Unable to install using conda

[kkhatri99]

I am trying to install this package as instructed but getting the following errors.

C:>conda install -c bioconda abnumber 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. This can take several minutes. Press CTRL-C to abort. failed

UnsatisfiableError:

[prihoda]

Hi @kkhatri99 thanks for reporting. These blank conda conflicts are notoriously hard to debug ☹️ Are you on Windows/Linux/Mac?

Can you try creating a dedicated environment?

conda create -n abnumber -c bioconda python=3.9 abnumber

You can also install ANARCI yourself (conda install -c bioconda anarci or https://github.com/oxpig/ANARCI)

And then install abnumber using pip from this github repo:

pip install git+https://github.com/prihoda/abnumber.git

[kkhatri99]

Hi @prihoda Thanks for your response! I am on Windows. I did try the solutions above but unfortunately none of them worked for me :(

[kkhatri99]

Hello @prihoda - I was able to install and use the library on Linux (WSL), so the issue appears to be limited to Windows. I am going to close this thread. Thanks for your help!

[prihoda]

Thanks, I added a note about this to the readme. Based on my investigation, this is because of the HMMER dependency which is not available on Windows.

[zmactep]

I have the same problem on my MacBook Pro (M1 Pro) even with a fresh environment:

Python 3.9

% conda create -n abnumber -c bioconda python=3.9 abnumber

Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: - 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                          

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python conflicts for:
abnumber -> anarci==2020.04.23 -> python[version='>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']
abnumber -> python[version='>=3.6']
python=3.9

Python 3.10

% conda create -n abnumber -c bioconda python=3.10 abnumber
Collecting package metadata (current_repodata.json): done
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: / 
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                          

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package python conflicts for:
python=3.10
abnumber -> anarci==2020.04.23 -> python[version='>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0']
abnumber -> python[version='>=3.6']

Step-by-step installation.

Create environment:

conda create -n abnumber python=3.10                     
Collecting package metadata (current_repodata.json): done
Solving environment: done
[...]
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate abnumber
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Trying to install abnumber:

% conda install -c bioconda abnumber
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.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                          

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Trying to install anarci:

% conda install -c bioconda anarci  
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.
This can take several minutes.  Press CTRL-C to abort.
failed                                                                          

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

[prihoda]

Hi @zmactep installing on Mac M1 is possible although tricky because HMMER for M1 is not on bioconda.

You can follow the HMMER README to install it manually, just add arch -x86_64 as suggested in this ticket.

wget http://eddylab.org/software/hmmer/hmmer.tar.gz
tar zxf hmmer.tar.gz
cd hmmer-3.3.2
arch -x86_64 ./configure --prefix /your/install/path
arch -x86_64 make
arch -x86_64 make check                 # optional: run automated tests
arch -x86_64 make install               # optional: install HMMER programs, man pages
(cd easel; make install)   # optional: install Easel tools

Then, you will need to install ANARCI and AbNumber python packages directly from the repository:

pip install git+https://github.com/oxpig/ANARCI.git@19d9de50b2ab7ca80f4d2c45fd113139f4cad311
pip install git+https://github.com/prihoda/abnumber

Test everything using ANARCI -h and then import abnumber from python