Closed constellation99 closed 3 months ago
I think I have the same issue as constellation99 has.
I could not install biom-format via conda install -c bioconda -c conda-forge biom-format
under Platform: osx-arm64, because of an error: PackagesNotFoundError: The following packages are not available from current channels:
I tried via 'pip install biom-format' as well but the installed program was not recognized well (no error during installation) since when I run biom
, it returned an error: NameError: name 'biom' is not defined
Any advice on this issue would be great!
Hi @masa-yoshizawa,
What version of Python is being used? And could you share the full output from the pip install
, which should have worked?
Best, Daniel
Hi Daniel, thank you for responding to my issue. I am using Python 3.11.7 here is the full output of pip install. Again thank you so much for your help for looking into!
In [4]: pip install biom-format
Requirement already satisfied: biom-format in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (2.1.15)
Requirement already satisfied: click in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from biom-format) (8.1.7)
Requirement already satisfied: numpy>=1.9.2 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from biom-format) (1.26.3)
Requirement already satisfied: scipy>=1.3.1 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from biom-format) (1.12.0)
Requirement already satisfied: pandas>=0.20.0 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from biom-format) (2.2.0)
Requirement already satisfied: h5py in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from biom-format) (3.10.0)
Requirement already satisfied: python-dateutil>=2.8.2 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from pandas>=0.20.0->biom-format) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from pandas>=0.20.0->biom-format) (2023.3.post1)
Requirement already satisfied: tzdata>=2022.7 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from pandas>=0.20.0->biom-format) (2023.4)
Requirement already satisfied: six>=1.5 in /Users/(user name)/anaconda3/envs/picrust2/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas>=0.20.0->biom-format) (1.16.0)
Note: you may need to restart the kernel to use updated packages.
[after restarting the kernel]
in [1]: biom
Traceback (most recent call last):
Cell In[1], line 1 biom
NameError: name 'biom' is not defined
Thanks, @masa-yoshizawa. Could you try import biom
? There is a program called biom
but it is intended to be run on the command line, whereas the output above suggests the use may be within a Python interpreter
Dear Daniel,
thank you so much for this advise! I imported biom and it seemed to work
In [2]: import biom as bio
In [3]:
that is great! However, in the same Python environment, the command line could not call biom
(singleCell) user@MacBook-Pro- ~ % biom
zsh: command not found: biom
The issue is that I cannot install picrust2 due to this issue.
Thank you for your thoughts!!!
It's odd that the biom
program is not accessible yet the library appears installed. My guess is an environment issue, where either pip
installed the program in an unusual location, or the install was done outside of the conda environment? If the general problem is with picrust2, would it be possible to open a help request with them?
I totally agree with you. It is so wired. I have installed biom-format by using pip of this version
pip --version
pip 23.3.1 from /Users/masato/anaconda3/envs/picrust2/lib/python3.11/site-packages/pip (python 3.11)
Thus, pip is under the same environment where I'd like to install biom-format... I will pose a question in the picrust2 site too. Thank you so much, Daniel!
Thanks, @masa-yoshizawa! Is there an associated issue with the picrust2 tracker to reference?
When trying to add biom-format support for aarch64 conda, I encountered the following error here, which caused the build to fail. The error message I received was "PackagesNotFoundError: The following packages are not available from current channels: biom-format". This occurred after including
biom-format
in the aarch64 conda requirements file for scikit-bio.Would it be possible to add support for aarch64 for biom?