Open amv33576 opened 8 months ago
I published today a maintenance update version 3.7.3 which should fix this issue.
If someone has to use 3.5.2, how can the numpy problem be addressed?
Go to the 3.5.2 release, and download the requirements.txt file: https://github.com/deeptools/HiCExplorer/blob/3.5.2/requirements.txt
Change now all >=
to ==
, and install HiCExplorer using the changed requirements.txt file: mamba create -n HiCExplorer3.5.2 --file requirements.txt hicexplorer=3.5.2
Yes, I already have a conda env for hicexplorer3.5.2. It shows: numpy 1.24.4
I get the np.int error when trying to use it. Do you know which file in the env needs to be modified or if there is another way around it?
Activate your environment and set the numpy version manually to an older one: conda install numpy=1.19
Unfortunately, there were too many conflicts to do this installation - the environment couldn't be resolved.
You can try either mamba instead of conda, or delete your non-working environment and set it up new with the requirements.txt file as explained above.
Dear all,
I am finding this problem when calculating a background model. Command in:
chicQualityControl -m matrix.nr.h5 --referencePoints RFpoints.bed --sparsity 0.025 --threads 20 --outFileName new_RPs.bed chicViewpointBackgroundModel -m matrix.nr.h5 --fixateRange 500000 --referencePoints new_RPs.bed --outFileName bgm.txt
ERROR:hicexplorer.chicViewpointBackgroundModel:An error occurred caused by one or many faulty reference points. ERROR:hicexplorer.chicViewpointBackgroundModel:Please run chicQualityControl to remove these from your reference point file: new_RPs.bed
ERROR:hicexplorer.chicViewpointBackgroundModel:module 'numpy' has no attribute 'int'.
np.int
was a deprecated alias for the builtinint
. To avoid this error in existing code, useint
by itself. Doing this will not modify any behavior and is safe. When replacingnp.int
, you may wish to use e.g.np.int64
ornp.int32
to specify the precision. If you wish to review your current use, check the release note link for additional information. The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecationsName Version Build Channel hicexplorer 3.7.2 pyhdfd78af_1 bioconda numpy 1.24.4 py38h59b608b_0 conda-forge python 3.8.18 hd12c33a_0_cpython conda-forge
Any advice?
Best,
A.