2025-09-08T19:06:16,944 Created temporary directory: /tmp/pip-build-tracker-_1czt53u
2025-09-08T19:06:16,945 Initialized build tracking at /tmp/pip-build-tracker-_1czt53u
2025-09-08T19:06:16,945 Created build tracker: /tmp/pip-build-tracker-_1czt53u
2025-09-08T19:06:16,945 Entered build tracker: /tmp/pip-build-tracker-_1czt53u
2025-09-08T19:06:16,945 Created temporary directory: /tmp/pip-wheel-1ppvbvpy
2025-09-08T19:06:16,948 Created temporary directory: /tmp/pip-ephem-wheel-cache-x83xihbr
2025-09-08T19:06:17,007 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-09-08T19:06:17,010 2 location(s) to search for versions of uga:
2025-09-08T19:06:17,010 * https://pypi.org/simple/uga/
2025-09-08T19:06:17,010 * https://www.piwheels.org/simple/uga/
2025-09-08T19:06:17,010 Fetching project page and analyzing links: https://pypi.org/simple/uga/
2025-09-08T19:06:17,010 Getting page https://pypi.org/simple/uga/
2025-09-08T19:06:17,012 Found index url https://pypi.org/simple/
2025-09-08T19:06:17,083 Fetched page https://pypi.org/simple/uga/ as application/vnd.pypi.simple.v1+json
2025-09-08T19:06:17,085 Found link https://files.pythonhosted.org/packages/4d/36/f482cd61f6203a95145fba1337b51dc4b8fcd6f17645fdc4971547a18f20/uga-2.0.tar.gz (from https://pypi.org/simple/uga/), version: 2.0
2025-09-08T19:06:17,085 Found link https://files.pythonhosted.org/packages/1c/d6/a97dd03cb53d33cf7c416104b018d86692ba0c2aabe0f8c0ccadf9e3e765/uga-2.0.1.tar.gz (from https://pypi.org/simple/uga/), version: 2.0.1
2025-09-08T19:06:17,085 Found link https://files.pythonhosted.org/packages/58/7b/5005fe02a229b5ce76c2a917d9460e0bf3540972392f8eaff38ab1a47e0b/uga-2.0.2.tar.gz (from https://pypi.org/simple/uga/), version: 2.0.2
2025-09-08T19:06:17,086 Found link https://files.pythonhosted.org/packages/d9/85/968d8552bd6c6199cea5842ee47db06558b1a7ce2a26e417fc40128b6d97/uga-2.0.3.tar.gz (from https://pypi.org/simple/uga/), version: 2.0.3
2025-09-08T19:06:17,086 Found link https://files.pythonhosted.org/packages/50/67/a01e7e269051d4b1ba45db5607d68471ccf471ce3c0cb9b2901e3da53854/uga-2.0.4.tar.gz (from https://pypi.org/simple/uga/), version: 2.0.4
2025-09-08T19:06:17,086 Found link https://files.pythonhosted.org/packages/1a/c0/99dfb28c44ba27be80436b5f1bb370fcb764ecbb4e69038d3eb7eacb247e/uga-2.0.5.tar.gz (from https://pypi.org/simple/uga/), version: 2.0.5
2025-09-08T19:06:17,086 Found link https://files.pythonhosted.org/packages/89/55/7ae9e605effe88754f29b901fe962391ca9e945cf527a11e24f4b60a3c11/uga-2.0.6.tar.gz (from https://pypi.org/simple/uga/), version: 2.0.6
2025-09-08T19:06:17,087 Found link https://files.pythonhosted.org/packages/49/34/6aab750c3cbd08ba7079b789bcedc045e8bdd6530eef5ca16a1a9988a1ca/uga-2.0.7.tar.gz (from https://pypi.org/simple/uga/), version: 2.0.7
2025-09-08T19:06:17,087 Fetching project page and analyzing links: https://www.piwheels.org/simple/uga/
2025-09-08T19:06:17,087 Getting page https://www.piwheels.org/simple/uga/
2025-09-08T19:06:17,088 Found index url https://www.piwheels.org/simple/
2025-09-08T19:06:17,179 Fetched page https://www.piwheels.org/simple/uga/ as text/html
2025-09-08T19:06:17,187 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.7-cp39-cp39-linux_armv6l.whl#sha256=b4fb6eb8856ba46db111a66a8eb2b11d1aea08b4eb620a3ea7274516893c3af5 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,187 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.7-cp39-cp39-linux_armv7l.whl#sha256=b4fb6eb8856ba46db111a66a8eb2b11d1aea08b4eb620a3ea7274516893c3af5 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,187 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.7-cp35-cp35m-linux_armv6l.whl#sha256=469d902ba03a1cef7b56d68e6e1f32dc7a5f3ae7a09b9368d37bc2f42a783582 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,187 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.7-cp35-cp35m-linux_armv7l.whl#sha256=469d902ba03a1cef7b56d68e6e1f32dc7a5f3ae7a09b9368d37bc2f42a783582 