8lYLcvmuKRR5pITBXnoQgY0= X-Google-Smtp-Source: ABdhPJz0DvgzxQ+InuU3MXIVKHXCtgROqnTDToK+F8WQlejl7AaJfdKDweCYWCKfbSheDlTuQXs6Ug== X-Received: by 2002:a17:906:a859:: with SMTP id dx25mr5333228ejb.459.1602106322292; Wed, 07 Oct 2020 14:32:02 -0700 (PDT) Received: from Morphium (ip-84-118-73-55.unity-media.net. [84.118.73.55]) by smtp.gmail.com with ESMTPSA id m7sm2673280edv.88.2020.10.07.14.32.01 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Wed, 07 Oct 2020 14:32:01 -0700 (PDT) From: Malte Frank Gerdes To: bug-guix@gnu.org Subject: gnu: python-shapely fails to build Date: Wed, 07 Oct 2020 23:32:01 +0200 Message-ID: <86h7r567u6.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain Received-SPF: pass client-ip=2a00:1450:4864:20::62c; envelope-from=malte.f.gerdes@gmail.com; helo=mail-ej1-x62c.google.com X-detected-operating-system: by eggs.gnu.org: No matching host in p0f cache. That's all we know. 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: 0.5 (/) 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 (--) Hi, python-shapely fails to build, because it can't find the c libary, the package definition was not complete (patch at the end). Now the package finds a C libary but the Test Suite fails with the follwoing error: --8<---------------cut here---------------start------------->8--- ====================================================================== FAIL: test_operations (tests.test_operations.OperationsTestCase) ---------------------------------------------------------------------- Traceback (most recent call last): File "/tmp/guix-build-python-shapely-1.6.4.post2.drv-0/Shapely-1.6.4.post2/tests/test_operations.py", line 25, in test_operations self.assertIsInstance(point.intersection(Point(-1, -1)), AssertionError: is not an instance of --8<---------------cut here---------------end--------------->8--- This package was last successfully built on 13th September. Malte --8<---------------cut here---------------start------------->8--- diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 459526941b..02744bfc6d 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -533,13 +533,16 @@ pidof, tty, taskset, pmap.") (let ((geos (assoc-ref inputs "geos")) (glibc (assoc-ref inputs ,(if (%current-target-system) "cross-libc" "libc")))) - (substitute* "shapely/geos.py" - (("_lgeos = load_dll\\('geos_c', fallbacks=.*\\)") - (string-append "_lgeos = load_dll('geos_c', fallbacks=['" - geos "/lib/libgeos_c.so'])")) - (("free = load_dll\\('c'\\)\\.free") - (string-append "free = load_dll('c', fallbacks=['" - glibc "/lib/libc.so.6']).free")))) + (map + (lambda (file) + (substitute* file + (("_lgeos = load_dll\\('geos_c', fallbacks=.*\\)") + (string-append "_lgeos = load_dll('geos_c', fallbacks=['" + geos "/lib/libgeos_c.so'])")) + (("free = load_dll\\('c'\\)\\.free") + (string-append "free = load_dll('c', fallbacks=['" + glibc "/lib/libc.so.6']).free")))) + '("shapely/geos.py" "shapely/_buildcfg.py"))) #t))))) (home-page "https://github.com/Toblerity/Shapely") (synopsis "Library for the manipulation and analysis of geometric objects") --8<---------------cut here---------------end--------------->8--- From debbugs-submit-bounces@debbugs.gnu.org Thu Oct 08 02:45:11 2020 Received: (at 43855) by debbugs.gnu.org; 8 Oct 2020 06:45:11 +0000 Received: from localhost ([127.0.0.1]:58524 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQPfr-0001ge-4j for submit@debbugs.gnu.org; Thu, 08 Oct 2020 02:45:11 -0400 Received: from flashner.co.il ([178.62.234.194]:37898) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQPfm-0001fl-As for 43855@debbugs.gnu.org; Thu, 08 Oct 2020 02:45:09 -0400 Received: from localhost (unknown [37.46.46.107]) by flashner.co.il (Postfix) with ESMTPSA id 0BAB84014A; Thu, 8 Oct 2020 06:44:59 +0000 (UTC) Date: Thu, 8 Oct 2020 09:44:27 +0300 From: Efraim Flashner To: Malte Frank Gerdes Subject: Re: bug#43855: gnu: python-shapely fails to build Message-ID: <20201008064427.GN21174@E5400> References: <86h7r567u6.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="TN8pJM9vJMHHFgJc" Content-Disposition: inline In-Reply-To: <86h7r567u6.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-Debbugs-Envelope-To: 43855 Cc: 43855@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 (-) --TN8pJM9vJMHHFgJc Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Wed, Oct 07, 2020 at 11:32:01PM +0200, Malte Frank Gerdes wrote: > Hi, >=20 > python-shapely fails to build, because it can't find the c libary, > the package definition was not complete (patch at the end). >=20 > Now the package finds a C libary but the Test Suite fails with the > follwoing error: >=20 > --8<---------------cut here---------------start------------->8--- > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > FAIL: test_operations (tests.test_operations.OperationsTestCase) > ---------------------------------------------------------------------- > Traceback (most recent call last): > File "/tmp/guix-build-python-shapely-1.6.4.post2.drv-0/Shapely-1.6.4.po= st2/tests/test_operations.py", line 25, in test_operations > self.assertIsInstance(point.intersection(Point(-1, -1)), > AssertionError: i= s not an instance of =20 > Malte >=20 > --8<---------------cut here---------------start------------->8--- > diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm > index 459526941b..02744bfc6d 100644 > --- a/gnu/packages/python-xyz.scm > +++ b/gnu/packages/python-xyz.scm > @@ -533,13 +533,16 @@ pidof, tty, taskset, pmap.") > (let ((geos (assoc-ref inputs "geos")) > (glibc (assoc-ref inputs ,(if (%current-target-system) > "cross-libc" "libc")))) > - (substitute* "shapely/geos.py" > - (("_lgeos =3D load_dll\\('geos_c', fallbacks=3D.*\\)") > - (string-append "_lgeos =3D load_dll('geos_c', fallback= s=3D['" > - geos "/lib/libgeos_c.so'])")) > - (("free =3D load_dll\\('c'\\)\\.free") > - (string-append "free =3D load_dll('c', fallbacks=3D['" > - glibc "/lib/libc.so.6']).free")))) > + (map > + (lambda (file) > + (substitute* file > + (("_lgeos =3D load_dll\\('geos_c', fallbacks=3D.*\\)= ") > + (string-append "_lgeos =3D load_dll('geos_c', fallb= acks=3D['" > + geos "/lib/libgeos_c.so'])")) > + (("free =3D load_dll\\('c'\\)\\.free") > + (string-append "free =3D load_dll('c', fallbacks=3D= ['" > + glibc "/lib/libc.so.6']).free")))) > + '("shapely/geos.py" "shapely/_buildcfg.py"))) > #t))))) > (home-page "https://github.com/Toblerity/Shapely") > (synopsis "Library for the manipulation and analysis of geometric ob= jects") > --8<---------------cut here---------------end--------------->8--- >=20 substitute* can take a list, so it would be simpler to write this as: