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Conda installation conflict #48

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ASUQ opened this issue May 14, 2024 · 0 comments
Open

Conda installation conflict #48

ASUQ opened this issue May 14, 2024 · 0 comments

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@ASUQ
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ASUQ commented May 14, 2024

While running

PanACoTA prepare --norefseq --min 0 --max 1 -o 1-prepare --cutn 125

after installing it by conda with the new environment, I got an error message

~/panacota/lib/python3.7/site-packages/python_utils/converters.py", line 89
    if match := regexp.search(input_):
              ^
SyntaxError: invalid syntax

This is probably because the python version that was installed was v3.7.12 but not newer than v3.8.
(walrus operator is available in python >= 3.8)

When I tried to update the python version with

mamba install -p <path to the environment> "python>=3.8"

I got

Could not solve for environment specs
The following packages are incompatible
├─ python >3.8  is installable with the potential options
│  ├─ python [3.8.1|3.8.10|...|3.8.8], which can be installed;
│  ├─ python [3.10.0|3.10.1|...|3.10.9], which can be installed;
│  ├─ python [3.11.0|3.11.1|...|3.11.9], which can be installed;
│  ├─ python [3.9.0|3.9.1|...|3.9.9], which can be installed;
│  ├─ python [3.12.0|3.12.1|3.12.2|3.12.3] conflicts with any installable versions previously reported;
│  └─ python 3.12.0rc3 would require
│     └─ _python_rc, which does not exist (perhaps a missing channel);
├─ python_abi is installable with the potential options
│  ├─ python_abi 3.7 would require
│  │  └─ python 3.7.* *_cpython, which can be installed;
│  ├─ python_abi 2.7 would require
│  │  └─ python 2.7.* , which conflicts with any installable versions previously reported;
│  ├─ python_abi 3.10 would require
│  │  └─ python 3.10.* , which can be installed;
│  ├─ python_abi 3.11 would require
│  │  └─ python 3.11.* , which can be installed;
│  ├─ python_abi 3.5 would require
│  │  └─ python 3.5.* , which conflicts with any installable versions previously reported;
│  ├─ python_abi 3.6 would require
│  │  └─ python 3.6.* , which conflicts with any installable versions previously reported;
│  ├─ python_abi 3.6 would require
│  │  └─ python 3.6.* *_73_pypy, which can be installed;
│  ├─ python_abi 3.7 would require
│  │  └─ python 3.7.* , which conflicts with any installable versions previously reported;
│  ├─ python_abi 3.7 would require
│  │  └─ python 3.7.* *_73_pypy, which can be installed;
│  ├─ python_abi 3.8 would require
│  │  └─ python 3.8.* , which can be installed;
│  ├─ python_abi 3.8 would require
│  │  └─ python 3.8.* *_73_pypy, which can be installed;
│  ├─ python_abi 3.9 would require
│  │  └─ python 3.9.* , which can be installed;
│  ├─ python_abi 3.9 would require
│  │  └─ python 3.9.* *_73_pypy, which can be installed;
│  ├─ python_abi 3.10 would require
│  │  └─ python 3.10.* *_cpython, which can be installed;
│  ├─ python_abi 3.10 would require
│  │  └─ python 3.10.* *_native230_graalpy, which can be installed;
│  ├─ python_abi 3.10 would require
│  │  └─ python 3.10.* *_native231_graalpy, which can be installed;
│  ├─ python_abi 3.11 would require
│  │  └─ python 3.11.* *_cpython, which can be installed;
│  ├─ python_abi 3.12 would require
│  │  └─ python 3.12.* *_cpython, which can be installed;
│  ├─ python_abi 3.8 would require
│  │  └─ python 3.8.* *_cpython, which can be installed;
│  ├─ python_abi 3.8 would require
│  │  └─ python 3.8.* *_native223_graalpy, which can be installed;
│  ├─ python_abi 3.8 would require
│  │  └─ python 3.8.* *_native38_graalpy, which can be installed;
│  └─ python_abi 3.9 would require
│     └─ python 3.9.* *_cpython, which can be installed;
└─ t_coffee is not installable because there are no viable options
   ├─ t_coffee 11.0.8 would require
   │  └─ python >=3.7,<3.8.0a0 , which conflicts with any installable versions previously reported;
   ├─ t_coffee 11.0.8 would require
   │  └─ python [2.7* |>=2.7,<2.8.0a0 ], which conflicts with any installable versions previously reported;
   ├─ t_coffee 11.0.8 would require
   │  └─ python 3.4* , which conflicts with any installable versions previously reported;
   ├─ t_coffee 11.0.8 would require
   │  └─ python [3.5* |>=3.5,<3.6.0a0 ], which conflicts with any installable versions previously reported;
   ├─ t_coffee 11.0.8 would require
   │  └─ python 3.6* , which conflicts with any installable versions previously reported;
   └─ t_coffee 11.0.8 would require
      └─ python >=3.6,<3.7.0a0 , which conflicts with any installable versions previously reported.