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,187 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.7-cp37-cp37m-linux_armv7l.whl#sha256=15ddf61614a47076c82b3d2423000d684b480af4e976f24336d2552977d8d359 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,187 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.7-cp37-cp37m-linux_armv6l.whl#sha256=15ddf61614a47076c82b3d2423000d684b480af4e976f24336d2552977d8d359 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,188 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.6-cp39-cp39-linux_armv6l.whl#sha256=19e6ca063f7eaa8a1c777d24590b2235a74e5bd0b4ebf6f9f84e18a5f275b703 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,188 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.6-cp39-cp39-linux_armv7l.whl#sha256=19e6ca063f7eaa8a1c777d24590b2235a74e5bd0b4ebf6f9f84e18a5f275b703 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,188 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.6-cp35-cp35m-linux_armv6l.whl#sha256=adb9c18a283dcfe8e1f43cf2868bbf7f3a3a66a7e61fda4b97c95e783f282aff (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,188 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.6-cp35-cp35m-linux_armv7l.whl#sha256=adb9c18a283dcfe8e1f43cf2868bbf7f3a3a66a7e61fda4b97c95e783f282aff (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,188 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.6-cp37-cp37m-linux_armv7l.whl#sha256=c2f1dcf8a76bb64180bd49b9b3aa6b024a4dc4544d1d60b2d43d20d7e079f281 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,188 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.6-cp37-cp37m-linux_armv6l.whl#sha256=c2f1dcf8a76bb64180bd49b9b3aa6b024a4dc4544d1d60b2d43d20d7e079f281 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,188 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.5-cp39-cp39-linux_armv6l.whl#sha256=f401f01d0e2d62702e3fe794e0068b94ad6f55f0a5d92c7f59c78fa17d748b32 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,188 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.5-cp39-cp39-linux_armv7l.whl#sha256=f401f01d0e2d62702e3fe794e0068b94ad6f55f0a5d92c7f59c78fa17d748b32 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,189 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.5-cp35-cp35m-linux_armv7l.whl#sha256=491a02ba97e9eb47d38732cd3ef41840a9aea5d14325b68144c7d2a48a026e0d (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,189 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.5-cp35-cp35m-linux_armv6l.whl#sha256=491a02ba97e9eb47d38732cd3ef41840a9aea5d14325b68144c7d2a48a026e0d (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,189 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.5-cp37-cp37m-linux_armv7l.whl#sha256=6bba3caa8c57b41d8f66eecd0f1eb41d0914362acd3664f88a33e63a9a0200f0 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,189 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.5-cp37-cp37m-linux_armv6l.whl#sha256=6bba3caa8c57b41d8f66eecd0f1eb41d0914362acd3664f88a33e63a9a0200f0 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,189 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.4-cp39-cp39-linux_armv6l.whl#sha256=1e2e4afcd27e57550da17b606b1ed1a3e10d00c042aec434ec39f668fd9b9673 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,189 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.4-cp39-cp39-linux_armv7l.whl#sha256=1e2e4afcd27e57550da17b606b1ed1a3e10d00c042aec434ec39f668fd9b9673 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,189 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.4-cp35-cp35m-linux_armv6l.whl#sha256=01d245dbc747468404c33a4e2da546fd8f8c16657d6ba518996349d745ddc12b (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,189 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.4-cp35-cp35m-linux_armv7l.whl#sha256=01d245dbc747468404c33a4e2da546fd8f8c16657d6ba518996349d745ddc12b (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,190 