Problem installing in fresh conda environment.

[Old-Green-Man]

I installed a fresh copy of miniconda on 5.15.0-58-generic #64-Ubuntu SMP Thu Jan 5 11:43:13 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux.

conda create -n gwas
conda activate gwas
conda info
active environment : gwas
active env location : /path/local/src/miniconda3/envs/gwas
shell level : 3
user config file : /path/.condarc
populated config files : /path/.condarc
conda version : 23.1.0
conda-build version : not installed
python version : 3.10.9.final.0
virtual packages : __archspec=1=x86_64
__glibc=2.35=0
__linux=5.15.0=0
__unix=0=0
base environment : /path/local/src/miniconda3 (writable)
conda av data dir : /path/local/src/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /path/local/src/miniconda3/pkgs
/path/.conda/pkgs
envs directories : /path/local/src/miniconda3/envs
/path/.conda/envs
platform : linux-64
user-agent : conda/23.1.0 requests/2.28.1 CPython/3.10.9 Linux/5.15.0-58-generic ubuntu/22.04.1 glibc/2.35
UID:GID : 1000:1000
netrc file : None
offline mode : False

conda install vcf2gwas -c conda-forge -c bioconda -c fvogt257

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: | Killed

On windows with a miniconda that's been installed for awhile but still creating a new gwas environment and activating it gave:

conda install vcf2gwas -c conda-forge -c bioconda -c fvogt257

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:

[frankvogt]

Could you retry with while adding verbosity flags (-v for INFO; -vv for DEBUG; -vvv for TRACE) to track down the issue?
Also on Windows, vcf2gwas can only be run via docker. Problems occurring there could be fixed by increasing the RAM size of the Virtual Machine.

[jennifercalawa]

Hi, I had the same problem trying to install on a Mac:

(myenv) jennifercalawa@U-KXNRWWJ417 ~ % conda install vcf2gwas -c conda-forge -c bioconda -c fvogt257
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:

(myenv) jennifercalawa@U-KXNRWWJ417 ~ % conda install vcf2gwas -c conda-forge -c bioconda -c fvogt257 -v -vv -vvv
Traceback (most recent call last):
File "/Users/jennifercalawa/anaconda3/lib/python3.10/site-packages/conda/gateways/logging.py", line 229, in set_verbosity
set_all_logger_level(VERBOSITY_LEVELS[verbosity_level])
IndexError: tuple index out of range

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/Users/jennifercalawa/anaconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1132, in call
return func(*args, **kwargs)
File "/Users/jennifercalawa/anaconda3/lib/python3.10/site-packages/conda/cli/main.py", line 62, in main_subshell
init_loggers(context)
File "/Users/jennifercalawa/anaconda3/lib/python3.10/site-packages/conda/cli/main.py", line 50, in init_loggers
set_verbosity(context.verbosity)
File "/Users/jennifercalawa/anaconda3/lib/python3.10/site-packages/conda/gateways/logging.py", line 231, in set_verbosity
raise CondaError("Invalid verbosity level: %(verbosity_level)s",
conda.CondaError: Invalid verbosity level: 6

[frankvogt]

Could you re run the command with only either -v, -vv, or -vvv (not all 3 in the same command)? Maybe try first with only -vv.

[jennifercalawa]

My scientific computing department was able to get it installed and it worked! Thanks!