conflict using conda and pip in miniconda environment

Question

I found that if I try to install tqdm in miniconda environment ( pip insall tqdm ), it will fail, and the error then will persist also for other libraries searched by pip

Update

I tried many test, I come to the conclusion that conda and pip install conflicts in miniconda environment.

Step to reproduce:

conda create --name mlvision 

test : is pandas and fastai there?

pip install pandas > pandas is there

now try to install opencv via conda

conda install opencv
[..]

now if I try pip install , I will get error:

pip install pandas
Collecting pandas
  Using cached https://files.pythonhosted.org/packages/fc/43/fd867e3347559845c8f993059d410c50a1e18709f1c4d4b3b47323a06a37/pandas-0.24.2-cp37-cp37m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
dyld: lazy symbol binding failed: Symbol not found: _fdopendir$INODE64
  Referenced from: /Users/gg4u/Sites/miniconda3/envs/mlvision/bin/python
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _fdopendir$INODE64
  Referenced from: /Users/gg4u/Sites/miniconda3/envs/mlvision/bin/python
  Expected in: /usr/lib/libSystem.B.dylib

All installations via pip are now broken:

pip install fastai
Collecting fastai
  Using cached https://files.pythonhosted.org/packages/7d/14/385382da888f7e3ba24c726d95ea05563eb5e984ed97d5a24e74197f7848/fastai-1.0.54-py3-none-any.whl
dyld: lazy symbol binding failed: Symbol not found: _fdopendir$INODE64
  Referenced from: /Users/gg4u/Sites/miniconda3/envs/mlvision/bin/python
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _fdopendir$INODE64
  Referenced from: /Users/gg4u/Sites/miniconda3/envs/mlvision/bin/python
  Expected in: /usr/lib/libSystem.B.dylib

also:

pip install --upgrade pip
Requirement already up-to-date: pip in ./envs/mlvision/lib/python3.7/site-packages (19.1.1)
dyld: lazy symbol binding failed: Symbol not found: _fdopendir$INODE64
  Referenced from: /Users/gg4u/Sites/miniconda3/envs/mlvision/bin/python
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _fdopendir$INODE64
  Referenced from: /Users/gg4u/Sites/miniconda3/envs/mlvision/bin/python
  Expected in: /usr/lib/libSystem.B.dylib

Trace/BPT trap: 5

I conclude that conda install may conflict with pip install...

not sure if only when using conda install opencv

The way around I found is to install opencv as last package, once used I may have the missing reference:

Expected in: /usr/lib/libSystem.B.dylib

and so I should install all packages via pip first, and last opencv...

How to solve conflicts in local conda environments ?

Tried to look at https://github.com/ContinuumIO/anaconda-issues/issues/1429 but could not yet solve the issue.

I cannot proceed to install all the packages I need (some via conda, some via pip)

---

note python correctly poiting to local env:

which python
[your path]/miniconda3/envs/mlvision/bin/python

conda --version conda 4.7.5

using Mac OS Mavericks 10.9.5 (if it matters)

Answer 1

Don't mix pip with conda if you can help it. Get everything you can from conda first. Then use pip only to install packages that you cannot get from conda .

The packages conda installs are created with the Anaconda toolchain. And they have dependencies that make sure that those were also created with a compatible Anaconda toolchain. If you mix in stuff with pip , it can install compiled libraries that are not compatible with what the Anaconda packages require.