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.4-cp37-cp37m-linux_armv6l.whl#sha256=6301b8317fda7159f64ff58c5b5a9535422c8f58b98440dd44eb9f1d049889cd (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,190 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.4-cp37-cp37m-linux_armv7l.whl#sha256=6301b8317fda7159f64ff58c5b5a9535422c8f58b98440dd44eb9f1d049889cd (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,190 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.3-cp39-cp39-linux_armv6l.whl#sha256=19595ba8c837169226774abafcd5d1796cfd63893d5df5993f6f02631cf3f9e8 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,190 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.3-cp39-cp39-linux_armv7l.whl#sha256=19595ba8c837169226774abafcd5d1796cfd63893d5df5993f6f02631cf3f9e8 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,190 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.3-cp35-cp35m-linux_armv6l.whl#sha256=4ae5094a5d2ac0045c05a95364489c3fef767b5ec34a527317e3eacd6889db30 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,190 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.3-cp35-cp35m-linux_armv7l.whl#sha256=4ae5094a5d2ac0045c05a95364489c3fef767b5ec34a527317e3eacd6889db30 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,190 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.3-cp37-cp37m-linux_armv7l.whl#sha256=9164b6be38accde172bb7d02e8236d78f4a524cd725964eacbac814d4c214cd8 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,190 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.3-cp37-cp37m-linux_armv6l.whl#sha256=9164b6be38accde172bb7d02e8236d78f4a524cd725964eacbac814d4c214cd8 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,191 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.2-cp39-cp39-linux_armv6l.whl#sha256=81c811d08f5395585ef4afb30b07f59f6696b27e91c2e7dfd250659b78e2b1fb (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,191 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.2-cp39-cp39-linux_armv7l.whl#sha256=81c811d08f5395585ef4afb30b07f59f6696b27e91c2e7dfd250659b78e2b1fb (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,191 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.2-cp35-cp35m-linux_armv6l.whl#sha256=8df33993e25739b0c2ecf50ba74014958c2b3a7ba2bb06c13894583ce07a6c5d (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,191 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.2-cp35-cp35m-linux_armv7l.whl#sha256=8df33993e25739b0c2ecf50ba74014958c2b3a7ba2bb06c13894583ce07a6c5d (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,191 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.2-cp37-cp37m-linux_armv6l.whl#sha256=5ad5c598603eba3a3905831df3b9dc6a6889d3baf37c0d6d657f24a48dd346c1 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,191 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.2-cp37-cp37m-linux_armv7l.whl#sha256=5ad5c598603eba3a3905831df3b9dc6a6889d3baf37c0d6d657f24a48dd346c1 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,191 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.1-cp39-cp39-linux_armv6l.whl#sha256=89b29333f3cdcb8d83850465197343059fc01a115bf3844569a14f9908a10c6e (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,191 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.1-cp39-cp39-linux_armv7l.whl#sha256=89b29333f3cdcb8d83850465197343059fc01a115bf3844569a14f9908a10c6e (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,191 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.1-cp35-cp35m-linux_armv6l.whl#sha256=0c73f6fdf7ecda943ac8a6d904970f0f1f773c23440b50de8e8fbc4ace03a3d5 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,192 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.1-cp35-cp35m-linux_armv7l.whl#sha256=0c73f6fdf7ecda943ac8a6d904970f0f1f773c23440b50de8e8fbc4ace03a3d5 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,192 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.1-cp37-cp37m-linux_armv7l.whl#sha256=95052aab0a69abd2738d368663a3ca61e9270aec462c54936e8ad838ed45de95 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,192 Skipping link: No binaries permitted for uga: https://archive1.piwheels.org/simple/uga/uga-2.0.1-cp37-cp37m-linux_armv6l.whl#sha256=95052aab0a69abd2738d368663a3ca61e9270aec462c54936e8ad838ed45de95 (from https://www.piwheels.org/simple/uga/)
