Problem with h5py (error: libhdf5.so: cannot open shared object file: No such file or directory)

I have a problem with h5py. I'm trying to install a package (P.E.P.P.E.R), but when trying to install, it will give an error.

error: libhdf5.so: cannot open shared object file: No such file or directory

This is an error I've seen a lot, which I tried fixing with these blogs first. But I cant seem to fix it. So I'm hoping one of you can give me the answer im looking for.

What I tried so far:

conda install -c anaconda h5pypip install h5pysudo apt-get install pkg-config libhdf5-100 libhdf5-devsudo apt-get install -y libhdf5-dev

I'm using anaconda, WSL (ubuntu), and VCS with python 3.10.9 in a local env.

The complete error log:

    (SNPcalling) stanaanhane@DESKTOP-L98RKGN:~/anaconda3/envs/SNPcalling/pepper$ make install. ./venv/bin/activate && pip install -r requirements.txtCollecting h5py==2.10.0  Using cached h5py-2.10.0.tar.gz (301 kB)  Preparing metadata (setup.py) ... doneRequirement already satisfied: numpy==1.22.0 in ./venv/lib/python3.10/site-packages (from -r requirements.txt (line 2)) (1.22.0)Requirement already satisfied: torch>1.10.0 in ./venv/lib/python3.10/site-packages (from -r requirements.txt (line 3)) (1.12.0+cu116)Requirement already satisfied: wget in ./venv/lib/python3.10/site-packages (from -r requirements.txt (line 4)) (3.2)Requirement already satisfied: torchvision in ./venv/lib/python3.10/site-packages (from -r requirements.txt (line 5)) (0.13.0+cu116)Requirement already satisfied: onnx in ./venv/lib/python3.10/site-packages (from -r requirements.txt (line 6)) (1.13.0)Collecting onnxruntime  Using cached onnxruntime-1.13.1-cp310-cp310-manylinux_2_27_x86_64.whl (4.5 MB)Collecting hyperopt==0.2  Using cached hyperopt-0.2-py3-none-any.whl (1.1 MB)Requirement already satisfied: cython>=0.29.12 in ./venv/lib/python3.10/site-packages (from -r requirements.txt (line 9)) (0.29.33)Requirement already satisfied: pyyaml in ./venv/lib/python3.10/site-packages (from -r requirements.txt (line 10)) (6.0)Collecting torchnet  Using cached torchnet-0.0.4-py3-none-any.whlRequirement already satisfied: intervaltree in ./venv/lib/python3.10/site-packages (from -r requirements.txt (line 12)) (3.1.0)Requirement already satisfied: pysam in ./venv/lib/python3.10/site-packages (from -r requirements.txt (line 13)) (0.20.0)Requirement already satisfied: six in ./venv/lib/python3.10/site-packages (from h5py==2.10.0->-r requirements.txt (line 1)) (1.16.0)Requirement already satisfied: cloudpickle in ./venv/lib/python3.10/site-packages (from hyperopt==0.2->-r requirements.txt (line 8)) (2.2.1)Requirement already satisfied: future in ./venv/lib/python3.10/site-packages (from hyperopt==0.2->-r requirements.txt (line 8)) (0.18.3)Requirement already satisfied: networkx==2.2 in ./venv/lib/python3.10/site-packages (from hyperopt==0.2->-r requirements.txt (line 8)) (2.2)        Collecting bson  Using cached bson-0.5.10-py3-none-any.whlRequirement already satisfied: tqdm in ./venv/lib/python3.10/site-packages (from hyperopt==0.2->-r requirements.txt (line 8)) (4.64.1)Requirement already satisfied: scipy in ./venv/lib/python3.10/site-packages (from hyperopt==0.2->-r requirements.txt (line 8)) (1.10.0)Requirement already satisfied: decorator>=4.3.0 in ./venv/lib/python3.10/site-packages (from networkx==2.2->hyperopt==0.2->-r requirements.txt (line 8)) (5.1.1)Requirement already satisfied: typing-extensions in ./venv/lib/python3.10/site-packages (from torch>1.10.0->-r requirements.txt (line 3)) (4.4.0)   Requirement already satisfied: requests in ./venv/lib/python3.10/site-packages (from torchvision->-r requirements.txt (line 5)) (2.28.2)Requirement already satisfied: pillow!=8.3.*,>=5.3.0 in ./venv/lib/python3.10/site-packages (from torchvision->-r requirements.txt (line 5)) (9.4.0)Requirement already satisfied: protobuf<4,>=3.20.2 in ./venv/lib/python3.10/site-packages (from onnx->-r requirements.txt (line 6)) (3.20.3)        Collecting coloredlogs  Using cached coloredlogs-15.0.1-py2.py3-none-any.whl (46 kB)Requirement already satisfied: packaging in ./venv/lib/python3.10/site-packages (from onnxruntime->-r requirements.txt (line 7)) (23.0)Requirement already satisfied: sympy in ./venv/lib/python3.10/site-packages (from onnxruntime->-r requirements.txt (line 7)) (1.11.1)Requirement already satisfied: flatbuffers in ./venv/lib/python3.10/site-packages (from onnxruntime->-r requirements.txt (line 7)) (23.1.4)Collecting visdom  Using cached visdom-0.2.3-py3-none-any.whlRequirement already satisfied: sortedcontainers<3.0,>=2.0 in ./venv/lib/python3.10/site-packages (from intervaltree->-r requirements.txt (line 12)) (2.4.0)Requirement already satisfied: python-dateutil>=2.4.0 in ./venv/lib/python3.10/site-packages (from bson->hyperopt==0.2->-r requirements.txt (line 8)) (2.8.2)Requirement already satisfied: humanfriendly>=9.1 in ./venv/lib/python3.10/site-packages (from coloredlogs->onnxruntime->-r requirements.txt (line 