2025-06-03T12:42:36,391 Created temporary directory: /tmp/pip-build-tracker-62owkba9
2025-06-03T12:42:36,392 Initialized build tracking at /tmp/pip-build-tracker-62owkba9
2025-06-03T12:42:36,393 Created build tracker: /tmp/pip-build-tracker-62owkba9
2025-06-03T12:42:36,393 Entered build tracker: /tmp/pip-build-tracker-62owkba9
2025-06-03T12:42:36,394 Created temporary directory: /tmp/pip-wheel-hijhemsc
2025-06-03T12:42:36,399 Created temporary directory: /tmp/pip-ephem-wheel-cache-atugol6i
2025-06-03T12:42:36,453 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
2025-06-03T12:42:36,455 2 location(s) to search for versions of dark-matter:
2025-06-03T12:42:36,455 * https://pypi.org/simple/dark-matter/
2025-06-03T12:42:36,455 * https://www.piwheels.org/simple/dark-matter/
2025-06-03T12:42:36,456 Fetching project page and analyzing links: https://pypi.org/simple/dark-matter/
2025-06-03T12:42:36,457 Getting page https://pypi.org/simple/dark-matter/
2025-06-03T12:42:36,458 Found index url https://pypi.org/simple/
2025-06-03T12:42:36,651 Fetched page https://pypi.org/simple/dark-matter/ as application/vnd.pypi.simple.v1+json
2025-06-03T12:42:36,701   Found link https://files.pythonhosted.org/packages/7a/5d/5704534d2e83673ec3c8534b39fe1a3f071291761d421803f6b2f04ca6b3/dark-matter-1.0.0.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.0
2025-06-03T12:42:36,702   Found link https://files.pythonhosted.org/packages/4a/50/cc5fbbe75b550d6819af04e15ffc633d99b636f2e2d3c22ca4fc09ba2380/dark-matter-1.0.11.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.11
2025-06-03T12:42:36,703   Found link https://files.pythonhosted.org/packages/12/38/d44b5b2e9c08c507a583accb8ee246ce0f98a57c553d06e0199943d0dbf4/dark-matter-1.0.12.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.12
2025-06-03T12:42:36,703   Found link https://files.pythonhosted.org/packages/42/69/f0d13d1e43ec50d1ca85b70c27cc5333f85186668700544a7661c4d6d374/dark-matter-1.0.13.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.13
2025-06-03T12:42:36,704   Found link https://files.pythonhosted.org/packages/30/5a/9c56b0639b13c2c78cad8ac304e9c5d834eed0cab07d0dcd780b7be47249/dark-matter-1.0.16.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.16
2025-06-03T12:42:36,705   Found link https://files.pythonhosted.org/packages/26/8d/eb629def26e051253c4070e70dfc7c8258d513b2685fe4e92bb975b6e613/dark-matter-1.0.19.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.19
2025-06-03T12:42:36,706   Found link https://files.pythonhosted.org/packages/6d/6f/755f4b72e91ce15571d5884761d34627eba8dc173005bc8d41a2e4d2ec81/dark-matter-1.0.27.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.27
2025-06-03T12:42:36,706   Found link https://files.pythonhosted.org/packages/c1/41/a8cb27f9a68dd388473a594c0a5cb162fb1518d16197c357ec3617e9631c/dark-matter-1.0.32.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.32
2025-06-03T12:42:36,707   Found link https://files.pythonhosted.org/packages/26/f5/ea2b1d090cd00bb769d4e07cc4b697373c58dac65a52cf442a4f60a833ba/dark-matter-1.0.34.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.34
2025-06-03T12:42:36,708   Found link https://files.pythonhosted.org/packages/1d/a3/954c4ab15080556dbb33a1c2053ce9028b51cb160099978332b9252b5f93/dark-matter-1.0.36.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.36
2025-06-03T12:42:36,709   Found link https://files.pythonhosted.org/packages/fd/f7/352dcf1f8fb13001175a73acb52fff4bc20760300f87459d7e1e967823a1/dark-matter-1.0.38.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.38
2025-06-03T12:42:36,709   Found link https://files.pythonhosted.org/packages/17/94/5d0c424a52cc3d16793cef2a6b38a8a3542c4bda072c49d61efd18a1ec60/dark-matter-1.0.40.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.40
2025-06-03T12:42:36,710   Found link https://files.pythonhosted.org/packages/4c/d7/9fa11fcb1f9923e3e980f1b493791ca3fbe6920a68a939971fb1eb333d05/dark-matter-1.0.41.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.41
2025-06-03T12:42:36,711   Found link https://files.pythonhosted.org/packages/1b/bb/9a2bffcc74c3bb8c2f45106443174a74dbe3424e45eb483ba7bf72da1fe2/dark-matter-1.0.42.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.42
2025-06-03T12:42:36,712   Found link https://files.pythonhosted.org/packages/e2/dd/cb0a17ce78d39d3b6d6dc93f54c49069b722569042312f7044143a67af30/dark-matter-1.0.43.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.43
2025-06-03T12:42:36,712   Found link https://files.pythonhosted.org/packages/88/ee/c6e7d4142ee1baca46ff0d7f295b7d5a4059648c815de4223f873f17a448/dark-matter-1.0.44.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.44
2025-06-03T12:42:36,713   Found link https://files.pythonhosted.org/packages/7e/71/19001567a982f1ea235095e6f2042990e0666c343bfd985b2c2b8a6a6edc/dark-matter-1.0.45.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.45
2025-06-03T12:42:36,714   Found link https://files.pythonhosted.org/packages/9b/71/0395a4c77fc9443e4b1c8d6d3787d527c2d06ecf56c75db9779bb602d594/dark-matter-1.0.46.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.46
2025-06-03T12:42:36,714   Found link https://files.pythonhosted.org/packages/85/3b/b68351e5280d2f65b26ca3e225a5a0385d921a6d25cef62563eeaec42343/dark-matter-1.0.47.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.47
2025-06-03T12:42:36,715   Found link https://files.pythonhosted.org/packages/fb/4c/6e27c41b817fc86240a956472978b226008da91e8c2b2b5dd991091c3a2d/dark-matter-1.0.48.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.48
2025-06-03T12:42:36,715   Found link https://files.pythonhosted.org/packages/07/65/1253b1fcd6c75fbbc19eee09982ec62023742959583d6687c666befffb71/dark-matter-1.0.49.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.49
2025-06-03T12:42:36,716   Found link https://files.pythonhosted.org/packages/ac/93/e94fa7a2455aa54ebc294bb5bd93c11aca3c461073aee1fab28b4ee380ae/dark-matter-1.0.50.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.50