2025-09-08T19:06:17,192 Skipping link: not a file: https://www.piwheels.org/simple/uga/
2025-09-08T19:06:17,192 Skipping link: not a file: https://pypi.org/simple/uga/
2025-09-08T19:06:17,215 Given no hashes to check 1 links for project 'uga': discarding no candidates
2025-09-08T19:06:17,216 Collecting uga==2.0.1
2025-09-08T19:06:17,218 Created temporary directory: /tmp/pip-unpack-6hbbm10t
2025-09-08T19:06:17,379 Downloading uga-2.0.1.tar.gz (727 kB)
2025-09-08T19:06:17,593 Added uga==2.0.1 from https://files.pythonhosted.org/packages/1c/d6/a97dd03cb53d33cf7c416104b018d86692ba0c2aabe0f8c0ccadf9e3e765/uga-2.0.1.tar.gz to build tracker '/tmp/pip-build-tracker-_1czt53u'
2025-09-08T19:06:17,595 Running setup.py (path:/tmp/pip-wheel-1ppvbvpy/uga_16df808151f3416cb95fb37b515861f6/setup.py) egg_info for package uga
2025-09-08T19:06:17,595 Created temporary directory: /tmp/pip-pip-egg-info-_d2f__gf
2025-09-08T19:06:17,595 Preparing metadata (setup.py): started
2025-09-08T19:06:17,596 Running command python setup.py egg_info
2025-09-08T19:06:18,124 /tmp/pip-wheel-1ppvbvpy/uga_16df808151f3416cb95fb37b515861f6/setup.py:2: SetuptoolsDeprecationWarning: The test command is disabled and references to it are deprecated.
2025-09-08T19:06:18,124 !!
2025-09-08T19:06:18,124 ********************************************************************************
2025-09-08T19:06:18,125 Please remove any references to `setuptools.command.test` in all supported versions of the affected package.
2025-09-08T19:06:18,125 This deprecation is overdue, please update your project and remove deprecated
2025-09-08T19:06:18,125 calls to avoid build errors in the future.
2025-09-08T19:06:18,125 ********************************************************************************
2025-09-08T19:06:18,125 !!
2025-09-08T19:06:18,125 from setuptools.command.test import test as TestCommand
2025-09-08T19:06:19,928 Error compiling Cython file:
2025-09-08T19:06:19,929 ------------------------------------------------------------
2025-09-08T19:06:19,929 ...
2025-09-08T19:06:19,929 ## along with this program. If not, see .
2025-09-08T19:06:19,929 import numpy as np
2025-09-08T19:06:19,929 import pandas as pd
2025-09-08T19:06:19,929 import Variant
2025-09-08T19:06:19,929 cimport Variant
2025-09-08T19:06:19,929 ^
2025-09-08T19:06:19,930 ------------------------------------------------------------
2025-09-08T19:06:19,930 uga/Geno.pxd:19:8: 'Variant.pxd' not found
2025-09-08T19:06:20,487 Error compiling Cython file:
2025-09-08T19:06:20,487 ------------------------------------------------------------
2025-09-08T19:06:20,487 ...
2025-09-08T19:06:20,487 cdef class Variants:
2025-09-08T19:06:20,487 cdef public bytes filename, sample_filename, region, group_id, method
2025-09-08T19:06:20,487 cdef public object handle, region_iter, snvgroup_map, results, header, cols, dtypes, snv_results_tagged, duplicated
2025-09-08T19:06:20,488 cdef public unsigned int chr, start, end
2025-09-08T19:06:20,488 cdef public np.ndarray genos, data, info, snv_chunk, snvgroup_chunk, snv_results, samples
2025-09-08T19:06:20,488 cpdef align(self, Variant.Ref ref)
2025-09-08T19:06:20,488 ^
2025-09-08T19:06:20,488 ------------------------------------------------------------
2025-09-08T19:06:20,488 uga/Geno.pxd:29:19: 'Ref' is not a type identifier
2025-09-08T19:06:20,511 Error compiling Cython file:
2025-09-08T19:06:20,511 ------------------------------------------------------------
2025-09-08T19:06:20,511 ...
