Closed xvazquezc closed 6 years ago
Hello. Thank you for bringing this to my attention. I have fixed the "warnings" issue. If you update PhyloRank to v0.0.35, it should install that latest version of biolib (v0.0.46) which fixes this issue. I have seen the issue regarding JSON serialization before. It appears to be specific to Anaconda. I assume you are on OS X? I haven't been able to reproduce this issue on Linux and am not sure what is causing the problem. Any insights you might have would be appreciated.
Hi,
Just updated to v0.0.36 but the JSON issue remains.
I use Ubuntu 16.04 and tried it within Anaconda and outside the conda environment in the main Python installation with no luck...
Initially I had installed the dependencies with conda install
so I remove them and added them again via pip
. Same error.
I tried in the HPC (CentOS) in Anaconda and after installing phylorank
it runs with no error.
I went through the 3 environments and check the Python libraries with pip freeze
comparing those in the HPC to the others... long story short: matplotlib
versions are different and downgrading it to matplotlib==2.0.0
fixes the problem. It works in my local Anaconda environment without error.
As a double-check I upgraded matplotlib
in the HPC and it stops working. Right now matplotlib==2.1.2
does not work for some reason.
Hello. Thank you for investigating this. I believe this is actually a mpld3 limitation and only indirectly related to PhyloRank. Perhaps the latest version of mpld3 works with the later versions of matplotlib? Anyway, this is excellent to know so I can direct people accordingly.
Hi @dparks1134,
I'm "playing around" with Phylorank and I get errors from most commands. e.g. with
phylorank outliers
This causes the program to terminate, but can be solved by removing the two
warnings=False
options inoutliers.py
. After this, the command goes further but still crashes with thisPS: I installed the program through pip, not from source