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bcgsc / physlr

:chains: Construct a Physical Map from Linked Reads
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Cannot install with Conda + Pypy 3.9 #194

Open davidlougheed opened 4 weeks ago

davidlougheed commented 4 weeks ago

Hello, I'm trying to install Physlr with Conda + Pypy 3.9 and I get the following error:

LibMambaUnsatisfiableError: Encountered problems while solving:
  - package physlr-1.0.4-py39h2df963e_0 requires tqdm, but none of the providers can be installed

Could not solve for environment specs
The following packages are incompatible
├─ physlr 1.0.4  is installable and it requires
│  └─ tqdm with the potential options
│     ├─ tqdm 4.7.2 would require
│     │  └─ python 3.6* , which can be installed;
│     └─ tqdm [4.10.0|4.11.0|...|4.9.0] conflicts with any installable versions previously reported;
└─ pin-1 is not installable because it requires
   └─ python 3.9.* , which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:
 - python 3.9.* (labeled as 'pin-1')

If I manually install TQDM, I instead get another error:

Could not solve for environment specs
The following packages are incompatible
├─ physlr 1.0.4**  is installable with the potential options
│  ├─ physlr 1.0.4 would require
│  │  ├─ pypy with the potential options
│  │  │  ├─ pypy 7.3.8 would require
│  │  │  │  └─ python 3.9.10 0_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.15 would require
│  │  │  │  └─ python 3.9.18 1_73_pypy, which can be installed;
│  │  │  ├─ pypy [7.3.0|7.3.1] would require
│  │  │  │  └─ python 3.6.9 0_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.1 would require
│  │  │  │  └─ python 3.6.9 1_73_pypy, which does not exist (perhaps a missing channel);
│  │  │  ├─ pypy 7.3.1 would require
│  │  │  │  └─ python 3.6.9 2_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.2 would require
│  │  │  │  └─ python 3.6.9 3_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.3 would require
│  │  │  │  └─ python 3.6.12 5_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.3 would require
│  │  │  │  └─ python 3.7.9 5_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.3 would require
│  │  │  │  └─ python 3.6.12 4_73_pypy, which can be installed;
│  │  │  ├─ pypy [7.3.4|7.3.5] would require
│  │  │  │  └─ python 3.7.10 0_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.5 would require
│  │  │  │  └─ python 3.7.10 1_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.7 would require
│  │  │  │  └─ python 3.7.12 0_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.8 would require
│  │  │  │  └─ python 3.8.12 0_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.9 would require
│  │  │  │  └─ python 3.8.13 0_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.9 would require
│  │  │  │  └─ python 3.9.12 0_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.11 would require
│  │  │  │  └─ python 3.8.16 0_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.11 would require
│  │  │  │  └─ python 3.9.16 0_73_pypy, which can be installed;
│  │  │  ├─ pypy 7.3.12 would require
│  │  │  │  └─ python 3.9.17 0_73_pypy, which can be installed;
│  │  │  └─ pypy 7.3.13 would require
│  │  │     └─ python 3.9.18 0_73_pypy, which can be installed;
│  │  └─ scikit-learn with the potential options
│  │     ├─ scikit-learn [0.17.1|0.18|...|0.20.4] would require
│  │     │  └─ python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
│  │     ├─ scikit-learn [0.17.1|0.18|0.18.2] would require
│  │     │  └─ python 3.4* , which can be installed;
│  │     ├─ scikit-learn [0.17.1|0.18|...|0.20.0] would require
│  │     │  └─ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
│  │     ├─ scikit-learn [0.18|0.18.1|...|0.19.2] would require
│  │     │  └─ python 3.6* , which can be installed;
│  │     ├─ scikit-learn [0.19.2|0.20.0|...|0.24.2] would require
│  │     │  └─ python >=3.6,<3.7.0a0 , which can be installed;
│  │     ├─ scikit-learn [0.20.0|0.20.1|...|1.0.2] would require
│  │     │  └─ python >=3.7,<3.8.0a0 , which can be installed;
│  │     ├─ scikit-learn [0.22|0.22.1|...|1.3.2] would require
│  │     │  └─ python >=3.8,<3.9.0a0 , which can be installed;
│  │     ├─ scikit-learn [0.23.2|0.24.0|...|1.5.0] would require