2025-09-08T19:06:20,511 self.data[:,i] = 2.0 - self.data[:,i].astype(float)
2025-09-08T19:06:20,512 def load_snvgroup_map(self, snvgroup_map):
2025-09-08T19:06:20,512 logger = logging.getLogger("Geno.Variants.load_snvgroup_map")
2025-09-08T19:06:20,512 logger.debug("load_snvgroup_map")
2025-09-08T19:06:20,512 print "loading snvgroup map " + os.path.basename(snvgroup_map)
2025-09-08T19:06:20,512 ^
2025-09-08T19:06:20,512 ------------------------------------------------------------
2025-09-08T19:06:20,512 uga/Geno.pyx:110:8: Syntax error in simple statement list
2025-09-08T19:06:20,516 Traceback (most recent call last):
2025-09-08T19:06:20,518 File "", line 2, in
2025-09-08T19:06:20,518 exec(compile('''
2025-09-08T19:06:20,518 ~~~~^^^^^^^^^^^^
2025-09-08T19:06:20,518 # This is -- a caller that pip uses to run setup.py
2025-09-08T19:06:20,519 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,519 ...<32 lines>...
2025-09-08T19:06:20,519 exec(compile(setup_py_code, filename, "exec"))
2025-09-08T19:06:20,519 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,519 ''' % ('/tmp/pip-wheel-1ppvbvpy/uga_16df808151f3416cb95fb37b515861f6/setup.py',), "", "exec"))
2025-09-08T19:06:20,519 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,519 File "", line 35, in
2025-09-08T19:06:20,519 File "/tmp/pip-wheel-1ppvbvpy/uga_16df808151f3416cb95fb37b515861f6/setup.py", line 21, in
2025-09-08T19:06:20,520 ext_modules = cythonize(["uga/Geno.pyx","uga/Geno.pxd","uga/Model.pyx","uga/Variant.pyx","uga/Variant.pxd"]),
2025-09-08T19:06:20,520 ~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,520 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1154, in cythonize
2025-09-08T19:06:20,520 cythonize_one(*args)
2025-09-08T19:06:20,520 ~~~~~~~~~~~~~^^^^^^^
2025-09-08T19:06:20,520 File "/usr/local/lib/python3.13/dist-packages/Cython/Build/Dependencies.py", line 1298, in cythonize_one
2025-09-08T19:06:20,520 raise CompileError(None, pyx_file)
2025-09-08T19:06:20,520 Cython.Compiler.Errors.CompileError: uga/Geno.pyx
2025-09-08T19:06:20,520 Compiling uga/Geno.pyx because it changed.
2025-09-08T19:06:20,521 Compiling uga/Model.pyx because it changed.
2025-09-08T19:06:20,521 Compiling uga/Variant.pyx because it changed.
2025-09-08T19:06:20,521 [1/3] Cythonizing uga/Geno.pyx
2025-09-08T19:06:20,841 ERROR: python setup.py egg_info exited with 1
2025-09-08T19:06:20,853 [bold magenta]full command[/]: [blue]/usr/bin/python3 -c '
2025-09-08T19:06:20,853 exec(compile('"'"''"'"''"'"'
2025-09-08T19:06:20,853 # This is -- a caller that pip uses to run setup.py
2025-09-08T19:06:20,853 #
2025-09-08T19:06:20,853 # - It imports setuptools before invoking setup.py, to enable projects that directly
2025-09-08T19:06:20,853 # import from `distutils.core` to work with newer packaging standards.
2025-09-08T19:06:20,853 # - It provides a clear error message when setuptools is not installed.
2025-09-08T19:06:20,853 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
2025-09-08T19:06:20,853 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
2025-09-08T19:06:20,853 # manifest_maker: standard file '"'"'-c'"'"' not found".
2025-09-08T19:06:20,853 # - It generates a shim setup.py, for handling setup.cfg-only projects.