2025-06-03T12:42:36,717   Found link https://files.pythonhosted.org/packages/b9/ce/7d74daae572ebb32ffdbd439440361f5bf39eb9f9d0f55654878cbd7cbb2/dark-matter-1.0.51.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.51
2025-06-03T12:42:36,718   Found link https://files.pythonhosted.org/packages/cd/fb/8ff473df5992d3cdfc57151ff5595561c42fff343fcc01c76f3b95cd1eb9/dark-matter-1.0.52.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.52
2025-06-03T12:42:36,719   Found link https://files.pythonhosted.org/packages/d4/a7/8e4a7fc079ce3324a605902fb7fe865ab846ba3376408987680cc68703c7/dark-matter-1.0.53.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.53
2025-06-03T12:42:36,719   Found link https://files.pythonhosted.org/packages/a8/50/55d45de9c1903904647e651a955b56dff452d61f9e095a5004a149ab2eca/dark-matter-1.0.54.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.54
2025-06-03T12:42:36,720   Found link https://files.pythonhosted.org/packages/47/41/cc272f599662d184f754abc67ee763ac9da02c5d9ef5d1155effe67d132f/dark-matter-1.0.55.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.55
2025-06-03T12:42:36,721   Found link https://files.pythonhosted.org/packages/d3/d8/250e7506219460c7da81f6f51bf93cce13d21b461392dcbfa1311e504a95/dark-matter-1.0.56.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.56
2025-06-03T12:42:36,722   Found link https://files.pythonhosted.org/packages/81/c7/3bf4ec17c4f0e02ca7741f7ede49d58680f12b48a4a7350031ffe8b38ba1/dark-matter-1.0.57.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.57
2025-06-03T12:42:36,722   Found link https://files.pythonhosted.org/packages/f1/d5/6e02cb418664b484f16ea42b60a86add44acf56dda4875001528957c27b2/dark-matter-1.0.58.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.58
2025-06-03T12:42:36,723   Found link https://files.pythonhosted.org/packages/5a/d3/a69ed2feeac3afcb852a8bcce6cadd5b541cd78de3756f0519a62ca29371/dark-matter-1.0.59.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.59
2025-06-03T12:42:36,724   Found link https://files.pythonhosted.org/packages/68/70/96bd4a89d1c5f40e05d734be94ae1571be35c0b4c4e19e22c0be893c9e1c/dark-matter-1.0.60.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.60
2025-06-03T12:42:36,725   Found link https://files.pythonhosted.org/packages/55/52/ab50ff5d12bb5efd1171a964a4f5baa03edb0091dfa5c79af08fbbe4da16/dark-matter-1.0.61.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.61
2025-06-03T12:42:36,726   Found link https://files.pythonhosted.org/packages/ab/de/cc9a342e642f66e60c8ff98d1786229d5cfcfb0306158f0c19ef61059303/dark-matter-1.0.62.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.62
2025-06-03T12:42:36,726   Found link https://files.pythonhosted.org/packages/cd/a5/713b8a9f25437fafe2a34291ca34f945c9e1394c2e600f73e5abd8e3282e/dark-matter-1.0.63.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.63
2025-06-03T12:42:36,727   Found link https://files.pythonhosted.org/packages/77/fe/320a21e0c4c116bd28487af7156a9937a90dcc44f70c4f720267e9b14291/dark-matter-1.0.64.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.64
2025-06-03T12:42:36,727   Found link https://files.pythonhosted.org/packages/a0/08/9be54a6570a6acf6f87d5ca8ff9f91660697fc32212d0be3601785e796b9/dark-matter-1.0.65.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.65
2025-06-03T12:42:36,728   Found link https://files.pythonhosted.org/packages/7b/61/46caedf674111789641d78a4252b26d1ea43d3d8c77f906b3abc7c638acc/dark-matter-1.0.66.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.66
2025-06-03T12:42:36,729   Found link https://files.pythonhosted.org/packages/97/54/fc8129e31460a4007b2d328e37efeb55a3488b7a7a34592e0c738ac27079/dark-matter-1.0.67.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.67
2025-06-03T12:42:36,729   Found link https://files.pythonhosted.org/packages/e5/33/890848c35cb392c57712943c79ffe317ce401bd2db2a616637719f8c5522/dark-matter-1.0.68.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.68
2025-06-03T12:42:36,730   Found link https://files.pythonhosted.org/packages/c2/23/5e4253583920bada6ee2f5204fbaf8a745527f8ba5c585ac8891fa959991/dark-matter-1.0.69.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.69
2025-06-03T12:42:36,731   Found link https://files.pythonhosted.org/packages/3d/6a/1cf82dcc5f77ac300a3ee4c1fce72edad81280795e42f0da80b67b3a1838/dark-matter-1.0.70.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.70
2025-06-03T12:42:36,732   Found link https://files.pythonhosted.org/packages/64/9a/ace6de00719320e68408c58f3abe036645a29901f17e3e1cd356260cb9f5/dark-matter-1.0.71.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.71
2025-06-03T12:42:36,733   Found link https://files.pythonhosted.org/packages/94/d0/a1e5aabab8ad66683757b3b0569d672da3528a5a8619f830f33c2d6bb179/dark-matter-1.0.72.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.72
2025-06-03T12:42:36,733   Found link https://files.pythonhosted.org/packages/a2/1a/f7d17f7e7d196b1fb5382a27adc6ae61bbc4c47ad812c9e78de890b61743/dark-matter-1.0.73.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.73
2025-06-03T12:42:36,734   Found link https://files.pythonhosted.org/packages/8e/dc/f8fbeb00d964a029f3e444ed65ba9ca0f69e83c4b19d93efb858ac9d67cf/dark-matter-1.0.74.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.74
2025-06-03T12:42:36,735   Found link https://files.pythonhosted.org/packages/26/50/60d51f6d26ec912a10cd058c4221c4794813080bcccd2f5af993a2bfe973/dark-matter-1.0.75.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.75
2025-06-03T12:42:36,735   Found link https://files.pythonhosted.org/packages/03/bb/45b48f894b2b3f2a08e9e3c3c07ce133db94e91a363688f3ab9ce4969d80/dark-matter-1.0.76.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.76
2025-06-03T12:42:36,736   Found link https://files.pythonhosted.org/packages/5a/b2/63dea9b0ab7517190dd58b390cd9f0c007da74ad33c1ce37a74e6640e62c/dark-matter-1.0.77.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.77
