My installation fails on "mamba env create -f conda_env.yaml". I have removed conda-forge from my channels in my ~/.condarc, but it didn't work. And then I've tried installing miniconda and mamba again, but it did not change anything. I got the following errors:
$ mamba env create -f conda_env.yaml
anaconda/noarch [====================] (00m:00s) No change
bioconda/noarch [====================] (00m:00s) No change
bioconda/linux-64 [====================] (00m:00s) No change
anaconda/linux-64 [====================] (00m:00s) No change
r/linux-64 [====================] (00m:00s) No change
r/noarch [====================] (00m:00s) No change
pkgs/main/linux-64 [====================] (00m:00s) No change
pkgs/r/linux-64 [====================] (00m:00s) No change
pkgs/r/noarch [====================] (00m:00s) No change
pkgs/main/noarch [====================] (00m:00s) No change
ohmeta/noarch [====================] (00m:00s) No change
conda-forge/noarch [====================] (00m:00s) Done
ohmeta/linux-64 [====================] (00m:00s) No change
conda-forge/linux-64 [====================] (00m:02s) Done
Traceback (most recent call last):
File "/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/lib/python3.8/site-packages/conda_env/cli/main.py", line 80, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/lib/python3.8/site-packages/conda_env/cli/main_create.py", line 111, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/lib/python3.8/site-packages/mamba/mamba_env.py", line 42, in mamba_install
index = load_channels(
File "/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/lib/python3.8/site-packages/mamba/utils.py", line 135, in load_channels
repo = subdir.create_repo(pool)
RuntimeError: Could not read JSON repodata file (/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/pkgs/cache/976d321b.json) parse error line 17356
active environment : base
active env location : /ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3
shell level : 1
user config file : /home/liangweiting/.condarc
I installed miniconda3 and mamba once again. This time I removed the ~/.condarc ~/.conda ~/.continum and anotationed conda setting in ~/.bashrc. I'm now able to progress in the install.
My installation fails on "mamba env create -f conda_env.yaml". I have removed conda-forge from my channels in my ~/.condarc, but it didn't work. And then I've tried installing miniconda and mamba again, but it did not change anything. I got the following errors:
$ mamba env create -f conda_env.yaml anaconda/noarch [====================] (00m:00s) No change bioconda/noarch [====================] (00m:00s) No change bioconda/linux-64 [====================] (00m:00s) No change anaconda/linux-64 [====================] (00m:00s) No change r/linux-64 [====================] (00m:00s) No change r/noarch [====================] (00m:00s) No change pkgs/main/linux-64 [====================] (00m:00s) No change pkgs/r/linux-64 [====================] (00m:00s) No change pkgs/r/noarch [====================] (00m:00s) No change pkgs/main/noarch [====================] (00m:00s) No change ohmeta/noarch [====================] (00m:00s) No change conda-forge/noarch [====================] (00m:00s) Done ohmeta/linux-64 [====================] (00m:00s) No change conda-forge/linux-64 [====================] (00m:02s) Done
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
$ /ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/bin/mamba create -f conda_env.yaml
environment variables: CIO_TEST=
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=base
CONDA_EXE=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/b
in/conda
CONDA_PREFIX=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3
CONDA_PROMPT_MODIFIER=(base)
CONDA_PYTHON_EXE=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/b
in/python
CONDA_ROOT=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3
CONDA_SHLVL=1
LD_LIBRARY_PATH=/opt/gridengine/lib/lx-amd64:/opt/openmpi/lib:/opt/python/lib
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
PATH=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/b
in:/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda
3/condabin:/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/m
iniconda3/bin:/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv/bi
n:/ldfssz1/ST_META/share/User/zhujie/.conda/envs/bioenv3.6/bin:/ldfssz
1/ST_META/share/User/zhujie/.conda/envs/bioenv2/bin:/ldfssz1/ST_META/s
hare/User/juyanmei/miniconda3/bin:/ldfssz1/ST_META/share/flow/biobaker
y-metaphlan2-d8ab9ca4244c:/opt/openmpi/bin:/usr/lib64/qt-3.3/bin:/usr/
local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/bio/ncbi/
bin:/opt/bio/mpiblast/bin:/opt/bio/EMBOSS/bin:/opt/bio/clustalw/bin:/o
pt/bio/tcoffee/bin:/opt/bio/hmmer/bin:/opt/bio/phylip/exe:/opt/bio/mrb
ayes:/opt/bio/fasta:/opt/bio/glimmer/bin:/opt/bio/glimmer/scripts:/opt
/bio/gromacs/bin:/opt/bio/gmap/bin:/opt/bio/tigr/bin:/opt/bio/autodock
suite/bin:/opt/bio/wgs/bin:/opt/ganglia/bin:/opt/ganglia/sbin:/usr/jav
a/latest/bin:/opt/rocks/bin:/opt/rocks/sbin:/opt/condor/bin:/opt/condo
r/sbin:/opt/gridengine/bin/lx-amd64:/home/liangweiting/bin
REQUESTS_CA_BUNDLE=
SPATH=/ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/stronginstal
l
SSL_CERT_FILE=
ftp_proxy=
http_proxy=
https_proxy=
no_proxy=
populated config files : /home/liangweiting/.condarc conda version : 4.8.3 conda-build version : not installed python version : 3.8.3.final.0 virtual packages : __glibc=2.17 base environment : /ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://conda.anaconda.org/ohmeta/linux-64 https://conda.anaconda.org/ohmeta/noarch 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 : /ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/pkgs envs directories : /ldfssz1/ST_META/P18Z10200N0127_GRJ/liangweiting/software/miniconda3/envs /home/liangweiting/.conda/envs platform : linux-64 user-agent : conda/4.8.3 requests/2.23.0 CPython/3.8.3 Linux/2.6.32-696.30.1.el6.x86_64 centos/6.9 glibc/2.17 UID:GID : 1000590:2782 netrc file : None offline mode : False
An unexpected error has occurred. Conda has prepared the above report.