2025-09-08T19:06:20,853 import os, sys, tokenize, traceback
2025-09-08T19:06:20,853
2025-09-08T19:06:20,853 try:
2025-09-08T19:06:20,853 import setuptools
2025-09-08T19:06:20,853 except ImportError:
2025-09-08T19:06:20,853 print(
2025-09-08T19:06:20,853 "ERROR: Can not execute `setup.py` since setuptools failed to import in "
2025-09-08T19:06:20,853 "the build environment with exception:",
2025-09-08T19:06:20,853 file=sys.stderr,
2025-09-08T19:06:20,853 )
2025-09-08T19:06:20,853 traceback.print_exc()
2025-09-08T19:06:20,853 sys.exit(1)
2025-09-08T19:06:20,853
2025-09-08T19:06:20,853 __file__ = %r
2025-09-08T19:06:20,853 sys.argv[0] = __file__
2025-09-08T19:06:20,853
2025-09-08T19:06:20,853 if os.path.exists(__file__):
2025-09-08T19:06:20,853 filename = __file__
2025-09-08T19:06:20,853 with tokenize.open(__file__) as f:
2025-09-08T19:06:20,853 setup_py_code = f.read()
2025-09-08T19:06:20,853 else:
2025-09-08T19:06:20,853 filename = ""
2025-09-08T19:06:20,853 setup_py_code = "from setuptools import setup; setup()"
2025-09-08T19:06:20,853
2025-09-08T19:06:20,853 exec(compile(setup_py_code, filename, "exec"))
2025-09-08T19:06:20,853 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-1ppvbvpy/uga_16df808151f3416cb95fb37b515861f6/setup.py'"'"',), "", "exec"))' egg_info --egg-base /tmp/pip-pip-egg-info-_d2f__gf[/]
2025-09-08T19:06:20,854 [bold magenta]cwd[/]: /tmp/pip-wheel-1ppvbvpy/uga_16df808151f3416cb95fb37b515861f6/
2025-09-08T19:06:20,854 Preparing metadata (setup.py): finished with status 'error'
2025-09-08T19:06:20,855 ERROR: metadata generation failed
2025-09-08T19:06:20,861 Exception information:
2025-09-08T19:06:20,861 Traceback (most recent call last):
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 63, in generate_metadata
2025-09-08T19:06:20,861 call_subprocess(
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~~~^
2025-09-08T19:06:20,861 args,
2025-09-08T19:06:20,861 ^^^^^
2025-09-08T19:06:20,861 ...<2 lines>...
2025-09-08T19:06:20,861 spinner=spinner,
2025-09-08T19:06:20,861 ^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 )
2025-09-08T19:06:20,861 ^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/utils/subprocess.py", line 209, in call_subprocess
2025-09-08T19:06:20,861 raise error
2025-09-08T19:06:20,861 pip._internal.exceptions.InstallationSubprocessError: python setup.py egg_info exited with 1
2025-09-08T19:06:20,861
2025-09-08T19:06:20,861 The above exception was the direct cause of the following exception:
2025-09-08T19:06:20,861
2025-09-08T19:06:20,861 Traceback (most recent call last):
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper
2025-09-08T19:06:20,861 status = _inner_run()
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run
2025-09-08T19:06:20,861 return self.run(options, args)
2025-09-08T19:06:20,861 ~~~~~~~~^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper
2025-09-08T19:06:20,861 return func(self, options, args)
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 147, in run
2025-09-08T19:06:20,861 requirement_set = resolver.resolve(reqs, check_supported_wheels=True)
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/resolver.py", line 96, in resolve
2025-09-08T19:06:20,861 result = self._result = resolver.resolve(
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~~~~^
2025-09-08T19:06:20,861 collected.requirements, max_rounds=limit_how_complex_resolution_can_be
2025-09-08T19:06:20,861 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 )
2025-09-08T19:06:20,861 ^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 515, in resolve
2025-09-08T19:06:20,861 state = resolution.resolve(requirements, max_rounds=max_rounds)
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 388, in resolve
2025-09-08T19:06:20,861 self._add_to_criteria(self.state.criteria, r, parent=None)
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/resolvers/resolution.py", line 141, in _add_to_criteria
2025-09-08T19:06:20,861 if not criterion.candidates:
2025-09-08T19:06:20,861 ^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_vendor/resolvelib/structs.py", line 194, in __bool__
2025-09-08T19:06:20,861 return bool(self._sequence)
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 163, in __bool__
2025-09-08T19:06:20,861 self._bool = any(self)
2025-09-08T19:06:20,861 ~~~^^^^^^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 147, in
2025-09-08T19:06:20,861 return (c for c in iterator if id(c) not in self._incompatible_ids)
2025-09-08T19:06:20,861 ^^^^^^^^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/found_candidates.py", line 37, in _iter_built
2025-09-08T19:06:20,861 candidate = func()
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 187, in _make_candidate_from_link
2025-09-08T19:06:20,861 base: Optional[BaseCandidate] = self._make_base_candidate_from_link(
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2025-09-08T19:06:20,861 link, template, name, version
2025-09-08T19:06:20,861 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 )
2025-09-08T19:06:20,861 ^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/factory.py", line 233, in _make_base_candidate_from_link
2025-09-08T19:06:20,861 self._link_candidate_cache[link] = LinkCandidate(
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~^
2025-09-08T19:06:20,861 link,
2025-09-08T19:06:20,861 ^^^^^
2025-09-08T19:06:20,861 ...<3 lines>...