2025-06-03T12:42:36,737   Found link https://files.pythonhosted.org/packages/56/a6/ff1dce2b4722ad0fd1dcc5914c1971bcfd1062b1ba50b118503ac201f1d9/dark-matter-1.0.78.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.78
2025-06-03T12:42:36,738   Found link https://files.pythonhosted.org/packages/a6/44/1c0e34e49e6901acc92553a511ac00b2c43efa03d09e290c51f22d1032f2/dark-matter-1.0.79.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.79
2025-06-03T12:42:36,739   Found link https://files.pythonhosted.org/packages/ec/c5/0b771560f096b6ceca2f42c737438d299cbfad32217b7bce5c49408109f2/dark-matter-1.0.80.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.80
2025-06-03T12:42:36,739   Found link https://files.pythonhosted.org/packages/d4/ed/efa93d8e4087caa880c8d66d6ef412eff016bb239ad2402f27159bda3319/dark-matter-1.0.81.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.81
2025-06-03T12:42:36,740   Found link https://files.pythonhosted.org/packages/9a/63/8b9c7378fa5ce52162eef0b86d55106651f7f991bf85081fae3d979e03b8/dark-matter-1.0.82.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.82
2025-06-03T12:42:36,741   Found link https://files.pythonhosted.org/packages/b8/9d/d679c7c2c2117f1a213befba627db8564b541a447e9aded15592c4d88187/dark-matter-1.0.83.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.83
2025-06-03T12:42:36,741   Found link https://files.pythonhosted.org/packages/c2/f4/27b0a93e98fffc72d8e2cefae3d7178d408245390e3165c61424b827ea7a/dark-matter-1.0.84.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.84
2025-06-03T12:42:36,742   Found link https://files.pythonhosted.org/packages/70/74/98991c35e08f4f9faa4c338678d15ecc22c7ada1cec8537a4013661783a7/dark-matter-1.0.85.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.85
2025-06-03T12:42:36,743   Found link https://files.pythonhosted.org/packages/f7/48/a8cb52ec943f30ab2eaa13fcbd13904248dbff48802e044cd13093415b8f/dark-matter-1.0.86.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.86
2025-06-03T12:42:36,744   Found link https://files.pythonhosted.org/packages/60/99/467e7afcc3816958f6b0b65b0b9d5d556901f5cc7505f32723142e23a730/dark-matter-1.0.87.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.87
2025-06-03T12:42:36,745   Found link https://files.pythonhosted.org/packages/96/eb/a304c4774203ca4915a031daf20ef7174fbb6441e5c72900885cee8238ab/dark-matter-1.0.88.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.88
2025-06-03T12:42:36,746   Found link https://files.pythonhosted.org/packages/95/a2/9b1b4b90bcba12dcb6bb46a618f031081b49cedcec407049cd13e0bad838/dark-matter-1.0.89.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.89
2025-06-03T12:42:36,746   Found link https://files.pythonhosted.org/packages/46/9e/932d303fb7765accb20878df3479fcc6f7fa9c3a789143e616d3968e529d/dark-matter-1.0.90.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.90
2025-06-03T12:42:36,747   Found link https://files.pythonhosted.org/packages/a1/8a/757d3cc5c174c076dd4de7b3462997f5686e06784fc7d05bc2d9ecbbed8c/dark-matter-1.0.91.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.91
2025-06-03T12:42:36,748   Found link https://files.pythonhosted.org/packages/34/b2/ba36a28e9d4d398b47609840176e75d245c06ef6f712a8ef2401810c5578/dark-matter-1.0.92.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.92
2025-06-03T12:42:36,749   Found link https://files.pythonhosted.org/packages/4e/be/05871de4f52e365957139663eafee1ea9317bdfa5552c32ebc9fe868d999/dark-matter-1.0.97.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.97
2025-06-03T12:42:36,750   Found link https://files.pythonhosted.org/packages/9a/c2/4637281c6c2cf72c7ae241068d7217b4f4ab239bfa6c859fe95ec32c411b/dark-matter-1.0.98.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.98
2025-06-03T12:42:36,750   Found link https://files.pythonhosted.org/packages/36/2f/6ea29741cda9df28e0e78e9ad5c46532d9c355a8658a33d08e89412d8263/dark-matter-1.0.99.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.99
2025-06-03T12:42:36,751   Found link https://files.pythonhosted.org/packages/bc/09/580b984f227a838207fa95aff9100435482287ae888d5adf7fbfa7b2bb5c/dark-matter-1.0.101.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.101
2025-06-03T12:42:36,752   Found link https://files.pythonhosted.org/packages/89/15/e31a2489ebf0badc0f02778ed22b68e35fe0158076901296f78eb85a2c3c/dark-matter-1.0.106.tar.gz (from https://pypi.org/simple/dark-matter/), version: 1.0.106
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2025-06-03T12:42:36,972   Found link https://files.pythonhosted.org/packages/9a/e9/8c1dc8e647e52fb620674a28892db9351e4b5ca607b481fce2ec626a3be7/dark-matter-5.0.21.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.21
2025-06-03T12:42:36,972   Found link https://files.pythonhosted.org/packages/b4/4c/2a8e32660dd2f21795b57489c87e85d724ecec956c2883f819eb289a3768/dark-matter-5.0.22.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.22
2025-06-03T12:42:36,973   Found link https://files.pythonhosted.org/packages/68/b9/bd3cfce28e78b49932e054d2e46efa773a514fdc225522757170d0e50c6e/dark-matter-5.0.23.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.23
2025-06-03T12:42:36,974   Found link https://files.pythonhosted.org/packages/dd/03/9f35f93d305b2ef93b2e7affd934a9a1755600009030988d683cc3e891e5/dark-matter-5.0.24.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.24
2025-06-03T12:42:36,975   Found link https://files.pythonhosted.org/packages/5e/0c/05ab1226f9c7256f51bab667713423abf1cc1d98e7e6b3953c8768322eb1/dark-matter-5.0.25.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.25
2025-06-03T12:42:36,976   Skipping link: No binaries permitted for dark-matter: https://files.pythonhosted.org/packages/11/1e/2ec303be07479099a0d51032ac00680c1c51547f0ebf266705f8c9e50623/dark_matter-5.0.25-py3-none-any.whl (from https://pypi.org/simple/dark-matter/)