Also when I tried to update the python version with conda,

conda install -p <path to the envirionment> "python>=3.8"

I got

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides _python_rc needed by python-3.12.0rc3-rc3_hab00c5b_1_cpython

Could not solve for environment specs
The following packages are incompatible
├─ panacota is installable with the potential options
│  ├─ panacota 1.4.0 would require
│  │  └─ prokka 1.14.5 , which requires
│  │     ├─ perl >=5.26.2,<5.26.3.0a0 , which can be installed;
│  │     └─ perl-bioperl >=1.7.2 , which requires
│  │        └─ perl-bio-tools-run-alignment-tcoffee with the potential options
│  │           ├─ perl-bio-tools-run-alignment-tcoffee 1.7.4 would require
│  │           │  └─ perl >=5.32.1,<6.0a0 *_perl5, which conflicts with any installable versions previously reported;
│  │           └─ perl-bio-tools-run-alignment-tcoffee 1.7.4 would require
│  │              └─ t_coffee with the potential options
│  │                 ├─ t_coffee 11.0.8 would require
│  │                 │  └─ python >=3.7,<3.8.0a0 , which can be installed;
│  │                 ├─ t_coffee 11.0.8 would require
│  │                 │  └─ python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
│  │                 ├─ t_coffee 11.0.8 would require
│  │                 │  └─ python 3.4* , which can be installed;
│  │                 ├─ t_coffee 11.0.8 would require
│  │                 │  └─ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
│  │                 ├─ t_coffee 11.0.8 would require
│  │                 │  └─ python 3.6* , which can be installed;
│  │                 └─ t_coffee 11.0.8 would require
│  │                    └─ python >=3.6,<3.7.0a0 , which can be installed;
│  └─ panacota [1.0.1.2|1.1.0|1.2.0|1.3.1] would require
│     └─ argparse with the potential options
│        ├─ argparse 1.4.0 would require
│        │  └─ python 2.6* , which can be installed;
│        ├─ argparse 1.4.0 would require
│        │  └─ python 2.7* , which can be installed;
│        ├─ argparse 1.4.0 would require
│        │  └─ python 3.4* , which can be installed;
│        ├─ argparse 1.4.0 would require
│        │  └─ python 3.5* , which can be installed;
│        └─ argparse 1.4.0 would require
│           └─ python 3.6* , which can be installed;
└─ python >=3.8  is not installable because there are no viable options
   ├─ python [3.10.0|3.10.1|...|3.9.9] conflicts with any installable versions previously reported;
   └─ python 3.12.0rc3 would require
      └─ _python_rc, which does not exist (perhaps a missing channel).

Environment:
CentOS Linux release 8.5.2111
Linux version 4.18.0
Conda version 23.9.0
Mamba version 1.5.6

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