These are chat archives for dereneaton/ipyrad
ImportError: /lib64/libpthread.so.0: version `GLIBC_2.12' not found (required by /home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/zmq/backend/cython/../../../../../libzmq.so.5)
conda install pyzmq=16 conda install ipyparallel=5.2
Encountered an unexpected error (see ./ipyrad_log.txt) Error message is below ------------------------------- Hub connection request timed out
ipcluster start -n 4. If it returns the console to you rather than blocking then ipcluster is messed up.
ERROR:tornado.application:Exception in callback (7, <function null_wrapper at 0x2aaab47bc9b0>) Traceback (most recent call last): File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/tornado/ioloop.py", line 1064, in start handler_func(fd_obj, events) File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/tornado/stack_context.py", line 276, in null_wrapper return fn(*args, **kwargs) File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyparallel/apps/launcher.py", line 310, in handle_stdout self.poll() File "/home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyparallel/apps/launcher.py", line 326, in poll self.poller.stop() AttributeError: 'NoneType' object has no attribute 'stop' 2018-06-05 12:52:08.963 [IPClusterStart] Removing pid file: /home1/02745/tdevitt/.ipython/profile_default/pid/ipcluster.pid
rm -rfyour miniconda directory, then do a
which pythonand make sure there is no other miniconda installed. Make sure $PYTHONPATH isn't set. It might be one strategy to contact someone with a known working minconda install and have them
tar -czv -f miniconda2.tgz miniconda2and then copy you the tgz file, then you can unpack it in your home directory and you should be good to go. This is somewhat hackish, but it's better than endlessly troubleshooting your own conda install if we know somebody who has one working (mariana for example).
@isaacovercast Just spoke with Mariana and I followed her directions to uninstall/reinstall, which seemed essentially the same as Edgardo's but I guess something was different. Everything is working again now. Whew. This is what I did:
rm -rf ~/miniconda2
rm -rf ~/.condarc ~/.conda ~/.continuum
conda install llvmlite=0.22
conda install -c ipyrad ipyrad
Still can't import the Python libraries in the Jupyter structure cookbook though.
import ipyrad.analysis as ipa ## ipyrad analysis toolkit
import ipyparallel as ipp ## parallel processing
import toyplot ## plotting library
IPyradErrorTraceback (most recent call last) <ipython-input-8-11fdbfdcd03d> in <module>() ----> 1 import ipyrad.analysis as ipa ## ipyrad analysis toolkit 2 ## import ipyparallel as ipp ## parallel processing 3 ## import toyplot ## plotting library /home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/__init__.py in <module>() 16 #from toytree import tree 17 #from .tetrad import Tetrad as tetrad ---> 18 from .structure import Structure as structure 19 from .treemix import Treemix as treemix 20 from .tetrad2 import Tetrad as tetrad /home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/structure.py in <module>() 10 import numpy as np 11 import pandas as pd ---> 12 from ipyrad.analysis.tetrad import get_spans 13 from ipyrad.assemble.util import Params, IPyradWarningExit 14 /home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/tetrad.py in <module>() 61 62 conda install toytree -c eaton-lab ---> 63 """) 64 65 /home1/02745/tdevitt/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/util.pyc in __init__(self, *args, **kwargs) 50 def __init__(self, *args, **kwargs): 51 if ipyrad.__interactive__: ---> 52 raise IPyradError(*args, **kwargs) 53 else: 54 SystemExit.__init__(self, *args, **kwargs) IPyradError: Error: tetrad requires the dependency 'toytree', which we haven't yet included in the ipyrad installation. For now, you can install toytree using conda with the following command: conda install toytree -c eaton-lab
conda install toytree -c eaton-lab. This might do the trick.
conda install toytree -c eaton-lab
File "<ipython-input-4-c4de7fdc2886>", line 5 conda install toytree -c eaton-lab ^ SyntaxError: invalid syntax
!conda install toytree -c eaton-lab