2025-06-03T12:42:36,977   Skipping link: No binaries permitted for dark-matter: https://files.pythonhosted.org/packages/df/e1/56c266df121b765097df89259769b777ee0ac2eacc97cbcfa6dda6376f5d/dark_matter-5.0.26-py3-none-any.whl (from https://pypi.org/simple/dark-matter/)
2025-06-03T12:42:36,977   Found link https://files.pythonhosted.org/packages/e7/2f/2fbd7d6ee78f8145c265120540ac9ae4079030ec6c8c9254539d2eb2056a/dark-matter-5.0.27.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.27
2025-06-03T12:42:36,978   Found link https://files.pythonhosted.org/packages/b1/08/2afe385c9945beabaaaaef4bf603ce55ff491d5b6fcc3c616d270073bd8e/dark-matter-5.0.28.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.28
2025-06-03T12:42:36,979   Found link https://files.pythonhosted.org/packages/3b/aa/92b96a5f82d397d6089ef19f96110391cd210ea1c809b354bc2225f5e904/dark-matter-5.0.29.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.29
2025-06-03T12:42:36,979   Found link https://files.pythonhosted.org/packages/42/30/4a5fa39b1f1dbd2fba6d79553aa5535eca6693995fa98d66e811616cb4d4/dark-matter-5.0.30.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.30
2025-06-03T12:42:36,980   Found link https://files.pythonhosted.org/packages/65/a2/6c128a1a6e5d4f637479bc59c847d001fe6563f913f9219b68c338badd14/dark-matter-5.0.31.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.31
2025-06-03T12:42:36,981   Found link https://files.pythonhosted.org/packages/74/d9/d427ce38ee8cac6fc313e23c39364500e28e67f50cdae07b4569d611bf7c/dark-matter-5.0.32.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.32
2025-06-03T12:42:36,982   Found link https://files.pythonhosted.org/packages/f4/d4/43c04d06003563721c453b2d4c6f98a0d5050cc34eeea90df567e8a63b40/dark_matter-5.0.33.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.33
2025-06-03T12:42:36,983   Found link https://files.pythonhosted.org/packages/ab/cc/8243ce21d1654c2d2cfa19e0b46df790ae0aa7c4e5778f7f5112ad697d99/dark_matter-5.0.34.tar.gz (from https://pypi.org/simple/dark-matter/), version: 5.0.34
2025-06-03T12:42:36,984   Found link https://files.pythonhosted.org/packages/53/bc/351a37fdb6bebc765349294462516f822c1e8186229c5dc303470eb1fbab/dark_matter-5.0.36.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.36
2025-06-03T12:42:36,984   Found link https://files.pythonhosted.org/packages/08/e5/13c645ff7936d85e3bdb8b25e3339a0604aed86e9be1c1f90e514d400f60/dark_matter-5.0.37.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.37
2025-06-03T12:42:36,985   Found link https://files.pythonhosted.org/packages/31/83/fcb8eb8e7337146222c16c431287fd7f94261a17a82110fd416976f67d45/dark_matter-5.0.38.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.38
2025-06-03T12:42:36,986   Found link https://files.pythonhosted.org/packages/44/f6/a7409ff4869f6236497c3bfbd69dfe4db1829528a651aaa9b832e636b43c/dark_matter-5.0.39.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.39
2025-06-03T12:42:36,986   Found link https://files.pythonhosted.org/packages/af/89/f46ab96454f6e4140449697c0c7cfdbf8377218be57b6930710768945273/dark_matter-5.0.40.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.40
2025-06-03T12:42:36,987   Found link https://files.pythonhosted.org/packages/3c/cd/6445d6215dce95936b2a43f5b2ff862df2f68a775d0175e5efdd4baee324/dark_matter-5.0.41.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.41
2025-06-03T12:42:36,988   Found link https://files.pythonhosted.org/packages/6c/e8/9f9383cde35b09fc0ca20482bf60c8a02ef4abca7288fc7e512bd7a3f987/dark_matter-5.0.42.tar.gz (from https://pypi.org/simple/dark-matter/) (requires-python:>=3.10), version: 5.0.42
2025-06-03T12:42:36,989 Fetching project page and analyzing links: https://www.piwheels.org/simple/dark-matter/
2025-06-03T12:42:36,990 Getting page https://www.piwheels.org/simple/dark-matter/
2025-06-03T12:42:36,992 Found index url https://www.piwheels.org/simple/
2025-06-03T12:42:37,153 WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/dark-matter/
2025-06-03T12:42:37,804 WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/dark-matter/
2025-06-03T12:42:38,975 WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/dark-matter/
2025-06-03T12:42:41,150 WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/dark-matter/
2025-06-03T12:42:45,319 WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))': /simple/dark-matter/
2025-06-03T12:42:45,494 Could not fetch URL https://www.piwheels.org/simple/dark-matter/: There was a problem confirming the ssl certificate: HTTPSConnectionPool(host='www.piwheels.org', port=443): Max retries exceeded with url: /simple/dark-matter/ (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: certificate is not yet valid (_ssl.c:992)'))) - skipping
2025-06-03T12:42:45,496 Skipping link: not a file: https://www.piwheels.org/simple/dark-matter/
2025-06-03T12:42:45,497 Skipping link: not a file: https://pypi.org/simple/dark-matter/
2025-06-03T12:42:45,556 Given no hashes to check 1 links for project 'dark-matter': discarding no candidates
2025-06-03T12:42:45,560 Collecting dark-matter==5.0.33
2025-06-03T12:42:45,562   Created temporary directory: /tmp/pip-unpack-b2czp7p9
2025-06-03T12:42:45,790   Downloading dark_matter-5.0.33.tar.gz (429 kB)
2025-06-03T12:42:46,407   Added dark-matter==5.0.33 from https://files.pythonhosted.org/packages/f4/d4/43c04d06003563721c453b2d4c6f98a0d5050cc34eeea90df567e8a63b40/dark_matter-5.0.33.tar.gz to build tracker '/tmp/pip-build-tracker-62owkba9'
2025-06-03T12:42:46,410   Running setup.py (path:/tmp/pip-wheel-hijhemsc/dark-matter_b93b5025476f45e29f8800791ac469c2/setup.py) egg_info for package dark-matter
2025-06-03T12:42:46,411   Created temporary directory: /tmp/pip-pip-egg-info-5sj09cx0
2025-06-03T12:42:46,411   Preparing metadata (setup.py): started
2025-06-03T12:42:46,413   Running command python setup.py egg_info
2025-06-03T12:42:47,309   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-03T12:42:47,309   !!