2025-09-08T19:06:20,861 version=version,
2025-09-08T19:06:20,861 ^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 )
2025-09-08T19:06:20,861 ^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 306, in __init__
2025-09-08T19:06:20,861 super().__init__(
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~~~~^
2025-09-08T19:06:20,861 link=link,
2025-09-08T19:06:20,861 ^^^^^^^^^^
2025-09-08T19:06:20,861 ...<4 lines>...
2025-09-08T19:06:20,861 version=version,
2025-09-08T19:06:20,861 ^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 )
2025-09-08T19:06:20,861 ^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 159, in __init__
2025-09-08T19:06:20,861 self.dist = self._prepare()
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~^^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 236, in _prepare
2025-09-08T19:06:20,861 dist = self._prepare_distribution()
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/resolution/resolvelib/candidates.py", line 317, in _prepare_distribution
2025-09-08T19:06:20,861 return preparer.prepare_linked_requirement(self._ireq, parallel_builds=True)
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 532, in prepare_linked_requirement
2025-09-08T19:06:20,861 return self._prepare_linked_requirement(req, parallel_builds)
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 647, in _prepare_linked_requirement
2025-09-08T19:06:20,861 dist = _get_prepared_distribution(
2025-09-08T19:06:20,861 req,
2025-09-08T19:06:20,861 ...<3 lines>...
2025-09-08T19:06:20,861 self.check_build_deps,
2025-09-08T19:06:20,861 )
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/operations/prepare.py", line 71, in _get_prepared_distribution
2025-09-08T19:06:20,861 abstract_dist.prepare_distribution_metadata(
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2025-09-08T19:06:20,861 finder, build_isolation, check_build_deps
2025-09-08T19:06:20,861 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 )
2025-09-08T19:06:20,861 ^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/distributions/sdist.py", line 69, in prepare_distribution_metadata
2025-09-08T19:06:20,861 self.req.prepare_metadata()
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~~~~~~~~~~~~~^^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/req/req_install.py", line 581, in prepare_metadata
2025-09-08T19:06:20,861 self.metadata_directory = generate_metadata_legacy(
2025-09-08T19:06:20,861 ~~~~~~~~~~~~~~~~~~~~~~~~^
2025-09-08T19:06:20,861 build_env=self.build_env,
2025-09-08T19:06:20,861 ^^^^^^^^^^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 ...<3 lines>...
2025-09-08T19:06:20,861 details=details,
2025-09-08T19:06:20,861 ^^^^^^^^^^^^^^^^
2025-09-08T19:06:20,861 )
2025-09-08T19:06:20,861 ^
2025-09-08T19:06:20,861 File "/usr/lib/python3/dist-packages/pip/_internal/operations/build/metadata_legacy.py", line 70, in generate_metadata
2025-09-08T19:06:20,861 raise MetadataGenerationFailed(package_details=details) from error
2025-09-08T19:06:20,861 pip._internal.exceptions.MetadataGenerationFailed: metadata generation failed
2025-09-08T19:06:20,883 Removed uga==2.0.1 from https://files.pythonhosted.org/packages/1c/d6/a97dd03cb53d33cf7c416104b018d86692ba0c2aabe0f8c0ccadf9e3e765/uga-2.0.1.tar.gz from build tracker '/tmp/pip-build-tracker-_1czt53u'
2025-09-08T19:06:20,883 Removed build tracker: '/tmp/pip-build-tracker-_1czt53u'