python3 setup.py install causes other packages to disappeaar

[NorseGaud]

🐛 Describe the bug

I'm running python3 setup.py install to build it out into my venv. I traced/logged the pip list output the entire process and watched to see what happens from start to finish.

I have the following packages:

root@844722c6e751:~# pip list
Package      Version
------------ -------------------------
bitsandbytes 0.45.2
einops       0.8.1
filelock     3.18.0
fsspec       2025.3.0
Jinja2       3.1.6
MarkupSafe   3.0.2
mpmath       1.3.0
networkx     3.4.2
pillow       11.1.0
pip          22.0.2
sympy        1.13.1
torch        2.6.0
xformers     0.0.30+1298453c.d20250326

When torchvision completes setup, it shows this for ~2 seconds

root@844722c6e751:~# pip list
Package      Version
------------ -------------------------
. . .
torchvision  0.21.0+7af6987
xformers     0.0.30+1298453c.d20250326

But then, xformers is gone after that.

The logs show a bunch of dependency related things happening at the end, around the time xformers disappears and I wonder if they're related. Here is the log

writing build/bdist.linux-aarch64/egg/EGG-INFO/native_libs.txt
creating dist
creating 'dist/torchvision-0.21.0+7af6987-py3.10-linux-aarch64.egg' and adding 'build/bdist.linux-aarch64/egg' to it
removing 'build/bdist.linux-aarch64/egg' (and everything under it)
Processing torchvision-0.21.0+7af6987-py3.10-linux-aarch64.egg
creating /root/wooly-client-venv/lib/python3.10/site-packages/torchvision-0.21.0+7af6987-py3.10-linux-aarch64.egg
Extracting torchvision-0.21.0+7af6987-py3.10-linux-aarch64.egg to /root/wooly-client-venv/lib/python3.10/site-packages
Adding torchvision 0.21.0+7af6987 to easy-install.pth file
detected new path './xformers-0.0.30+1298453c.d20250326-py3.10-linux-aarch64.egg'
detected new path './numpy-2.2.4-py3.10-linux-aarch64.egg'

Installed /root/wooly-client-venv/lib/python3.10/site-packages/torchvision-0.21.0+7af6987-py3.10-linux-aarch64.egg
Processing dependencies for torchvision==0.21.0+7af6987
Searching for numpy
Reading https://pypi.org/simple/numpy/
Downloading https://files.pythonhosted.org/packages/4c/22/fb1be710a14434c09080dd4a0acc08939f612ec02efcb04b9e210474782d/numpy-2.2.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl#sha256=7716e4a9b7af82c06a2543c53ca476fa0b57e4d760481273e09da04b74ee6ee2
Best match: numpy 2.2.4
Processing numpy-2.2.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl
removing '/root/wooly-client-venv/lib/python3.10/site-packages/numpy-2.2.4-py3.10-linux-aarch64.egg' (and everything under it)
Installing numpy-2.2.4-cp310-cp310-manylinux_2_17_aarch64.manylinux2014_aarch64.whl to /root/wooly-client-venv/lib/python3.10/site-packages
Adding numpy 2.2.4 to easy-install.pth file
detected new path './torchvision-0.21.0+7af6987-py3.10-linux-aarch64.egg'
Installing f2py script to /root/wooly-client-venv/bin
Installing numpy-config script to /root/wooly-client-venv/bin

Installed /root/wooly-client-venv/lib/python3.10/site-packages/numpy-2.2.4-py3.10-linux-aarch64.egg
Searching for pillow==11.1.0
Best match: pillow 11.1.0
Processing pillow-11.1.0-py3.10-linux-aarch64.egg
Adding pillow 11.1.0 to easy-install.pth file

Using /root/wooly-client-venv/lib/python3.10/site-packages/pillow-11.1.0-py3.10-linux-aarch64.egg
Searching for torch==2.6.0
Best match: torch 2.6.0
Adding torch 2.6.0 to easy-install.pth file
Installing torchfrtrace script to /root/wooly-client-venv/bin
Installing torchrun script to /root/wooly-client-venv/bin

Using /root/wooly-client-venv/lib/python3.10/site-packages
Searching for sympy==1.13.1
Best match: sympy 1.13.1
Processing sympy-1.13.1-py3.10.egg
Adding sympy 1.13.1 to easy-install.pth file
Installing isympy script to /root/wooly-client-venv/bin