substitute* '("shapely/geos.py" "shapely/_buildcfg.py") --=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 --TN8pJM9vJMHHFgJc Content-Type: application/pgp-signature; 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[84.118.73.55]) by smtp.gmail.com with ESMTPSA id cw15sm3916944ejb.47.2020.10.08.05.05.50 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 08 Oct 2020 05:05:51 -0700 (PDT) From: Malte Frank Gerdes To: 43855@debbugs.gnu.org Subject: Re: bug#43855: gnu: python-shapely fails to build References: <86h7r567u6.fsf@gmail.com> <20201008064427.GN21174@E5400> Date: Thu, 08 Oct 2020 14:05:50 +0200 In-Reply-To: <20201008064427.GN21174@E5400> (Efraim Flashner's message of "Thu, 8 Oct 2020 09:44:27 +0300") Message-ID: <87tuv4vs69.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.1 (gnu/linux) MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43855 Cc: Efraim Flashner 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 (-) Efraim Flashner writes: > 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=/gnu/store/q9rm8h9imazsq2c4qiv2yjpvlvliywqb-python-3.8.2/lib > 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/vectorized/_vectorized.cpython-38-x86_64-linux-gnu.so > warning: no library file corresponding to > '/gnu/store/603imkkh2bqs01z8ik0b2ndgpdz0jghk-python-numpy-1.17.3/lib/python3.8/site-packages/numpy/core/include' > found (skipping) > warning: no library file corresponding to > '/gnu/store/603imkkh2bqs01z8ik0b2ndgpdz0jghk-python-numpy-1.17.3/lib/python3.8/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__='setup.py';f=getattr(tokenize, 'open', > open)(__file__);code=f.read().replace('\\r\\n', > '\\n');f.close();exec(compile(code, __file__, 'exec'))" "test" failed with > 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-1.7.1.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/2yz1ybl0156canhfz4vhay0g473c5nwv-python-shapely-1.7.1.drv' failed > > Do you want to take a stab at updating python-shapely to 1.7.1? 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? :) > substitute* can take a list, so it would be simpler to write this as: > substitute* '("shapely/geos.py" > "shapely/_buildcfg.py") One more thing i've learned :) Malte From debbugs-submit-bounces@debbugs.gnu.org Thu Oct 08 14:26:01 2020 Received: (at 43855) by debbugs.gnu.org; 8 Oct 2020 18:26:01 +0000 Received: from localhost ([127.0.0.1]:33129 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQac5-0006vu-6j for submit@debbugs.gnu.org; Thu, 08 Oct 2020 14:26:01 -0400 Received: from mail-ej1-f52.google.com ([209.85.218.52]:35931) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQac2-0006vd-3B for 43855@debbugs.gnu.org; Thu, 08 Oct 2020 14:25:59 -0400 Received: by mail-ej1-f52.google.com with SMTP id qp15so9515248ejb.3 for <43855@debbugs.gnu.org>; Thu, 08 Oct 2020 11:25:58 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20161025; h=from:to:subject:date:message-id:user-agent:mime-version; bh=ZtIMedwO+adI4QHTuAyzKWuji0gvJs74wsy+lo8z0nc=; b=kTSyx6rahRMxOLZLpuvb/6LbqBzdt2nZ9WoS/PWYiyRWCcdKvhNsBrYM7CUFx0vVD9 /IMFsODlErpBiOd+Mn8ucbRSITGHPoD1Puy3mkOsMkOPA2mYgEEKuYku8HBfZYM1mzEZ sjYDnqYxiv6uzRhLmBiNpNQyDdmOlyiiU12IYzk17lt2vGnsDe0BbTEqTsN6ma0U+nDA wWiCrpzrT4QV58+O+9ofWw2yJwfe6sNBUUQa8gYPt9IW8mlno4N41FaD37t8tOGUMGMB pv/y8L1hXTqR3cw26HlcS8W40VpfJq4IOA0PrzzinRGbvGzxRM1wCfD7onPBtFCkc3q6 