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BCCDC-PHL / fluviewer-nf

Nextflow pipeline for influenza A whole genome sequence analysis
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Version conflict between Matplotlib et numpy #40

Closed EricFournier3 closed 2 months ago

EricFournier3 commented 2 months ago

Hi,

when I run the following command

nextflow run BCCDC-PHL/fluviewer-nf -r v0.3.0 -profile conda --cache /data/devel/fluviewer/conda --fastq_input /data/devel/fluviewer/fastq --db /data/devel/fluviewer/db/FluViewer_db_v_0_1_8.fa --outdir /data/devel/fluviewer/out

fluviewer.nf produces the following Import Error

Traceback (most recent call last): File "/data/devel/fluviewer/conda/fluviewer-nf-FluViewer-98a3cd0cef99579de0b5ca640a2e19df/bin/fluviewer", line 5, in from fluviewer.fluviewer import main File "/data/devel/fluviewer/conda/fluviewer-nf-FluViewer-98a3cd0cef99579de0b5ca640a2e19df/lib/python3.9/site-packages/fluviewer/fluviewer.py", line 23, in from . import plots File "/data/devel/fluviewer/conda/fluviewer-nf-FluViewer-98a3cd0cef99579de0b5ca640a2e19df/lib/python3.9/site-packages/fluviewer/plots.py", line 9, in import seaborn as sb File "/data/devel/fluviewer/conda/fluviewer-nf-FluViewer-98a3cd0cef99579de0b5ca640a2e19df/lib/python3.9/site-packages/seaborn/init.py", line 2, in from .rcmod import * # noqa: F401,F403 File "/data/devel/fluviewer/conda/fluviewer-nf-FluViewer-98a3cd0cef99579de0b5ca640a2e19df/lib/python3.9/site-packages/seaborn/rcmod.py", line 3, in import matplotlib as mpl File "/data/devel/fluviewer/conda/fluviewer-nf-FluViewer-98a3cd0cef99579de0b5ca640a2e19df/lib/python3.9/site-packages/matplotlib/init.py", line 263, in _check_versions() File "/data/devel/fluviewer/conda/fluviewer-nf-FluViewer-98a3cd0cef99579de0b5ca640a2e19df/lib/python3.9/site-packages/matplotlib/init.py", line 259, in _check_versions raise ImportError(f"Matplotlib requires {modname}>={minver}; " ImportError: Matplotlib requires numpy>=1.23; you have 1.22.4

Yet, as you can see in my fluviewer-nf-FluViewer-98a3cd0cef99579de0b5ca640a2e19df conda environment the version of numpy is 1.26.4 (not 1.22.4)

(base) [site-packages]$ pwd
/data/devel/fluviewer/conda/fluviewer-nf-FluViewer-98a3cd0cef99579de0b5ca640a2e19df/lib/python3.9/site-packages
(base) [site-packages]$ ls -d numpy*/
numpy/  numpy-1.26.4.dist-info/

Do you have any idea regarding this issue?

Thanks Eric

EricFournier3 commented 2 months ago

I finally found the cause. I will close this issue