Using /root/wooly-client-venv/lib/python3.10/site-packages/sympy-1.13.1-py3.10.egg
Searching for typing-extensions==4.12.2
Best match: typing-extensions 4.12.2
Adding typing-extensions 4.12.2 to easy-install.pth file

Using /root/wooly-client-venv/lib/python3.10/site-packages/setuptools/_vendor
Searching for networkx==3.4.2
Best match: networkx 3.4.2
Processing networkx-3.4.2-py3.10.egg
Adding networkx 3.4.2 to easy-install.pth file

Using /root/wooly-client-venv/lib/python3.10/site-packages/networkx-3.4.2-py3.10.egg
Searching for jinja2==3.1.6
Best match: jinja2 3.1.6
Processing jinja2-3.1.6-py3.10.egg
Adding jinja2 3.1.6 to easy-install.pth file

Using /root/wooly-client-venv/lib/python3.10/site-packages/jinja2-3.1.6-py3.10.egg
Searching for fsspec==2025.3.0
Best match: fsspec 2025.3.0
Processing fsspec-2025.3.0-py3.10.egg
Adding fsspec 2025.3.0 to easy-install.pth file

Using /root/wooly-client-venv/lib/python3.10/site-packages/fsspec-2025.3.0-py3.10.egg
Searching for filelock==3.18.0
Best match: filelock 3.18.0
Processing filelock-3.18.0-py3.10.egg
Adding filelock 3.18.0 to easy-install.pth file

Using /root/wooly-client-venv/lib/python3.10/site-packages/filelock-3.18.0-py3.10.egg
Searching for mpmath==1.3.0
Best match: mpmath 1.3.0
Processing mpmath-1.3.0-py3.10.egg
Adding mpmath 1.3.0 to easy-install.pth file

Using /root/wooly-client-venv/lib/python3.10/site-packages/mpmath-1.3.0-py3.10.egg
Searching for MarkupSafe==3.0.2
Best match: MarkupSafe 3.0.2
Processing MarkupSafe-3.0.2-py3.10-linux-aarch64.egg
Adding MarkupSafe 3.0.2 to easy-install.pth file

Using /root/wooly-client-venv/lib/python3.10/site-packages/MarkupSafe-3.0.2-py3.10-linux-aarch64.egg
Finished processing dependencies for torchvision==0.21.0+7af6987

