Installation error
Hi @sirarredondo ,
Thank you for a great resource! I am trying to install the software on the compute cluster and I am running into the following error, any suggestions?
Code-
python -m pip install -e .
Error-
Installing build dependencies ... done
Checking if build backend supports build_editable ... done
Getting requirements to build editable ... done
Preparing editable metadata (pyproject.toml) ... done
Collecting opentsne (from mge-cluster==1.1.0)
Downloading openTSNE-1.0.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 8.0 MB/s eta 0:00:00
Collecting hdbscan (from mge-cluster==1.1.0)
Downloading hdbscan-0.8.33.tar.gz (5.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.2/5.2 MB 26.7 MB/s eta 0:00:00
Installing build dependencies ... done
Getting requirements to build wheel ... done
Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: pandas in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from mge-cluster==1.1.0) (2.0.2)
Collecting unitig-caller (from mge-cluster==1.1.0)
Downloading unitig-caller-1.2.0.tar.gz (12 kB)
Preparing metadata (setup.py) ... done
Requirement already satisfied: cython<3,>=0.27 in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from hdbscan->mge-cluster==1.1.0) (0.29.35)
Requirement already satisfied: numpy>=1.20 in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from hdbscan->mge-cluster==1.1.0) (1.24.3)
Requirement already satisfied: scipy>=1.0 in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from hdbscan->mge-cluster==1.1.0) (1.10.1)
Requirement already satisfied: scikit-learn>=0.20 in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from hdbscan->mge-cluster==1.1.0) (1.2.2)
Requirement already satisfied: joblib>=1.0 in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from hdbscan->mge-cluster==1.1.0) (1.2.0)
Requirement already satisfied: python-dateutil>=2.8.2 in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from pandas->mge-cluster==1.1.0) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from pandas->mge-cluster==1.1.0) (2023.3)
Requirement already satisfied: tzdata>=2022.1 in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from pandas->mge-cluster==1.1.0) (2023.3)
Requirement already satisfied: six>=1.5 in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from python-dateutil>=2.8.2->pandas->mge-cluster==1.1.0) (1.16.0)
Requirement already satisfied: threadpoolctl>=2.0.0 in /home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages (from scikit-learn>=0.20->hdbscan->mge-cluster==1.1.0) (3.1.0)
Building wheels for collected packages: mge-cluster, hdbscan, unitig-caller
Building editable for mge-cluster (pyproject.toml) ... done
Created wheel for mge-cluster: filename=mge_cluster-1.1.0-0.editable-py3-none-any.whl size=10141 sha256=402860865ac78050b1b9ba79d099bc1587d74a17accce3b392f3bee2a24e5836
Stored in directory: /tmp/pip-ephem-wheel-cache-leeh420p/wheels/5a/15/c7/f279ac46b1a8d0a942c40b82b813095bef638e58ae2007118d
Building wheel for hdbscan (pyproject.toml) ... done
Created wheel for hdbscan: filename=hdbscan-0.8.33-cp311-cp311-linux_x86_64.whl size=3840157 sha256=48696392e004b9bfa5cc0f111355eb4156e46e06d00bece720400e2dc8cd2018
Stored in directory: /home/jigyasaa/.cache/pip/wheels/4e/8c/6f/d0495e4e40cbd27a8c7330d4e963837e099d6e16014dbdcdb5
Building wheel for unitig-caller (setup.py) ... error
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [54 lines of output]
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-cpython-311
creating build/lib.linux-x86_64-cpython-311/unitig_caller
copying unitig_caller/__main__.py -> build/lib.linux-x86_64-cpython-311/unitig_caller
copying unitig_caller/__init__.py -> build/lib.linux-x86_64-cpython-311/unitig_caller
copying unitig_caller/bifrost.py -> build/lib.linux-x86_64-cpython-311/unitig_caller
running build_ext
CMake Error: The source directory "/tmp/pip-install-tgoswkb5/unitig-caller_55f2e3f36616404ca6b415bb853caf43" does not appear to contain CMakeLists.txt.
Specify --help for usage, or press the help button on the CMake GUI.
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "<pip-setuptools-caller>", line 34, in <module>
File "/tmp/pip-install-tgoswkb5/unitig-caller_55f2e3f36616404ca6b415bb853caf43/setup.py", line 82, in <module>
setup(
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/__init__.py", line 87, in setup
return distutils.core.setup(**attrs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 185, in setup
return run_commands(dist)
^^^^^^^^^^^^^^^^^^
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 201, in run_commands
dist.run_commands()
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 968, in run_commands
self.run_command(cmd)
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/wheel/bdist_wheel.py", line 343, in run
self.run_command("build")
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
self.distribution.run_command(command)
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/_distutils/command/build.py", line 132, in run
self.run_command(cmd_name)
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 319, in run_command
self.distribution.run_command(command)
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/dist.py", line 1217, in run_command
super().run_command(command)
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 987, in run_command
cmd_obj.run()
File "/tmp/pip-install-tgoswkb5/unitig-caller_55f2e3f36616404ca6b415bb853caf43/setup.py", line 49, in run
self.build_extension(ext)
File "/tmp/pip-install-tgoswkb5/unitig-caller_55f2e3f36616404ca6b415bb853caf43/setup.py", line 74, in build_extension
subprocess.check_call(['cmake', ext.sourcedir] + cmake_args, cwd=self.build_temp, env=env)
File "/home/jigyasaa/.pyenv/versions/3.11.3/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['cmake', '/tmp/pip-install-tgoswkb5/unitig-caller_55f2e3f36616404ca6b415bb853caf43', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/tmp/pip-install-tgoswkb5/unitig-caller_55f2e3f36616404ca6b415bb853caf43/build/lib.linux-x86_64-cpython-311', '-DPYTHON_EXECUTABLE=/home/jigyasaa/.pyenv/versions/3.11.3/bin/python', '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON', '-DCMAKE_BUILD_TYPE=Release']' returned non-zero exit status 1.
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for unitig-caller
Running setup.py clean for unitig-caller
Successfully built mge-cluster hdbscan
Failed to build unitig-caller
ERROR: Could not build wheels for unitig-caller, which is required to install pyproject.toml-based projects
[notice] A new release of pip is available: 23.1.2 -> 24.0
[notice] To update, run: pip install --upgrade pip