7)) (10.0)Requirement already satisfied: certifi>=2017.4.17 in ./venv/lib/python3.10/site-packages (from requests->torchvision->-r requirements.txt (line 5)) (2022.12.7)Requirement already satisfied: urllib3<1.27,>=1.21.1 in ./venv/lib/python3.10/site-packages (from requests->torchvision->-r requirements.txt (line 5)) (1.26.14)Requirement already satisfied: idna<4,>=2.5 in ./venv/lib/python3.10/site-packages (from requests->torchvision->-r requirements.txt (line 5)) (3.4) Requirement already satisfied: charset-normalizer<4,>=2 in ./venv/lib/python3.10/site-packages (from requests->torchvision->-r requirements.txt (line 5)) (3.0.1)Requirement already satisfied: mpmath>=0.19 in ./venv/lib/python3.10/site-packages (from sympy->onnxruntime->-r requirements.txt (line 7)) (1.2.1)Requirement already satisfied: jsonpatch in ./venv/lib/python3.10/site-packages (from visdom->torchnet->-r requirements.txt (line 11)) (1.32)Requirement already satisfied: tornado in ./venv/lib/python3.10/site-packages (from visdom->torchnet->-r requirements.txt (line 11)) (6.2)Requirement already satisfied: websocket-client in ./venv/lib/python3.10/site-packages (from visdom->torchnet->-r requirements.txt (line 11)) (1.4.2)Requirement already satisfied: jsonpointer>=1.9 in ./venv/lib/python3.10/site-packages (from jsonpatch->visdom->torchnet->-r requirements.txt (line 11)) (2.3)Building wheels for collected packages: h5py  Building wheel for h5py (setup.py) ... error  error: subprocess-exited-with-error× python setup.py bdist_wheel did not run successfully.│ exit code: 1╰─> [66 lines of output]      /home/stanaanhane/anaconda3/envs/SNPcalling/pepper/venv/lib/python3.10/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.        warnings.warn(      running bdist_wheel      running build      running build_py      creating build      creating build/lib.linux-x86_64-3.10      creating build/lib.linux-x86_64-3.10/h5py      copying h5py/ipy_completer.py -> build/lib.linux-x86_64-3.10/h5py      copying h5py/highlevel.py -> build/lib.linux-x86_64-3.10/h5py      copying h5py/h5py_warnings.py -> build/lib.linux-x86_64-3.10/h5py      copying h5py/__init__.py -> build/lib.linux-x86_64-3.10/h5py      copying h5py/version.py -> build/lib.linux-x86_64-3.10/h5py      creating build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/filters.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/selections.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/vds.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/dims.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/files.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/compat.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/base.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/group.py -> build/lib.linux-x86_64-3.10/h5py/_hl      creating build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_base.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_selections.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5t.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_attribute_create.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_attrs_data.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5f.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_objects.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_attrs.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/__init__.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_filters.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dimension_scales.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5pl.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_datatype.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_file_image.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_completions.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_group.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5p.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_file.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/common.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_deprecation.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dataset.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_threads.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_file2.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dtype.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_slicing.py -> build/lib.linux-x86_64-3.10/h5py/tests      creating build/lib.linux-x86_64-3.10/h5py/tests/test_vds      copying h5py/tests/test_vds/__init__.py -> build/lib.linux-x86_64-3.10/h5py/tests/test_vds      copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-x86_64-3.10/h5py/tests/test_vds      copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-x86_64-3.10/h5py/tests/test_vds      copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-x86_64-3.10/h5py/tests/test_vds      running build_ext      Loading library to get version: libhdf5.so      error: libhdf5.so: cannot open shared object file: No such file or directory      [end of output]  note: This error originates from a subprocess, and is likely not a problem with pip.  