2025-06-03T12:42:47,310           ********************************************************************************
2025-06-03T12:42:47,311           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-03T12:42:47,312           License :: OSI Approved :: MIT License

2025-06-03T12:42:47,313           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-03T12:42:47,314           ********************************************************************************

2025-06-03T12:42:47,315   !!
2025-06-03T12:42:47,315     self._finalize_license_expression()
2025-06-03T12:42:47,339   running egg_info
2025-06-03T12:42:47,366   creating /tmp/pip-pip-egg-info-5sj09cx0/dark_matter.egg-info
2025-06-03T12:42:47,367   writing /tmp/pip-pip-egg-info-5sj09cx0/dark_matter.egg-info/PKG-INFO
2025-06-03T12:42:47,370   writing dependency_links to /tmp/pip-pip-egg-info-5sj09cx0/dark_matter.egg-info/dependency_links.txt
2025-06-03T12:42:47,372   writing requirements to /tmp/pip-pip-egg-info-5sj09cx0/dark_matter.egg-info/requires.txt
2025-06-03T12:42:47,373   writing top-level names to /tmp/pip-pip-egg-info-5sj09cx0/dark_matter.egg-info/top_level.txt
2025-06-03T12:42:47,375   writing manifest file '/tmp/pip-pip-egg-info-5sj09cx0/dark_matter.egg-info/SOURCES.txt'
2025-06-03T12:42:47,504   reading manifest file '/tmp/pip-pip-egg-info-5sj09cx0/dark_matter.egg-info/SOURCES.txt'
2025-06-03T12:42:47,505   adding license file 'LICENSE'
2025-06-03T12:42:47,514   writing manifest file '/tmp/pip-pip-egg-info-5sj09cx0/dark_matter.egg-info/SOURCES.txt'
2025-06-03T12:42:47,619   Preparing metadata (setup.py): finished with status 'done'
2025-06-03T12:42:47,852   Source in /tmp/pip-wheel-hijhemsc/dark-matter_b93b5025476f45e29f8800791ac469c2 has version 5.0.33, which satisfies requirement dark-matter==5.0.33 from https://files.pythonhosted.org/packages/f4/d4/43c04d06003563721c453b2d4c6f98a0d5050cc34eeea90df567e8a63b40/dark_matter-5.0.33.tar.gz
2025-06-03T12:42:47,853   Removed dark-matter==5.0.33 from https://files.pythonhosted.org/packages/f4/d4/43c04d06003563721c453b2d4c6f98a0d5050cc34eeea90df567e8a63b40/dark_matter-5.0.33.tar.gz from build tracker '/tmp/pip-build-tracker-62owkba9'
2025-06-03T12:42:47,868 Created temporary directory: /tmp/pip-unpack-4x1fcten
2025-06-03T12:42:47,870 Created temporary directory: /tmp/pip-unpack-43e433p9
2025-06-03T12:42:47,870 Building wheels for collected packages: dark-matter
2025-06-03T12:42:47,875   Created temporary directory: /tmp/pip-wheel-ttmzyw_y
2025-06-03T12:42:47,876   DEPRECATION: Building 'dark-matter' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'dark-matter'. Discussion can be found at https://github.com/pypa/pip/issues/6334
2025-06-03T12:42:47,878   Building wheel for dark-matter (setup.py): started
2025-06-03T12:42:47,879   Destination directory: /tmp/pip-wheel-ttmzyw_y
2025-06-03T12:42:47,879   Running command python setup.py bdist_wheel
2025-06-03T12:42:48,726   /usr/local/lib/python3.11/dist-packages/setuptools/dist.py:759: SetuptoolsDeprecationWarning: License classifiers are deprecated.
2025-06-03T12:42:48,727   !!

2025-06-03T12:42:48,728           ********************************************************************************
2025-06-03T12:42:48,728           Please consider removing the following classifiers in favor of a SPDX license expression:

2025-06-03T12:42:48,730           License :: OSI Approved :: MIT License

2025-06-03T12:42:48,731           See https://packaging.python.org/en/latest/guides/writing-pyproject-toml/#license for details.
2025-06-03T12:42:48,732           ********************************************************************************

2025-06-03T12:42:48,733   !!
