Dear all
I have been using conda environments for years on my server that is installed with a CentOS 7 distribution currently with version 3.10.0-1160.99.1.el7.x86_64 of the kernel. My system depends on an old python version, 2.7.18, that I was told to not change for proper OS function. I have thus been using miniconda2 to install all my conda environments up to recently. The problem I encounter since the last part of 2023 is that I cannot create any more new environments. I have many already created environments that my bioinformatics work heavily depends upon that are essential for versioning control of our pipelines, so I am highly reluctant to modify things that could imperil the currently functioning environments. I suspect however that my inability to create new environments may stem from the use of an outdated version of python eventually combined with a system update of some component, even though I have not been able to identify if the problem directly followed a system update because I create only rarely new conda environments.
I have not been able to identify an answer to this problem on various forums.
Does anyone knows about this problem and could propose a solution to circumvent it while preserving formerly created conda environments?
The full error message is at the end of this mail. It is one resulting from a specific conda environment creation attempt but the message is not specific to that environment creation attempt and these errors occur whatever I want to create.
Thanks
Thierry
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/grange/miniconda2b/lib/python2.7/site-packages/conda/exceptions.py", line 1074, in __call__
return func(*args, **kwargs)
File "/home/grange/miniconda2b/lib/python2.7/site-packages/conda/cli/main.py", line 84, in _main
exit_code = do_call(args, p)
File "/home/grange/miniconda2b/lib/python2.7/site-packages/conda/cli/conda_argparse.py", line 82, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/grange/miniconda2b/lib/python2.7/site-packages/conda/cli/main_create.py", line 37, in execute
install(args, parser, 'create')
File "/home/grange/miniconda2b/lib/python2.7/site-packages/conda/cli/install.py", line 116, in install
if context.use_only_tar_bz2:
File "/home/grange/miniconda2b/lib/python2.7/site-packages/conda/base/context.py", line 666, in use_only_tar_bz2
import conda_package_handling.api
File "/home/grange/miniconda2b/lib/python2.7/site-packages/conda_package_handling/api.py", line 7, in <module>
import tqdm as _tqdm
File "/home/grange/miniconda2b/lib/python2.7/site-packages/tqdm/__init__.py", line 3, in <module>
from .cli import main # TODO: remove in v5.0.0
File "/home/grange/miniconda2b/lib/python2.7/site-packages/tqdm/cli.py", line 202
sys.stderr.write(f"Error:Unknown argument:{argv[0]}\n{help_short}")
^
SyntaxError: invalid syntax
$ /home/grange/miniconda2b/bin/conda create -n ancIBD -c anaconda python=3.10.10 numpy pandas h5pi psutil matplotlib
environment variables:
CIO_TEST=
CONDA_DEFAULT_ENV=base
CONDA_EXE=/home/grange/miniconda2b/bin/conda
CONDA_PREFIX=/home/grange/miniconda2b
CONDA_PREFIX_1=/home/grange/miniconda2
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/home/grange/miniconda2b/bin/python
CONDA_ROOT=/home/grange/miniconda2b
CONDA_SHLVL=2
GOPATH=/home/grange/go
PATH=/home/grange/miniconda2b/bin:/home/grange/miniconda2b/bin:/usr/local/g
o/bin:/home/grange/miniconda2b/bin:/home/grange/miniconda2/condabin:/h
ome/grange/Software/sratoolkit.3.0.10-centos_linux64/bin:/home/grange/
Software/FREEC-11.6b/src:/home/grange/Software/samtools-1.18:/home/gra
nge/Software/htslib-1.18:/home/grange/Software/bcftools-1.18:/home/gra
nge/Software/ELAI/src:/home/grange/Software/crimap2.507:/home/grange/S
oftware/AdmixSim2/src:/home/grange/Software/pbwt:/home/grange/Software
/bioinformatics-cafe/fastaRegexFinder:/home/grange/Software/leeHom/src
:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/
home/grange/go/bin:/home/grange/.local/bin:/home/grange/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
active environment : base
active env location : /home/grange/miniconda2b
shell level : 2
user config file : /home/grange/.condarc
populated config files : /home/grange/.condarc
conda version : 4.7.12
conda-build version : not installed
python version : 2.7.17.final.0
virtual packages :
base environment : /home/grange/miniconda2b (writable)
channel URLs : anaconda/linux-64
long list of URLs I had to delete
package cache : /home/grange/miniconda2b/pkgs
/home/grange/.conda/pkgs
envs directories : /home/grange/miniconda2b/envs
/home/grange/.conda/envs
platform : linux-64
user-agent : conda/4.7.12 requests/2.25.1 CPython/2.7.17 Linux/3.10.0-1160.99.1.el7.x86_64 centos/7.9.2009 glibc/2.17
UID:GID : 1000:1000
netrc file : None
offline mode : False