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phylo42 / PEWO

Phylogenetic Placement Evaluation Workflows : Benchmark placement software and different reference trees
MIT License
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Conflict between local pip and conda pip for package taxtastic #1

Open blinard-BIOINFO opened 4 years ago

blinard-BIOINFO commented 4 years ago

If taxtastic is installed locally via pip, it mingles with the taxtastic installation of the conda environment. Conda has its own internal pip command but somehow, it cannot isolate both ?

Example: taxtastic 0.8.5 installed locally via pip + 0.8.11 install via PEWO conda environement:

Traceback (most recent call last):
  File "/home/benclaff/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 578, in _build_master
    ws.require(__requires__)
  File "/home/benclaff/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 895, in require
    needed = self.resolve(parse_requirements(requirements))
  File "/home/benclaff/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 786, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.VersionConflict: (taxtastic 0.8.5 (/home/benclaff/.local/lib/python3.6/site-packages), Requirement.parse('taxtastic==0.8.11'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/benclaff/softwares/miniconda3/envs/PEWO/bin/taxit", line 6, in <module>
    from pkg_resources import load_entry_point
  File "/home/benclaff/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3112, in <module>
    @_call_aside
  File "/home/benclaff/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3096, in _call_aside
    f(*args, **kwargs)
  File "/home/benclaff/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 3125, in _initialize_master_working_set
    working_set = WorkingSet._build_master()
  File "/home/benclaff/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 580, in _build_master
    return cls._build_from_requirements(__requires__)
  File "/home/benclaff/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 593, in _build_from_requirements
    dists = ws.resolve(reqs, Environment())
  File "/home/benclaff/.local/lib/python3.6/site-packages/pkg_resources/__init__.py", line 781, in resolve
    raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'taxtastic==0.8.11' distribution was not found and is required by the application
blinard-BIOINFO commented 4 years ago

So far, the only solution is to completely unistall taxtastic from the local pip installation, keeping only the conda installation...