Bug: cannot install MACS3 by conda

[Bencshan]

Describe the bug
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I tried to install MACS3 by running: conda install -c bioconda macs3 . It did not work.
To Reproduce
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Expected behavior
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Install easily and successfully.

Screenshots
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HP-Z440-Workstation:~# conda install -c bioconda macs3
Channels:

• bioconda
• defaults
  Platform: linux-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides python 3.4* needed by hmmlearn-20151031-py34_0

Could not solve for environment specs
The following packages are incompatible
├─ macs3 =* * is installable with the potential options
│ ├─ macs3 [3.0.1|3.0.2|3.0.3] would require
│ │ └─ python_abi =3.10 *_cp310, which does not exist (perhaps a missing channel);
│ ├─ macs3 [3.0.1|3.0.2] would require
│ │ └─ python_abi =3.11 *_cp311, which does not exist (perhaps a missing channel);
│ ├─ macs3 3.0.1 would require
│ │ └─ hmmlearn =0.3 *, which does not exist (perhaps a missing channel);
│ ├─ macs3 [3.0.1|3.0.2|3.0.3] would require
│ │ └─ python_abi =3.9 *_cp39, which does not exist (perhaps a missing channel);
│ ├─ macs3 [3.0.2|3.0.3] would require
│ │ └─ libzlib >=1.3.1,<2.0a0 *, which does not exist (perhaps a missing channel);
│ └─ macs3 3.0.2 would require
│ └─ hmmlearn >=0.3.2 * with the potential options
│ ├─ hmmlearn 20151031 would require
│ │ └─ python [=2.7 *|>=2.7,<2.8.0a0 *], which can be installed;
│ ├─ hmmlearn 20151031 would require
│ │ └─ python =3.4 *, which does not exist (perhaps a missing channel);
│ ├─ hmmlearn 20151031 would require
│ │ └─ python [=3.5 *|>=3.5,<3.6.0a0 *], which can be installed;
│ └─ hmmlearn 20151031 would require
│ └─ python [=3.6 |>=3.6,<3.7.0a0 ], which can be installed;
└─ pin on python 3.12. = * is not installable because it requires
└─ python =3.12 *, which conflicts with any installable versions previously reported.

Pins seem to be involved in the conflict. Currently pinned specs:

• python=3.12

System (please complete the following information):

• OS: --name option ignored when using -nolambda option (running macs14 on Ubuntu12.10) #17~24.04.2-Ubuntu
• Python 3.12.2

Additional context
Add any other context about the problem here.

[taoliu]

It seems the Python version is 3.4 in your conda environment? How about creating a clean new conda environment and install macs3 there?

You can use conda create -n MACS3 to create a new environment called ‘MACS3’ then switch to this environment with conda activate MACS3. Then use conda install.

[Bencshan]

Still not working:

(MACS3) root@hancs-HP-Z440-Workstation:~# conda install -c bioconda macs3
Channels:

• bioconda
• defaults
  Platform: linux-64
  Collecting package metadata (repodata.json): done
  Solving environment: failed

LibMambaUnsatisfiableError: Encountered problems while solving:

• nothing provides libgcc-ng >=12 needed by macs3-3.0.1-py310h1af8fb7_3

Could not solve for environment specs
The following packages are incompatible
└─ macs3 =* * is not installable because there are no viable options
├─ macs3 3.0.1 would require
│ └─ libgcc-ng >=12 *, which does not exist (perhaps a missing channel);
├─ macs3 3.0.1 would require
│ └─ libzlib >=1.2.13,<1.3.0a0 *, which does not exist (perhaps a missing channel);
├─ macs3 3.0.2 would require
│ └─ python_abi =3.10 *_cp310, which does not exist (perhaps a missing channel);
├─ macs3 [3.0.2|3.0.3] would require
│ └─ libgcc >=13 *, which does not exist (perhaps a missing channel);
├─ macs3 3.0.2 would require
│ └─ libzlib >=1.2.13,<2.0a0 *, which does not exist (perhaps a missing channel);
└─ macs3 3.0.2 would require
└─ python_abi =3.9 *_cp39, which does not exist (perhaps a missing channel).

[philippadoherty]

hi @Bencshan can you either:

1. Provide additional info on your environment, and your commands/full error messages? What version of python are you using in your conda environment? You mentioned you are running on linux-64, we test with Python 3.9 through 3.12 on x64 and our install is passing with those tests, so we want to figure out why it is failing

2. Try installing using another method
   possibly with pip (and try specifying the python version when creating the env):
   conda create -n myenv python=3.10
conda activate myenv
pip install macs3

Thanks! Please let us know if this works

[ansonkn]

Hi thank you for the wonderful package.

For anyone else having the same issue, python version 3.9 is the only one that worked for me:

conda create -n myenv python=3.9
conda activate myenv
pip install macs3