From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 169E41382C5 for ; Fri, 19 Mar 2021 14:31:49 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 0FCC3E0893; Fri, 19 Mar 2021 14:31:48 +0000 (UTC) Received: from bumble.maple.relay.mailchannels.net (bumble.maple.relay.mailchannels.net [23.83.214.25]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 88E56E0893 for ; Fri, 19 Mar 2021 14:31:47 +0000 (UTC) X-Sender-Id: dreamhost|x-authsender|marcvinyals@velodius.com Received: from relay.mailchannels.net (localhost [127.0.0.1]) by relay.mailchannels.net (Postfix) with ESMTP id F40C77E3183 for ; Fri, 19 Mar 2021 14:31:45 +0000 (UTC) X-Sender-Id: dreamhost|x-authsender|marcvinyals@velodius.com Received: from pdx1-sub0-mail-a32.g.dreamhost.com (pop.dreamhost.com [64.90.62.162]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384) by 100.96.13.54 (trex/6.1.1); Fri, 19 Mar 2021 14:31:45 +0000 X-MC-Relay: Neutral X-MailChannels-SenderId: dreamhost|x-authsender|marcvinyals@velodius.com X-MailChannels-Auth-Id: dreamhost X-Industry-Abaft: 690bbc5758e5bd8c_1616164305384_1018337594 X-MC-Loop-Signature: 1616164305384:901859160 X-MC-Ingress-Time: 1616164305383 Received: from pdx1-sub0-mail-a32.g.dreamhost.com (localhost [127.0.0.1]) by pdx1-sub0-mail-a32.g.dreamhost.com (Postfix) with ESMTP id BAFA27E0BC for ; Fri, 19 Mar 2021 07:31:42 -0700 (PDT) DKIM-Signature: v=1; a=rsa-sha1; c=relaxed; d=velodius.com; h=date:from :to:subject:message-id:in-reply-to:references:mime-version :content-type:content-transfer-encoding; s=velodius.com; bh=OJ6n L/5ViiM4xbENeGHY4q5xEG4=; b=aJ7JZFZBAGeExNGfcT/XJpCt3Z2WlIGHGfzN ccFV37vpnXM0d8HOhu3ievQQh5sIMyni8GCQ5pos03gbkMzWrXpND5OmsCpT3MqO m4WW8FWNOeZkdxvsHcndlSqNj3nTu5Z8YUb2ycQiBUhLhqipX3Q5J7u+OM2O9kWq lO7XrQ8= Date: Fri, 19 Mar 2021 16:31:36 +0200 X-DH-BACKEND: pdx1-sub0-mail-a32 From: Marc Vinyals To: gentoo-science@lists.gentoo.org Subject: Re: [gentoo-science] ImportError with latest python-igraph Message-ID: <20210319163136.24b270bc@clevo-marc> In-Reply-To: References: <20210319020757.69892299@clevo-marc> X-Mailer: Claws Mail 3.17.8 (GTK+ 2.24.32; x86_64-pc-linux-gnu) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-science@lists.gentoo.org Reply-to: gentoo-science@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable X-Archives-Salt: 8cee2746-65df-4148-9af5-1e3ea5d7a34d X-Archives-Hash: e748aee10a79c75aeb8cfef7ea67a044 Sure: $ LANG=3DC readelf -d /usr/lib/python3.8/site-packages/igraph/_igraph.cpyth= on-38-x86_64-linux-gnu.so Dynamic section at offset 0x8ac60 contains 25 entries: Tag Type Name/Value 0x0000000000000001 (NEEDED) Shared library: [libigraph.so.0] 0x0000000000000001 (NEEDED) Shared library: [libc.so.6] 0x000000000000000c (INIT) 0x1e000 0x000000000000000d (FINI) 0x4e96c 0x0000000000000019 (INIT_ARRAY) 0x8bc50 0x000000000000001b (INIT_ARRAYSZ) 8 (bytes) 0x000000000000001a (FINI_ARRAY) 0x8bc58 0x000000000000001c (FINI_ARRAYSZ) 8 (bytes) 0x000000006ffffef5 (GNU_HASH) 0x200 0x0000000000000005 (STRTAB) 0x7e88 0x0000000000000006 (SYMTAB) 0x1c18 0x000000000000000a (STRSZ) 28749 (bytes) 0x000000000000000b (SYMENT) 24 (bytes) 0x0000000000000003 (PLTGOT) 0x8c000 0x0000000000000002 (PLTRELSZ) 14712 (bytes) 0x0000000000000014 (PLTREL) RELA 0x0000000000000017 (JMPREL) 0x1a368 0x0000000000000007 (RELA) 0xf760 0x0000000000000008 (RELASZ) 44040 (bytes) 0x0000000000000009 (RELAENT) 24 (bytes) 0x000000006ffffffe (VERNEED) 0xf710 0x000000006fffffff (VERNEEDNUM) 1 0x000000006ffffff0 (VERSYM) 0xeed6 0x000000006ffffff9 (RELACOUNT) 1387 0x0000000000000000 (NULL) 0x0 Also, the missing symbol appears to be in the library: $ nm -D -g /usr/lib/python3.8/site-packages/igraph/_igraph.cpython-38-x86_6= 4-linux-gnu.so | grep igraph_subcomponent U igraph_subcomponent El Fri, 19 Mar 2021 19:15:09 +1300 Fran=C3=A7ois Bissey va escriure el seg=C3=BCent: > Can you post the output of=20 > readelf -d > /usr/lib/python3.8/site-packages/igraph/_igraph.cpython-38-x86_64-linux-g= nu.so > with version 0.9.0? >=20 > > On 19/03/2021, at 13:09, Marc Vinyals > > wrote: > >=20 > > Hi all, > >=20 > > I am running into trouble when trying to use > > dev-python/python-igraph-0.9.0 with dev-libs/igraph-0.9.0: > >=20 > > $ python3 > > Python 3.8.8 (default, Mar 14 2021, 23:44:05)=20 > > [GCC 9.3.0] on linux > > Type "help", "copyright", "credits" or "license" for more > > information. =20 > >>>> import igraph =20 > > Traceback (most recent call last): > > File "", line 1, in > > File "/usr/lib/python3.8/site-packages/igraph/__init__.py", line > > 31, in from igraph._igraph import ( > > ImportError: > > /usr/lib/python3.8/site-packages/igraph/_igraph.cpython-38-x86_64-linux= -gnu.so: > > undefined symbol: igraph_subcomponent > >=20 > > To get this to work I have to downgrade both igraph and > > python-igraph to version 0.8.3 (mixing and matching do not work > > either because of different reasons, but that would be a separate > > issue). I did not try igraph-0.8.5. > >=20 > > I did not find any reports of this issue upstream and this looks too > > basic to remain unnoticed, so I suspect the problem is somewhere > > else on my side, but just in case can anyone reproduce it? > >=20 > > Best, > > Marc > > =20 >=20 >=20