conda installation fails: ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21' not found

[fidelram]

After installing leidenalg with conda I got the following error:

ImportError: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.21'  not found

I could solve it by downgrading to libgcc==5.2.0 (my original version was 7.2.0)

Initially, I tried to install with pip but got the error: Could not download and compile the C core of igraph.. Probably, I could have solve this issue by setting the source of igraph but I tried conda instead.

Maybe this is helpful if anyone has the same problem.

[vtraag]

Thanks for reporting the issue! Could I ask what OS your are on?

[fidelram]

Scientific Linux. However, most software comes from my own Anaconda installation.

[vtraag]

I can't seem to reproduce the problem. When I setup a Docker of Scientific Linux (7) from https://hub.docker.com/r/scientificlinux/sl/, install miniconda 3 and do

conda install -c conda-forge igraph python-igraph
conda install -c vtraag leidenalg

everything works correctly. Could you perhaps report exactly how to reproduce the problem from scratch (i.e. from a clean Scientific Linux docker)?

[fidelram]

For me, to trigger the error I do:
conda install libgcc==7.2.0

[vtraag]

I'm, sorry, but also using

conda install libgcc==7.2.0

everything works as expected when installing on a clean Scientific Linux (7) docker image. Perhaps it is something concerning the configuration of Scientific Linux outside of Anaconda?

[fidelram]

Something nasty is probably happening on my installation. I hope that at least this issue could help anyone else having the same problem.

Thanks for your time on checking this issue.

[vtraag]

Thanks for reporting. Hope it will help some others indeed!

[kaizen89]

I also got this error message

Cannot find the C core of igraph on this system using pkg-config.
    We will now try to download and compile the C core from scratch.
    Version number of the C core: 0.7.1.post6
    We will also try: 0.7.1

What do you advise?

[vtraag]

@kaizen89, I assume you are not trying to install using conda? It is probably a separate issue from the one reported here.

The problem is that the C core of igraph needs to be installed and compiled separately from the python-igraph interface, and the leidenalg package which is developed on top of that. If you are on a Unix type system, it should be feasible to compile this. If you are on Windows, this is more difficult, and it is by far the easiest to simply install the package using conda.

[kaizen89]

I'm on Linux, I tried with Conda and I got this

UnsatisfiableError: The following specifications were found to be incompatible with each other:                                                 



Package wheel conflicts for:
leidenalg -> python[version='>=3.6,<3.7.0a0'] -> pip -> wheel
python=3.7 -> pip -> wheel
Package ca-certificates conflicts for:
python=3.7 -> openssl[version='>=1.1.1a,<1.1.2a'] -> ca-certificates
leidenalg -> python[version='>=3.6,<3.7.0a0'] -> openssl=1.0 -> ca-certificates
Package setuptools conflicts for:
leidenalg -> python[version='>=3.6,<3.7.0a0'] -> pip -> setuptools
python=3.7 -> pip -> setuptools
Package pip conflicts for:
python=3.7 -> pip
leidenalg -> python[version='>=3.6,<3.7.0a0'] -> pip
Package python conflicts for:
python=3.7
Package certifi conflicts for:
leidenalg -> python[version='>=3.6,<3.7.0a0'] -> pip -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
python=3.7 -> pip -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
Package python-igraph conflicts for:
leidenalg -> python-igraph[version='>=0.7.1.0']

[vtraag]

OK, thanks for the report. I'll have to look into it.

[kaizen89]

I was able to install it after I installed the core library from https://igraph.org/c/#downloads.
Thanks

[vtraag]

Good to hear! I'll look into the conflict with versions nonetheless...