│  │     │  └─ python_abi 3.9.* *_cp39 but there are no viable options
│  │     │     ├─ python_abi 3.9 would require
│  │     │     │  └─ pypy <0a0 , which conflicts with any installable versions previously reported;
│  │     │     └─ python_abi 3.9 would require
│  │     │        └─ python 3.9.* *_cpython, which conflicts with any installable versions previously reported;
│  │     ├─ scikit-learn [1.0.1|1.0.2|...|1.5.0] would require
│  │     │  └─ python >=3.10,<3.11.0a0 , which can be installed;
│  │     ├─ scikit-learn [1.1.3|1.2.0|...|1.5.0] would require
│  │     │  └─ python >=3.11,<3.12.0a0 , which can be installed;
│  │     ├─ scikit-learn [1.3.1|1.3.2|...|1.5.0] would require
│  │     │  └─ python >=3.12,<3.13.0a0 , which can be installed;
│  │     └─ scikit-learn [0.19.0|0.19.1|...|1.4.2] conflicts with any installable versions previously reported;
│  └─ physlr 1.0.4 would require
│     └─ scikit-learn with the potential options
│        ├─ scikit-learn [0.17.1|0.18|...|0.20.4], which can be installed (as previously explained);
│        ├─ scikit-learn [0.17.1|0.18|0.18.2], which can be installed (as previously explained);
│        ├─ scikit-learn [0.17.1|0.18|...|0.20.0], which can be installed (as previously explained);
│        ├─ scikit-learn [0.18|0.18.1|...|0.19.2], which can be installed (as previously explained);
│        ├─ scikit-learn [0.19.2|0.20.0|...|0.24.2], which can be installed (as previously explained);
│        ├─ scikit-learn [0.20.0|0.20.1|...|1.0.2], which can be installed (as previously explained);
│        ├─ scikit-learn [0.22|0.22.1|...|1.3.2], which can be installed (as previously explained);
│        ├─ scikit-learn [0.23.2|0.24.0|...|1.5.0], which cannot be installed (as previously explained);
│        ├─ scikit-learn [1.0.1|1.0.2|...|1.5.0], which can be installed (as previously explained);
│        ├─ scikit-learn [1.1.3|1.2.0|...|1.5.0], which can be installed (as previously explained);
│        ├─ scikit-learn [1.3.1|1.3.2|...|1.5.0], which can be installed (as previously explained);
│        └─ scikit-learn [0.19.0|0.19.1|...|1.4.2] conflicts with any installable versions previously reported;
├─ pin-1 is not installable because it requires
│  └─ python 3.9.* , which conflicts with any installable versions previously reported;
└─ pypy is installable with the potential options
   ├─ pypy 7.3.8, which can be installed (as previously explained);
   ├─ pypy 7.3.15, which can be installed (as previously explained);
   ├─ pypy [7.3.0|7.3.1], which can be installed (as previously explained);
   ├─ pypy 7.3.1, which cannot be installed (as previously explained);
   ├─ pypy 7.3.1, which can be installed (as previously explained);
   ├─ pypy 7.3.2, which can be installed (as previously explained);
   ├─ pypy 7.3.3, which can be installed (as previously explained);
   ├─ pypy 7.3.3, which can be installed (as previously explained);
   ├─ pypy 7.3.3, which can be installed (as previously explained);
   ├─ pypy [7.3.4|7.3.5], which can be installed (as previously explained);
   ├─ pypy 7.3.5, which can be installed (as previously explained);
   ├─ pypy 7.3.7, which can be installed (as previously explained);
   ├─ pypy 7.3.8, which can be installed (as previously explained);
   ├─ pypy 7.3.9, which can be installed (as previously explained);
   ├─ pypy 7.3.9, which can be installed (as previously explained);
   ├─ pypy 7.3.11, which can be installed (as previously explained);
   ├─ pypy 7.3.11, which can be installed (as previously explained);
   ├─ pypy 7.3.12, which can be installed (as previously explained);
   └─ pypy 7.3.13, which can be installed (as previously explained).

Pins seem to be involved in the conflict. Currently pinned specs:
 - python 3.9.* (labeled as 'pin-1')

Any suggestions as to best next steps?

lcoombe commented 5 days ago

Hi @davidlougheed,

Could you let us know the exact sequence of conda commands you tried?

On my end (on a linux machine), I was able to install physlr with these commands:

conda create -n physlr_test # Make a fresh conda environment
conda activate physlr_test # Activate the fresh conda environment
conda install mamba pypy3.9
mamba install physlr
(physlr_test) [lcoombe@hpce704 git]$ physlr version
physlr 1.0.4

Thank you for your interest in physlr! Lauren