2025-06-03T12:42:48,733     self._finalize_license_expression()
2025-06-03T12:42:48,734   running bdist_wheel
2025-06-03T12:42:48,865   running build
2025-06-03T12:42:48,865   running build_py
2025-06-03T12:42:48,897   creating build/lib/dark
2025-06-03T12:42:48,899   copying dark/titles.py -> build/lib/dark
2025-06-03T12:42:48,902   copying dark/simplify.py -> build/lib/dark
2025-06-03T12:42:48,904   copying dark/distance.py -> build/lib/dark
2025-06-03T12:42:48,906   copying dark/trees.py -> build/lib/dark
2025-06-03T12:42:48,908   copying dark/sam.py -> build/lib/dark
2025-06-03T12:42:48,912   copying dark/alignments.py -> build/lib/dark
2025-06-03T12:42:48,915   copying dark/proteins.py -> build/lib/dark
2025-06-03T12:42:48,918   copying dark/entrez.py -> build/lib/dark
2025-06-03T12:42:48,920   copying dark/__init__.py -> build/lib/dark
2025-06-03T12:42:48,921   copying dark/errors.py -> build/lib/dark
2025-06-03T12:42:48,923   copying dark/genomes.py -> build/lib/dark
2025-06-03T12:42:48,925   copying dark/process.py -> build/lib/dark
2025-06-03T12:42:48,928   copying dark/hsp.py -> build/lib/dark
2025-06-03T12:42:48,930   copying dark/bowtie2.py -> build/lib/dark
2025-06-03T12:42:48,933   copying dark/dna.py -> build/lib/dark
2025-06-03T12:42:48,936   copying dark/summarize.py -> build/lib/dark
2025-06-03T12:42:48,938   copying dark/database.py -> build/lib/dark
2025-06-03T12:42:48,940   copying dark/score.py -> build/lib/dark
2025-06-03T12:42:48,943   copying dark/taxonomy.py -> build/lib/dark
2025-06-03T12:42:48,946   copying dark/genbank.py -> build/lib/dark
2025-06-03T12:42:48,948   copying dark/ipynb.py -> build/lib/dark
2025-06-03T12:42:48,951   copying dark/html.py -> build/lib/dark
2025-06-03T12:42:48,953   copying dark/sqlite3.py -> build/lib/dark
2025-06-03T12:42:48,955   copying dark/sequence.py -> build/lib/dark
2025-06-03T12:42:48,957   copying dark/consensus.py -> build/lib/dark
2025-06-03T12:42:48,961   copying dark/codonDistance.py -> build/lib/dark
2025-06-03T12:42:48,963   copying dark/colors.py -> build/lib/dark
2025-06-03T12:42:48,965   copying dark/graphics.py -> build/lib/dark
2025-06-03T12:42:48,968   copying dark/fastq.py -> build/lib/dark
2025-06-03T12:42:48,970   copying dark/ncbidb.py -> build/lib/dark
2025-06-03T12:42:48,972   copying dark/aligners.py -> build/lib/dark
2025-06-03T12:42:48,974   copying dark/fasta_ss.py -> build/lib/dark
2025-06-03T12:42:48,976   copying dark/reads.py -> build/lib/dark
2025-06-03T12:42:48,980   copying dark/filter.py -> build/lib/dark
2025-06-03T12:42:48,983   copying dark/mutations.py -> build/lib/dark
2025-06-03T12:42:48,986   copying dark/aaVars.py -> build/lib/dark
2025-06-03T12:42:48,989   copying dark/btop.py -> build/lib/dark
2025-06-03T12:42:48,991   copying dark/local_align.py -> build/lib/dark
2025-06-03T12:42:48,994   copying dark/fpcache.py -> build/lib/dark
2025-06-03T12:42:48,996   copying dark/orfs.py -> build/lib/dark
2025-06-03T12:42:48,997   copying dark/idutils.py -> build/lib/dark
2025-06-03T12:42:48,999   copying dark/features.py -> build/lib/dark
2025-06-03T12:42:49,002   copying dark/dimension.py -> build/lib/dark
2025-06-03T12:42:49,004   copying dark/cigar.py -> build/lib/dark
2025-06-03T12:42:49,006   copying dark/analyze_reads.py -> build/lib/dark
2025-06-03T12:42:49,008   copying dark/utils.py -> build/lib/dark
2025-06-03T12:42:49,011   copying dark/progress.py -> build/lib/dark
2025-06-03T12:42:49,013   copying dark/fasta.py -> build/lib/dark
2025-06-03T12:42:49,017   copying dark/consensus-with-debugging.py -> build/lib/dark
2025-06-03T12:42:49,020   copying dark/windowedIdentity.py -> build/lib/dark
2025-06-03T12:42:49,022   copying dark/intervals.py -> build/lib/dark
2025-06-03T12:42:49,025   copying dark/baseimage.py -> build/lib/dark
2025-06-03T12:42:49,027   copying dark/aa.py -> build/lib/dark
2025-06-03T12:42:49,030   creating build/lib/dark/blast
2025-06-03T12:42:49,031   copying dark/blast/params.py -> build/lib/dark/blast
2025-06-03T12:42:49,034   copying dark/blast/records.py -> build/lib/dark/blast
2025-06-03T12:42:49,036   copying dark/blast/alignments.py -> build/lib/dark/blast
2025-06-03T12:42:49,038   copying dark/blast/__init__.py -> build/lib/dark/blast
2025-06-03T12:42:49,040   copying dark/blast/hsp.py -> build/lib/dark/blast
2025-06-03T12:42:49,042   copying dark/blast/score.py -> build/lib/dark/blast
2025-06-03T12:42:49,044   copying dark/blast/hacks.py -> build/lib/dark/blast
2025-06-03T12:42:49,046   copying dark/blast/conversion.py -> build/lib/dark/blast
2025-06-03T12:42:49,050   creating build/lib/dark/diamond
2025-06-03T12:42:49,051   copying dark/diamond/sam.py -> build/lib/dark/diamond
2025-06-03T12:42:49,054   copying dark/diamond/alignments.py -> build/lib/dark/diamond
2025-06-03T12:42:49,056   copying dark/diamond/__init__.py -> build/lib/dark/diamond
2025-06-03T12:42:49,058   copying dark/diamond/hsp.py -> build/lib/dark/diamond
2025-06-03T12:42:49,061   copying dark/diamond/run.py -> build/lib/dark/diamond
2025-06-03T12:42:49,063   copying dark/diamond/conversion.py -> build/lib/dark/diamond
2025-06-03T12:42:49,066   creating build/lib/dark/civ
2025-06-03T12:42:49,067   copying dark/civ/proteins.py -> build/lib/dark/civ
2025-06-03T12:42:49,074   copying dark/civ/__init__.py -> build/lib/dark/civ
2025-06-03T12:42:49,076   copying dark/civ/html.py -> build/lib/dark/civ
2025-06-03T12:42:49,079   copying dark/civ/graphics.py -> build/lib/dark/civ
2025-06-03T12:42:49,088   running build_scripts
2025-06-03T12:42:49,089   creating build/scripts-3.11
2025-06-03T12:42:49,090   copying and adjusting bin/aa-info.py -> build/scripts-3.11
2025-06-03T12:42:49,092   copying and adjusting bin/aa-to-dna.py -> build/scripts-3.11
2025-06-03T12:42:49,093   copying and adjusting bin/aa-to-properties.py -> build/scripts-3.11
2025-06-03T12:42:49,095   copying and adjusting bin/adaptor-distances.py -> build/scripts-3.11
2025-06-03T12:42:49,097   copying and adjusting bin/alignment-panel-civ.py -> build/scripts-3.11
2025-06-03T12:42:49,099   copying and adjusting bin/alignments-per-read.py -> build/scripts-3.11
2025-06-03T12:42:49,101   copying and adjusting bin/bit-score-to-e-value.py -> build/scripts-3.11
2025-06-03T12:42:49,102   copying and adjusting bin/cat-json-blast-records.py -> build/scripts-3.11
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2025-06-03T12:42:49,117   copying bin/convert-sam-to-fastq.sh -> build/scripts-3.11
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2025-06-03T12:42:49,121   copying and adjusting bin/curate-tree-ete3.py -> build/scripts-3.11
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2025-06-03T12:42:49,126   copying and adjusting bin/dark-matter-version.py -> build/scripts-3.11
2025-06-03T12:42:49,127   copying and adjusting bin/describe-protein-database.py -> build/scripts-3.11
2025-06-03T12:42:49,129   copying and adjusting bin/dna-to-aa.py -> build/scripts-3.11
2025-06-03T12:42:49,131   copying bin/download-genbank.sh -> build/scripts-3.11
2025-06-03T12:42:49,134   copying bin/download-refseq-viral-fasta.sh -> build/scripts-3.11