OUxA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:from:to:subject:date:message-id:user-agent :mime-version; bh=ZtIMedwO+adI4QHTuAyzKWuji0gvJs74wsy+lo8z0nc=; b=UIAKDoo9S3UnCYK8LkhGbpt2wNdg/VKZie+XqIpJO7WdkPVybjydM+W0E/FBeY1j7U WT0zRV5XXLH2EGDhDOmqmOaBU9uyotqMPl3BoOd3v2GFEzKW/En2UawYMrjLybRiZ2Ra /Xvgh1TAsyskjnK2hdbRRB27K9IKpa0hsG64vTD0hdDWqcYPbqePaSU/tSekyu3QkyT6 Df2i/fJZ3yNcQO+v1VNX3VNsLdmMyrwa//ZgO/5f+VEms/D+AssAvSY5RlG8hkyFm/bv aUCrTDIevnFCh02Fsk74b9E9UzmgdmG/YLrBIh5iqyajrA2hGWTcgnFP+KF5PX94fy5R PADQ== X-Gm-Message-State: AOAM531AGqDMatiIuI0OKrNAL/7HluXouyycAFpw1YBZg2I+qK3hEI0j bqbwrxFW2duPupQUzZ6tSggvNqDLSAoGew== X-Google-Smtp-Source: ABdhPJwzmCIFswZL28ab9f/O8m36JnYFKawSfh2FN90ftXxZZ/odB3YQDfIkXc1rZFL9i8pK58IJoA== X-Received: by 2002:a17:906:28db:: with SMTP id p27mr10354445ejd.424.1602181551951; Thu, 08 Oct 2020 11:25:51 -0700 (PDT) Received: from Morphium (ip-84-118-73-55.unity-media.net. [84.118.73.55]) by smtp.gmail.com with ESMTPSA id ck19sm4620998ejb.99.2020.10.08.11.25.50 for <43855@debbugs.gnu.org> (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Thu, 08 Oct 2020 11:25:51 -0700 (PDT) From: Malte Frank Gerdes To: 43855@debbugs.gnu.org Subject: [PATCH] gnu: python-shapely: Update to 1.7.1. Date: Thu, 08 Oct 2020 20:25:50 +0200 Message-ID: <86lfgglglt.fsf@gmail.com> User-Agent: Gnus/5.13 (Gnus v5.13) Emacs/27.1 (gnu/linux) MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="=-=-=" X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 43855 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 (-) --=-=-= Content-Type: text/plain It seems python-shapely assumes musl libc, because the store path of glibc was missing in one place. Now the Test suite runs without failure. Malte --=-=-= Content-Type: text/x-patch Content-Disposition: inline; filename=0001-gnu-python-shapely-Update-to-1.7.1.patch >From a320ab014d60f5401f409eb37ccb16aa23c32cf1 Mon Sep 17 00:00:00 2001 From: Malte Frank Gerdes Date: Thu, 8 Oct 2020 20:20:12 +0200 Subject: [PATCH] gnu: python-shapely: Update to 1.7.1. * gnu/packages/python-xyz.scm (python-shapely): Update to 1.7.1. --- gnu/packages/python-xyz.scm | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/gnu/packages/python-xyz.scm b/gnu/packages/python-xyz.scm index 459526941b..fa4a4f4954 100644 --- a/gnu/packages/python-xyz.scm +++ b/gnu/packages/python-xyz.scm @@ -507,14 +507,14 @@ pidof, tty, taskset, pmap.") (define-public python-shapely (package (name "python-shapely") - (version "1.6.4.post2") + (version "1.7.1") (source (origin (method url-fetch) (uri (pypi-uri "Shapely" version)) (sha256 (base32 - "03r42fmd9alp6r3q95ad6rldq2f7n1wimrw53zy5kpn33yv7pf64")))) + "0adiz4jwmwxk7k1awqifb1a9bj5x4nx4gglb5dz9liam21674h8n")))) (build-system python-build-system) (native-inputs `(("python-cython" ,python-cython) @@ -533,11 +533,14 @@ pidof, tty, taskset, pmap.") (let ((geos (assoc-ref inputs "geos")) (glibc (assoc-ref inputs ,(if (%current-target-system) "cross-libc" "libc")))) - (substitute* "shapely/geos.py" + (substitute* '("shapely/geos.py" "shapely/_buildcfg.py") (("_lgeos = load_dll\\('geos_c', fallbacks=.*\\)") (string-append "_lgeos = load_dll('geos_c', fallbacks=['" geos "/lib/libgeos_c.so'])")) (("free = load_dll\\('c'\\)\\.free") + (string-append "free = load_dll('c', fallbacks=['" + glibc "/lib/libc.so.6']).free")) + (("free = load_dll\\('c', fallbacks=.