ERROR: Failed building wheel for h5py  Running setup.py clean for h5pyFailed to build h5pyInstalling collected packages: h5py, coloredlogs, visdom, onnxruntime, bson, torchnet, hyperopt  Running setup.py install for h5py ... error  error: subprocess-exited-with-error× Running setup.py install for h5py did not run successfully.│ exit code: 1╰─> [68 lines of output]      /home/stanaanhane/anaconda3/envs/SNPcalling/pepper/venv/lib/python3.10/site-packages/setuptools/installer.py:27: SetuptoolsDeprecationWarning: setuptools.installer is deprecated. Requirements should be satisfied by a PEP 517 installer.        warnings.warn(      running install      /home/stanaanhane/anaconda3/envs/SNPcalling/pepper/venv/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.        warnings.warn(      running build      running build_py      creating build      creating build/lib.linux-x86_64-3.10      creating build/lib.linux-x86_64-3.10/h5py      copying h5py/ipy_completer.py -> build/lib.linux-x86_64-3.10/h5py      copying h5py/highlevel.py -> build/lib.linux-x86_64-3.10/h5py      copying h5py/h5py_warnings.py -> build/lib.linux-x86_64-3.10/h5py      copying h5py/__init__.py -> build/lib.linux-x86_64-3.10/h5py      copying h5py/version.py -> build/lib.linux-x86_64-3.10/h5py      creating build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/filters.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/selections.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/attrs.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/selections2.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/__init__.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/vds.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/datatype.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/dims.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/dataset.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/files.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/compat.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/base.py -> build/lib.linux-x86_64-3.10/h5py/_hl      copying h5py/_hl/group.py -> build/lib.linux-x86_64-3.10/h5py/_hl      creating build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dataset_getitem.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_base.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_selections.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5t.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_attribute_create.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_attrs_data.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5f.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5d_direct_chunk.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_objects.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_attrs.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/__init__.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_filters.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dimension_scales.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dims_dimensionproxy.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5pl.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_datatype.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_file_image.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dataset_swmr.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_completions.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_group.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_h5p.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_file.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/common.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_deprecation.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dataset.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_threads.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_file2.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_dtype.py -> build/lib.linux-x86_64-3.10/h5py/tests      copying h5py/tests/test_slicing.py -> build/lib.linux-x86_64-3.10/h5py/tests      creating build/lib.linux-x86_64-3.10/h5py/tests/test_vds      copying h5py/tests/test_vds/__init__.py -> build/lib.linux-x86_64-3.10/h5py/tests/test_vds      copying h5py/tests/test_vds/test_lowlevel_vds.py -> build/lib.linux-x86_64-3.10/h5py/tests/test_vds      copying h5py/tests/test_vds/test_virtual_source.py -> build/lib.linux-x86_64-3.10/h5py/tests/test_vds      copying h5py/tests/test_vds/test_highlevel_vds.py -> build/lib.linux-x86_64-3.10/h5py/tests/test_vds      running build_ext      Loading library to get version: libhdf5.so      error: libhdf5.so: cannot open shared object file: No such file or directory      [end of output]  note: This error originates from a subprocess, and is likely not a problem with pip.error: legacy-install-failure× Encountered error while trying to install package.╰─> h5py

Thank you in advance!