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2025-06-03T12:42:49,366   changing mode of build/scripts-3.11/trim-reads.py from 644 to 755
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2025-06-03T12:42:49,388   /usr/local/lib/python3.11/dist-packages/setuptools/_distutils/cmd.py:90: SetuptoolsDeprecationWarning: setup.py install is deprecated.
2025-06-03T12:42:49,388   !!

2025-06-03T12:42:49,390           ********************************************************************************
2025-06-03T12:42:49,390           Please avoid running ``setup.py`` directly.
2025-06-03T12:42:49,391           Instead, use pypa/build, pypa/installer or other
2025-06-03T12:42:49,391           standards-based tools.

2025-06-03T12:42:49,393           By 2025-Oct-31, you need to update your project and remove deprecated calls
2025-06-03T12:42:49,393           or your builds will no longer be supported.

2025-06-03T12:42:49,394           See https://blog.ganssle.io/articles/2021/10/setup-py-deprecated.html for details.
2025-06-03T12:42:49,395           ********************************************************************************

2025-06-03T12:42:49,396   !!
2025-06-03T12:42:49,397     self.initialize_options()
2025-06-03T12:42:49,417   installing to build/bdist.linux-armv7l/wheel
2025-06-03T12:42:49,417   running install
2025-06-03T12:42:49,442   running install_lib
2025-06-03T12:42:49,470   creating build/bdist.linux-armv7l/wheel
2025-06-03T12:42:49,473   creating build/bdist.linux-armv7l/wheel/dark
2025-06-03T12:42:49,474   copying build/lib/dark/titles.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,476   copying build/lib/dark/simplify.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,478   copying build/lib/dark/distance.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,480   copying build/lib/dark/trees.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,482   copying build/lib/dark/sam.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,485   copying build/lib/dark/alignments.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,488   copying build/lib/dark/proteins.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,491   copying build/lib/dark/entrez.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,492   copying build/lib/dark/__init__.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,494   copying build/lib/dark/errors.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,496   copying build/lib/dark/genomes.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,498   copying build/lib/dark/process.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,500   copying build/lib/dark/hsp.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,503   copying build/lib/dark/bowtie2.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,505   copying build/lib/dark/dna.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,508   copying build/lib/dark/summarize.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,511   copying build/lib/dark/database.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,512   copying build/lib/dark/score.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,514   copying build/lib/dark/taxonomy.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,517   copying build/lib/dark/genbank.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,520   copying build/lib/dark/ipynb.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,522   copying build/lib/dark/html.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,525   copying build/lib/dark/sqlite3.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,527   copying build/lib/dark/sequence.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,530   creating build/bdist.linux-armv7l/wheel/dark/diamond
2025-06-03T12:42:49,531   copying build/lib/dark/diamond/sam.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-03T12:42:49,535   copying build/lib/dark/diamond/alignments.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-03T12:42:49,537   copying build/lib/dark/diamond/__init__.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-03T12:42:49,539   copying build/lib/dark/diamond/hsp.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-03T12:42:49,542   copying build/lib/dark/diamond/run.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-03T12:42:49,544   copying build/lib/dark/diamond/conversion.py -> build/bdist.linux-armv7l/wheel/./dark/diamond
2025-06-03T12:42:49,547   copying build/lib/dark/consensus.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,550   copying build/lib/dark/codonDistance.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,552   copying build/lib/dark/colors.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,555   creating build/bdist.linux-armv7l/wheel/dark/civ
2025-06-03T12:42:49,557   copying build/lib/dark/civ/proteins.py -> build/bdist.linux-armv7l/wheel/./dark/civ
2025-06-03T12:42:49,562   copying build/lib/dark/civ/__init__.py -> build/bdist.linux-armv7l/wheel/./dark/civ
2025-06-03T12:42:49,563   copying build/lib/dark/civ/html.py -> build/bdist.linux-armv7l/wheel/./dark/civ
2025-06-03T12:42:49,566   copying build/lib/dark/civ/graphics.py -> build/bdist.linux-armv7l/wheel/./dark/civ
2025-06-03T12:42:49,569   copying build/lib/dark/graphics.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,572   copying build/lib/dark/fastq.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,574   copying build/lib/dark/ncbidb.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,576   copying build/lib/dark/aligners.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,578   copying build/lib/dark/fasta_ss.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,580   copying build/lib/dark/reads.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,584   copying build/lib/dark/filter.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,587   copying build/lib/dark/mutations.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,590   copying build/lib/dark/aaVars.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,592   copying build/lib/dark/btop.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,595   copying build/lib/dark/local_align.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,597   copying build/lib/dark/fpcache.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,599   copying build/lib/dark/orfs.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,601   copying build/lib/dark/idutils.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,603   copying build/lib/dark/features.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,606   copying build/lib/dark/dimension.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,608   copying build/lib/dark/cigar.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,610   copying build/lib/dark/analyze_reads.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,613   copying build/lib/dark/utils.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,615   copying build/lib/dark/progress.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,618   copying build/lib/dark/fasta.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,620   copying build/lib/dark/consensus-with-debugging.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,623   copying build/lib/dark/windowedIdentity.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,627   creating build/bdist.linux-armv7l/wheel/dark/blast
