Comments (4)
Hi Gavin,
I forgot to run the pip install --editable .
. Sorry to bother you with this.
Thanks a lot!
Yakshi
from picrust2.
Did you install PICRUSt2 based on the instructions here: https://github.com/picrust/picrust2/wiki/Installation?
If so then just to double-check, did you run pip install --editable .
? It seems like the scripts aren't installed correctly.
Gavin
from picrust2.
Hi
When running pytest it indicates the following errors:
_________________________________________________________________________________ ERROR collecting tests/test_workflow.py __________________________________________________________________________________
import file mismatch:
imported module 'tests.test_workflow' has this file attribute:
/home/dell/picrust2-2.4.1/picrust2-2.4.1/tests/test_workflow.py
which is not the same as the test file we want to collect:
/home/dell/picrust2-2.4.1/tests/test_workflow.py
HINT: remove pycache / .pyc files and/or use a unique basename for your test file modules
========================================================================================= short test summary info ==========================================================================================
ERROR tests/test_hsp.py
ERROR tests/test_metagenome_pipeline.py
ERROR tests/test_pathway_pipeline.py
ERROR tests/test_place_seqs.py
ERROR tests/test_util.py
ERROR tests/test_workflow.py
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 6 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
How can i fix this?
Thanks!
from picrust2.
Hi @Beta-INC,
The first thing I would try is to re-download the the source repository as perhaps something was corrupted. Otherwise you can make sure there aren't any pycache or .pyc files in the test directory.
Cheers,
Gavin
from picrust2.
Related Issues (20)
- Installing problem into MacBook Air m1 terminal HOT 9
- help please : Error running picrust2_pipeline.py HOT 2
- maximum recursion depth exceeded while calling a Python object
- Question about previous filtering of otu table HOT 3
- Customize database guidance HOT 4
- running picrust2 on ITS HOT 2
- metagenome contributions analysis HOT 2
- Running picrust on shotgun output from bracken HOT 2
- Error runnig picrust due to cannot import name '_convert_node_to_root_polytomy' HOT 2
- Absolute abundance data for picrust2 HOT 3
- pytest fails 1 test on test_place_seqs.py HOT 2
- Macbook M1 chip pytest error (sqlite3 import??) HOT 2
- Assign general function from KEGG pathway in pathways_out HOT 1
- PICRTUST 2 No such file or directory: 'hmmalign' HOT 2
- Gene family abundances per ASV rather than per sample HOT 1
- UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte HOT 3
- During pytest place_seqs.py fails and cannot run the full pipeline HOT 6
- complex definition effect on abundance calculation HOT 1
- Please help for picrust2 tutorial: cannot download the data set HOT 4
- Running picrust on full geomes HOT 3
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from picrust2.