Re: [igraph] Problem installation

[Tamas Nepusz]

Hello,

This is an ongoing issue without a definite resolution yet; here's the
corresponding bug report on Github:

https://github.com/igraph/igraph/issues/598

The important part is this comment:

https://github.com/igraph/igraph/issues/598#issuecomment-58337488

This gives you a patched setup.py, which does *not* solve your problem yet, but
takes you almost all the way there. The key point is that the patched setup.py
allows one to exclude certain libraries from being linked statically when
igraph is compiled. Look for the following line:

buildcfg.replace_static_libraries(exclusions=["m"])

and replace it with something like this:

buildcfg.replace_static_libraries(exclusions=["m", "xml2"])

Then remove any "build" directories that the previous build attempts may have
created, and then try to run "python setup.py install --user" again. Hopefully
it does the trick.

All the best,
T.

On 11/10, José Manuel Monroy Kuhn wrote:
> Hello!!
> 
> I need python igraph to run trans ABySS. I am installing it on a cluster
> where I dont have root access.
> I tried to do as follows
> 
> python setup.py install --user
> But I got this error
> 
> /usr/bin/ld: /usr/lib64/libxml2.a(entities.o): relocation R_X86_64_32
> against `.text' can not be used when making a shared object; recompile
> with -fPIC
> /usr/lib64/libxml2.a: could not read symbols: Bad value
> collect2: error: ld returned 1 exit status
> error: command 'gcc' failed with exit status 1
> 
> I know from here
> https://lists.nongnu.org/archive/html/igraph-help/2014-05/msg00045.html that
> the static version of libxml2 on my system was not compiled with the -fPIC
> option enabled, so it cannot be linked to a dynamic library. The problem is
> I cannot do what they suggest because I do not have root privileges.
> I tried to compile libxml2 with -fPIC option eneabled on my home directory
> and add it to my PATH but I get the same error. I dont know haw to make it
> use the libxml2 installed in my home directory.
> Is it possible? Is there any other way?
> 
> Thank you for your time
> Cheers
> 
> J. Manuel

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-- 
T.