yinshiyi
(Shiyi Yin)
October 17, 2024, 6:52pm
1
I use conda.yml file for a process.
The process run fine under my dev account and test.
I do not want to give other user write access to the nextflow repo.
The user is running into errors that conda want to write a temp file in the location where environment.yml is located.
Any idea how to get around this?
Conda version 23.5
nextflow latest edge.
A similar bug is reported in Conda
opened 09:18PM - 22 Jul 20 UTC
closed 10:18PM - 22 Feb 22 UTC
locked
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## Current Behavior
<!-- What actually happens?
If you want to include console output, please use "Steps to Reproduce" below. -->
`conda run` writes an activation script to a temporary file _in the target environment directory_, which means it can't be used with shared environments (unless all users have write access to the conda location - not a good idea)
### Steps to Reproduce
<!-- If the current behavior is a bug, please provide specific, minimal steps to independently reproduce.
Include the exact conda commands that reproduce the issue and their output between the ticks below. -->
```
$ export CONDA_TEST_SAVE_TEMPS=true
$ conda run -n drugs_and_money cylc --version
WARNING conda.cli.main_run:execute(39): CONDA_TEST_SAVE_TEMPS :: retaining main_run script_caller \
/home/oliverh/miniconda3/envs/drugs_and_money/.tmprsaedgg3
8.0a2
$ cat /home/oliverh/miniconda3/envs/drugs_and_money/.tmprsaedgg3
eval "$(/home/oliverh/miniconda3/bin/conda shell.posix hook)"
conda activate /home/oliverh/miniconda3/envs/drugs_and_money
cylc --version
```
## Expected Behavior
`conda run` should write the temporary activation script to a standard temp file location for the user.
## Environment Information
<details open><summary><code>`conda info`</code></summary><p>
```
active environment : /tmp
active env location : /tmp
shell level : 0
user config file : /home/oliverh/.condarc
populated config files : /home/oliverh/.condarc
conda version : 4.8.3
conda-build version : not installed
python version : 3.7.7.final.0
virtual packages : __glibc=2.17
base environment : /home/oliverh/miniconda3 (writable)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /home/oliverh/miniconda3/pkgs
/home/oliverh/.conda/pkgs
envs directories : /home/oliverh/miniconda3/envs
/home/oliverh/.conda/envs
platform : linux-64
user-agent : conda/4.8.3 requests/2.24.0 CPython/3.7.7 Linux/3.10.0-1127.13.1.el7.x86_64 centos/7.8.2003 glibc/2.17
UID:GID : 8560:10000
netrc file : None
offline mode : False
```
</p></details>
<details open><summary><code>`conda config --show-sources`</code></summary><p>
```
auto_activate_base: False
ssl_verify: True
channel_priority: disabled
channels:
- conda-forge
unsatisfiable_hints: True
anaconda_upload: False
```
</p></details>
<details><summary><code>`conda list --show-channel-urls`</code></summary><p>
```
conda list --show-channel-urls
# packages in environment at /home/oliverh/miniconda3:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main defaults
brotlipy 0.7.0 py37h7b6447c_1000 defaults
ca-certificates 2020.6.24 0 defaults
certifi 2020.6.20 py37_0 defaults
cffi 1.14.0 py37he30daa8_1 defaults
chardet 3.0.4 py37_1003 defaults
conda 4.8.3 py37_0 defaults
conda-package-handling 1.6.0 py37h8f50634_2 conda-forge
cryptography 2.9.2 py37h1ba5d50_0 defaults
idna 2.10 py_0 defaults
ld_impl_linux-64 2.34 h53a641e_7 conda-forge
libedit 3.1.20191231 h14c3975_1 defaults
libffi 3.3 he6710b0_2 defaults
libgcc-ng 9.2.0 hdf63c60_0 conda-forge
libstdcxx-ng 9.2.0 hdf63c60_2 conda-forge
ncurses 6.2 he6710b0_1 defaults
openssl 1.1.1g h7b6447c_0 defaults
pip 20.1.1 py37_1 defaults
pycosat 0.6.3 py37h7b6447c_0 defaults
pycparser 2.20 py_2 defaults
pyopenssl 19.1.0 py_1 defaults
pysocks 1.7.1 py37_1 defaults
python 3.7.7 hcff3b4d_5 defaults
python_abi 3.7 1_cp37m conda-forge
readline 8.0 h7b6447c_0 defaults
requests 2.24.0 py_0 defaults
ruamel_yaml 0.15.87 py37h7b6447c_1 defaults
setuptools 49.2.0 py37_0 defaults
six 1.15.0 py_0 defaults
sqlite 3.32.3 h62c20be_0 defaults
tk 8.6.10 hbc83047_0 defaults
tqdm 4.48.0 pyh9f0ad1d_0 conda-forge
urllib3 1.25.9 py_0 defaults
wheel 0.34.2 py37_0 defaults
xz 5.2.5 h7b6447c_0 defaults
yaml 0.2.5 h7b6447c_0 defaults
zlib 1.2.11 h7b6447c_3 defaults
```
</p></details>
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
PermissionError: [Errno 13] Permission denied: 'nextflow_repo/config/condaenv.bbgfzbg4.requirements.txt'