The xformers directory is however there under site-packages and looks complete

root@fc2813de016d:~# ll wooly-client-venv/lib/python3.10/site-packages/
total 396
drwxr-xr-x  1 1000 1000   4096 Mar 26 15:34 ./
drwxr-xr-x  1 1000 1000   4096 Mar 26 14:58 ../
drwxr-xr-x  4 root root   4096 Mar 26 15:33 MarkupSafe-3.0.2-py3.10-linux-aarch64.egg/
drwxr-xr-x  2 root root   4096 Mar 26 15:24 MarkupSafe-3.0.2.dist-info/
drwxr-xr-x  2 root root   4096 Mar 26 14:58 PyYAML-6.0.2.dist-info/
drwxr-xr-x  1 root root   4096 Mar 26 15:24 __pycache__/
drwxr-xr-x  3 1000 1000   4096 Mar 26 14:58 _distutils_hack/
drwxr-xr-x  3 root root   4096 Mar 26 14:58 _yaml/
drwxr-xr-x  9 root root   4096 Mar 26 15:24 bitsandbytes/
drwxr-xr-x  3 root root   4096 Mar 26 15:24 bitsandbytes-0.45.2.dist-info/
-rw-r--r--  1 1000 1000    152 Mar 26 14:58 distutils-precedence.pth
-rw-r--r--  1 root root     95 Mar 26 15:34 easy-install.pth
drwxr-xr-x  3 root root   4096 Mar 26 15:24 filelock/
drwxr-xr-x  4 root root   4096 Mar 26 15:33 filelock-3.18.0-py3.10.egg/
drwxr-xr-x  3 root root   4096 Mar 26 15:24 filelock-3.18.0.dist-info/
drwxr-xr-x  5 root root   4096 Mar 26 15:24 fsspec/
drwxr-xr-x  4 root root   4096 Mar 26 15:33 fsspec-2025.3.0-py3.10.egg/
drwxr-xr-x  3 root root   4096 Mar 26 15:24 fsspec-2025.3.0.dist-info/
drwxr-xr-x  8 root root   4096 Mar 26 15:24 functorch/
-rw-r--r--  1 root root  11207 Mar 26 15:24 isympy.py
drwxr-xr-x  3 root root   4096 Mar 26 15:24 jinja2/
drwxr-xr-x  4 root root   4096 Mar 26 15:33 jinja2-3.1.6-py3.10.egg/
drwxr-xr-x  3 root root   4096 Mar 26 15:24 jinja2-3.1.6.dist-info/
drwxr-xr-x  3 root root   4096 Mar 26 15:24 markupsafe/
drwxr-xr-x  8 root root   4096 Mar 26 15:24 mpmath/
drwxr-xr-x  4 root root   4096 Mar 26 15:33 mpmath-1.3.0-py3.10.egg/
drwxr-xr-x  2 root root   4096 Mar 26 15:24 mpmath-1.3.0.dist-info/
drwxr-xr-x 11 root root   4096 Mar 26 15:24 networkx/
drwxr-xr-x  4 root root   4096 Mar 26 15:33 networkx-3.4.2-py3.10.egg/
drwxr-xr-x  2 root root   4096 Mar 26 15:24 networkx-3.4.2.dist-info/
drwxr-xr-x 25 root root   4096 Mar 26 14:58 numpy/
drwxr-xr-x  2 root root   4096 Mar 26 14:58 numpy-2.2.4.dist-info/
drwxr-xr-x  2 root root   4096 Mar 26 14:58 numpy.libs/
drwxr-xr-x  4 root root   4096 Mar 26 14:58 packaging/
drwxr-xr-x  2 root root   4096 Mar 26 14:58 packaging-24.2.dist-info/
drwxr-xr-x  5 root root   4096 Mar 26 15:34 pillow-11.1.0-py3.10-linux-aarch64.egg/
drwxr-xr-x  5 1000 1000   4096 Mar 26 14:58 pip/
drwxr-xr-x  2 1000 1000   4096 Mar 26 14:58 pip-22.0.2.dist-info/
drwxr-xr-x  6 1000 1000   4096 Mar 26 14:58 pkg_resources/
drwxr-xr-x  7 1000 1000   4096 Mar 26 14:58 setuptools/
drwxr-xr-x  2 1000 1000   4096 Mar 26 14:58 setuptools-59.6.0.dist-info/
drwxr-xr-x 43 root root   4096 Mar 26 15:24 sympy/
drwxr-xr-x  5 root root   4096 Mar 26 15:33 sympy-1.13.1-py3.10.egg/
drwxr-xr-x  2 root root   4096 Mar 26 15:24 sympy-1.13.1.dist-info/
drwxr-xr-x 63 root root   4096 Mar 26 15:24 torch/
drwxr-xr-x  2 root root   4096 Mar 26 15:24 torch-2.6.0a0+gitd398019.egg-info/
drwxr-xr-x 11 root root   4096 Mar 26 15:24 torchgen/
drwxr-xr-x  4 root root   4096 Mar 26 15:34 torchvision-0.21.0+7af6987-py3.10-linux-aarch64.egg/
drwxr-xr-x  3 root root   4096 Mar 26 14:58 typing_extensions-4.13.0.dist-info/
-rw-r--r--  1 root root 171956 Mar 26 14:58 typing_extensions.py
drwxr-xr-x  5 root root   4096 Mar 26 14:58 wheel/
drwxr-xr-x  2 root root   4096 Mar 26 14:58 wheel-0.45.1.dist-info/
drwxr-xr-x  4 root root   4096 Mar 26 15:33 xformers-0.0.30+1298453c.d20250326-py3.10-linux-aarch64.egg/
drwxr-xr-x  3 root root   4096 Mar 26 14:58 yaml/

I checked the setup.py and I didn't see it doing anything that could cause this, but I'm also a pip/python newbie in a few ways.

Anyone know what I'm missing here? What could cause the packages to disappear after torchvision setup finishes?

Versions

0.21.0