tetrad install in python 3.9 fails

[joqb]

Hi @eaton-lab

I have an issue with installing tetrad, error with the latest python (3.9):

-bash-4.2$ conda install tetrad -c eaton-lab -c conda-forge
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.                           failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - tetrad -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0']

Your python: python=3.9

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.17=0
  - feature:|@/linux-64::__glibc==2.17=0

Your installed version is: 2.17

Downgrading to python 3.7 installs tetrad and ipyrad (conda install -c conda-forge -c bioconda ipyrad) but give me an error when importing ipyrad...

(py37) -bash-4.2$ python
Python 3.7.11 (default, Jul 27 2021, 14:32:16)
[GCC 7.5.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import ipyrad.analysis as ipa
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/ipyrad/__init__.py", line 4, in <module>
    from .core.assembly import Assembly, merge
  File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/ipyrad/core/assembly.py", line 20, in <module>
    from ipyrad.assemble.utils import IPyradError, ObjDict, BADCHARS
  File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/ipyrad/assemble/__init__.py", line 9, in <module>
    from . import consens_se
  File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/ipyrad/assemble/consens_se.py", line 33, in <module>
    import h5py
  File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/h5py/__init__.py", line 33, in <module>
    from . import version
  File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/h5py/version.py", line 15, in <module>
    from . import h5 as _h5
  File "h5py/h5.pyx", line 1, in init h5py.h5
ImportError: /home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/h5py/defs.cpython-37m-x86_64-linux-gnu.so: undefined symbol: H5Pset_fapl_ros3

Any suggestions? What environment is working for both ipyrad and tetrad?

[eaton-lab]

Hi jobq,

Thanks for letting me know. Looks like the conda recipe needs to be updated for the latest Python (3.9). I will try to make this available as soon as I can.

Best, Deren

On 12/14/21 8:49 AM, joqb wrote:

Hi @eaton-lab https://github.com/eaton-lab

I have an issue with installing tetrad, error with the latest python (3.9):

|-bash-4.2$ conda install tetrad -c eaton-lab -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: \ Found conflicts! Looking for incompatible packages. failed UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment: Specifications: - tetrad -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|>=3.7,<3.8.0a0'] Your python: python=3.9 If python is on the left-most side of the chain, that's the version you've asked for. When python appears to the right, that indicates that the thing on the left is somehow not available for the python version you are constrained to. Note that conda will not change your python version to a different minor version unless you explicitly specify that. The following specifications were found to be incompatible with your system: - feature:/linux-64::glibc==2.17=0 - feature:|@/linux-64::glibc==2.17=0 Your installed version is: 2.17 |

Downgrading to python 3.7 installs tetrad and ipyrad (conda install -c conda-forge -c bioconda ipyrad) but give me an error when importing ipyrad...

|(py37) -bash-4.2$ python Python 3.7.11 (default, Jul 27 2021, 14:32:16) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information. >>> import ipyrad.analysis as ipa Traceback (most recent call last): File "", line 1, in File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/ipyrad/init.py", line 4, in from .core.assembly import Assembly, merge File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/ipyrad/core/assembly.py", line 20, in from ipyrad.assemble.utils import IPyradError, ObjDict, BADCHARS File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/ipyrad/assemble/init.py", line 9, in from . import consens_se File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/ipyrad/assemble/consens_se.py", line 33, in import h5py File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/h5py/init.py", line 33, in from . import version File "/home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/h5py/version.py", line 15, in from . import h5 as _h5 File "h5py/h5.pyx", line 1, in init h5py.h5 ImportError: /home/bernhardt/miniconda3/envs/py37/lib/python3.7/site-packages/h5py/defs.cpython-37m-x86_64-linux-gnu.so: undefined symbol: H5Pset_fapl_ros3 |

Any suggestions? What environment is working for both ipyrad and tetrad?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/eaton-lab/tetrad/issues/7, or unsubscribe https://github.com/notifications/unsubscribe-auth/AGEVUG74DVF4BHXS6COKDIDUQ5DM7ANCNFSM5KA6BVXQ. Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Deren Eaton, Ph.D. Assistant Professor, Ecology, Evolution, and Environmental Biology Affiliate Member, Data Science Institute Columbia University https://eaton-lab.org

[joqb]

Hi @eaton-lab, any update on this? I seem to still be unable to run tetrad. How can I run tetrad?

Best, joqb

[isaacovercast]

One alternative is to clone the repository and the:

cd tetrad
pip install -e .

That should work.