* [gentoo-science] ImportError with latest python-igraph
@ 2021-03-19 0:09 Marc Vinyals
2021-03-19 6:15 ` François Bissey
0 siblings, 1 reply; 4+ messages in thread
From: Marc Vinyals @ 2021-03-19 0:09 UTC (permalink / raw
To: gentoo-science
Hi all,
I am running into trouble when trying to use
dev-python/python-igraph-0.9.0 with dev-libs/igraph-0.9.0:
$ python3
Python 3.8.8 (default, Mar 14 2021, 23:44:05)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import igraph
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.8/site-packages/igraph/__init__.py", line 31,
in <module> from igraph._igraph import (
ImportError:
/usr/lib/python3.8/site-packages/igraph/_igraph.cpython-38-x86_64-linux-gnu.so:
undefined symbol: igraph_subcomponent
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.
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?
Best,
Marc
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [gentoo-science] ImportError with latest python-igraph
2021-03-19 0:09 [gentoo-science] ImportError with latest python-igraph Marc Vinyals
@ 2021-03-19 6:15 ` François Bissey
2021-03-19 14:31 ` Marc Vinyals
0 siblings, 1 reply; 4+ messages in thread
From: François Bissey @ 2021-03-19 6:15 UTC (permalink / raw
To: gentoo-science
Can you post the output of
readelf -d /usr/lib/python3.8/site-packages/igraph/_igraph.cpython-38-x86_64-linux-gnu.so
with version 0.9.0?
> On 19/03/2021, at 13:09, Marc Vinyals <marcvinyals@velodius.com> wrote:
>
> Hi all,
>
> I am running into trouble when trying to use
> dev-python/python-igraph-0.9.0 with dev-libs/igraph-0.9.0:
>
> $ python3
> Python 3.8.8 (default, Mar 14 2021, 23:44:05)
> [GCC 9.3.0] on linux
> Type "help", "copyright", "credits" or "license" for more information.
>>>> import igraph
> Traceback (most recent call last):
> File "<stdin>", line 1, in <module>
> File "/usr/lib/python3.8/site-packages/igraph/__init__.py", line 31,
> in <module> from igraph._igraph import (
> ImportError:
> /usr/lib/python3.8/site-packages/igraph/_igraph.cpython-38-x86_64-linux-gnu.so:
> undefined symbol: igraph_subcomponent
>
> 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.
>
> 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?
>
> Best,
> Marc
>
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [gentoo-science] ImportError with latest python-igraph
2021-03-19 6:15 ` François Bissey
@ 2021-03-19 14:31 ` Marc Vinyals
2021-03-19 18:55 ` François Bissey
0 siblings, 1 reply; 4+ messages in thread
From: Marc Vinyals @ 2021-03-19 14:31 UTC (permalink / raw
To: gentoo-science
Sure:
$ LANG=C readelf -d /usr/lib/python3.8/site-packages/igraph/_igraph.cpython-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_64-linux-gnu.so | grep igraph_subcomponent
U igraph_subcomponent
El Fri, 19 Mar 2021 19:15:09 +1300
François Bissey <fbissey@slingshot.co.nz> va escriure el següent:
> Can you post the output of
> readelf -d
> /usr/lib/python3.8/site-packages/igraph/_igraph.cpython-38-x86_64-linux-gnu.so
> with version 0.9.0?
>
> > On 19/03/2021, at 13:09, Marc Vinyals <marcvinyals@velodius.com>
> > wrote:
> >
> > Hi all,
> >
> > I am running into trouble when trying to use
> > dev-python/python-igraph-0.9.0 with dev-libs/igraph-0.9.0:
> >
> > $ python3
> > Python 3.8.8 (default, Mar 14 2021, 23:44:05)
> > [GCC 9.3.0] on linux
> > Type "help", "copyright", "credits" or "license" for more
> > information.
> >>>> import igraph
> > Traceback (most recent call last):
> > File "<stdin>", line 1, in <module>
> > File "/usr/lib/python3.8/site-packages/igraph/__init__.py", line
> > 31, in <module> from igraph._igraph import (
> > ImportError:
> > /usr/lib/python3.8/site-packages/igraph/_igraph.cpython-38-x86_64-linux-gnu.so:
> > undefined symbol: igraph_subcomponent
> >
> > 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.
> >
> > 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?
> >
> > Best,
> > Marc
> >
>
>
^ permalink raw reply [flat|nested] 4+ messages in thread* Re: [gentoo-science] ImportError with latest python-igraph
2021-03-19 14:31 ` Marc Vinyals
@ 2021-03-19 18:55 ` François Bissey
0 siblings, 0 replies; 4+ messages in thread
From: François Bissey @ 2021-03-19 18:55 UTC (permalink / raw
To: gentoo-science
> On 20/03/2021, at 03:31, Marc Vinyals <marcvinyals@velodius.com> wrote:
>
> $ nm -D -g /usr/lib/python3.8/site-packages/igraph/_igraph.cpython-38-x86_64-linux-gnu.so | grep igraph_subcomponent
>
> U igraph_subcomponent
“U” is for undefined I think. So, it needs to be in one of the loaded
libraries. Since you know how to use “nm” can you do the search on libigraph?
It looks like an upstream issue or possibly a subtle fault in the build system
for the library.
François
^ permalink raw reply [flat|nested] 4+ messages in thread
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2021-03-19 0:09 [gentoo-science] ImportError with latest python-igraph Marc Vinyals
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2021-03-19 14:31 ` Marc Vinyals
2021-03-19 18:55 ` François Bissey
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