*\\)\\.free") (string-append "free = load_dll('c', fallbacks=['" glibc "/lib/libc.so.6']).free")))) #t))))) -- 2.28.0 --=-=-=-- From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 09 01:00:18 2020 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 To: Malte Frank Gerdes Subject: Re: bug#43855: gnu: python-shapely fails to build 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-Debbugs-Envelope-To: 43855 Cc: 43855@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 (-) --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-- From debbugs-submit-bounces@debbugs.gnu.org Fri Oct 09 01:02:08 2020 Received: (at 43855-done) by debbugs.gnu.org; 9 Oct 2020 05:02:08 +0000 Received: from localhost ([127.0.0.1]:33928 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQkXg-0001L4-0t for submit@debbugs.gnu.org; Fri, 09 Oct 2020 01:02:08 -0400 Received: from flashner.co.il ([178.62.234.194]:41086) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1kQkXd-0001F7-PE for 43855-done@debbugs.gnu.org; Fri, 09 Oct 2020 01:02:06 -0400 Received: from localhost (unknown [141.226.15.20]) by flashner.co.il (Postfix) with ESMTPSA id D9B184059A; Fri, 9 Oct 2020 05:01:59 +0000 (UTC) Date: Fri, 9 Oct 2020 08:01:27 +0300 From: Efraim Flashner To: Malte Frank Gerdes Subject: Re: bug#43855: [PATCH] gnu: python-shapely: Update to 1.7.1. Message-ID: <20201009050127.GC1157@E5400> References: <86h7r567u6.fsf@gmail.com> <86lfgglglt.fsf@gmail.com> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="BI5RvnYi6R4T2M87" Content-Disposition: inline In-Reply-To: <86lfgglglt.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-Debbugs-Envelope-To: 43855-done Cc: 43855-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 (-) --BI5RvnYi6R4T2M87 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable On Thu, Oct 08, 2020 at 08:25:50PM +0200, Malte Frank Gerdes wrote: > It seems python-shapely assumes musl libc, because the store path of > glibc was missing in one place. Now the Test suite runs without failure. >=20 > Malte >=20 Looks good! Certainly a smaller patch than I was expecting. I added a copyright line for you and pushed the patch. --=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 --BI5RvnYi6R4T2M87 Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQIzBAABCgAdFiEEoov0DD5VE3JmLRT3Qarn3Mo9g1EFAl9/7qcACgkQQarn3Mo9 g1H+fQ/9FihrYSwl/+cQ7wk2LsrN92Vmp/PcV9fJSpIQaJtsbLcps8fd8QYNUJjA P+JTo4YD4IrxFzJXKCUkj4pXcnoSVzi4x8o9mQkhYSy8gUopH0wtR13wMpyCAfsj 6J5HoLlbvZkY7yDGqVnyV1ncWxuDYOWfu+gqjtoMDL/8vg9NSs/u9u4J/QWbMwDx 24jQYKVKze7nuVKyu+8mjutqlfVoza+XaMx4wLeGzMOqUm55kxMsu+zIY2l+jg0/ Ra0myaAx7dXk2wzCqpoJDUBp8W/HuKxl+zQ7ZNv8dXJad0Zwmv/AQvmQ4G/u6p1X 6gG1HNVOjESraFwW7gqmc0oSiBel39Io069t1cay7QQnaz64U4XKfTb0lzwdAUY3 ESg5DFCsNurY77gyABVwWol0nkzC0IpCSbUC1WPnzvkgYQezxiaOAxT/pvltgmv7 mV5KxGRZlGlSSxqWA53zQ11AyeEcqr4xwyGWzNJs3dGgnr4QUqeFsk2yv25pl3uD W8Xhd6RTd13WNhrHIK7Dk4JSh7soXj4k/KIlcVowObc5EDaNnAAzVJE0b9WS8H3J 82qYZFGnIecDGRMI4SZoqdMAW+yc9W44+vFDVuAL2RwEftfGL+HdarVoZ0oNy2/2 YmtiJdrhD2cb/RoQMGb56b3WFFumUT1mCXPWmaMOV1X949Xhnc4= =nIf1 -----END PGP SIGNATURE----- --BI5RvnYi6R4T2M87-- From unknown Sat Jun 21 03:23:43 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, 06 Nov 2020 12:24:06 +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