2025-06-03T12:42:49,628   copying build/lib/dark/blast/params.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-03T12:42:49,630   copying build/lib/dark/blast/records.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-03T12:42:49,632   copying build/lib/dark/blast/alignments.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-03T12:42:49,635   copying build/lib/dark/blast/__init__.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-03T12:42:49,637   copying build/lib/dark/blast/hsp.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-03T12:42:49,640   copying build/lib/dark/blast/score.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-03T12:42:49,642   copying build/lib/dark/blast/hacks.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-03T12:42:49,644   copying build/lib/dark/blast/conversion.py -> build/bdist.linux-armv7l/wheel/./dark/blast
2025-06-03T12:42:49,646   copying build/lib/dark/intervals.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,649   copying build/lib/dark/baseimage.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,651   copying build/lib/dark/aa.py -> build/bdist.linux-armv7l/wheel/./dark
2025-06-03T12:42:49,653   running install_egg_info
2025-06-03T12:42:49,692   running egg_info
2025-06-03T12:42:49,721   writing dark_matter.egg-info/PKG-INFO
2025-06-03T12:42:49,725   writing dependency_links to dark_matter.egg-info/dependency_links.txt
2025-06-03T12:42:49,727   writing requirements to dark_matter.egg-info/requires.txt
2025-06-03T12:42:49,728   writing top-level names to dark_matter.egg-info/top_level.txt
2025-06-03T12:42:49,771   reading manifest file 'dark_matter.egg-info/SOURCES.txt'
2025-06-03T12:42:49,786   adding license file 'LICENSE'
2025-06-03T12:42:49,797   writing manifest file 'dark_matter.egg-info/SOURCES.txt'
2025-06-03T12:42:49,799   Copying dark_matter.egg-info to build/bdist.linux-armv7l/wheel/./dark_matter-5.0.33-py3.11.egg-info
2025-06-03T12:42:49,809   running install_scripts
2025-06-03T12:42:49,812   creating build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,814   copying build/scripts-3.11/run-bowtie2.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,817   copying build/scripts-3.11/describe-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,819   copying build/scripts-3.11/convert-diamond-to-sam.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,821   copying build/scripts-3.11/convert-diamond-to-json.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,824   copying build/scripts-3.11/summarize-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,827   copying build/scripts-3.11/fasta-subset.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,830   copying build/scripts-3.11/e-value-to-bit-score.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,833   copying build/scripts-3.11/cat-json-blast-records.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,835   copying build/scripts-3.11/curate-trees.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,838   copying build/scripts-3.11/ids.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,840   copying build/scripts-3.11/write-htcondor-job-spec.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,843   copying build/scripts-3.11/read-blast-xml.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,846   copying build/scripts-3.11/newick-to-ascii.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,848   copying build/scripts-3.11/fasta-base-indices.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,850   copying build/scripts-3.11/get-taxonomy.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,853   copying build/scripts-3.11/alignments-per-read.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,855   copying build/scripts-3.11/download-refseq-viral-gbff.sh -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,857   copying build/scripts-3.11/parse-genbank-flat-file.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,859   copying build/scripts-3.11/reverse-complement.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,861   copying build/scripts-3.11/download-genbank.sh -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,864   copying build/scripts-3.11/window-split-alignment.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,866   copying build/scripts-3.11/position-summary.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,869   copying build/scripts-3.11/codon-distance.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,871   copying build/scripts-3.11/aa-to-properties.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,873   copying build/scripts-3.11/relabel-newick-tree.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,876   copying build/scripts-3.11/reference-read-scores-to-JSON.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,878   copying build/scripts-3.11/subset-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,881   copying build/scripts-3.11/local-align.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,883   copying build/scripts-3.11/compare-sequences.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,886   copying build/scripts-3.11/sam-references.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,888   copying build/scripts-3.11/get-features.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,890   copying build/scripts-3.11/compare-consensuses.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,893   copying build/scripts-3.11/alignment-panel-civ.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,896   copying build/scripts-3.11/fasta-count.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,898   copying build/scripts-3.11/fasta-subtraction.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,900   copying build/scripts-3.11/fasta-ids.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,902   copying build/scripts-3.11/fasta-to-phylip.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,905   copying build/scripts-3.11/make-fasta-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,907   copying build/scripts-3.11/format-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,909   copying build/scripts-3.11/fasta-join.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,911   copying build/scripts-3.11/fasta-diff.sh -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,913   copying build/scripts-3.11/filter-reads-alignments.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,915   copying build/scripts-3.11/dark-matter-version.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,917   copying build/scripts-3.11/genome-protein-summary.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,920   copying build/scripts-3.11/fasta-split-by-id.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,921   copying build/scripts-3.11/make-protein-database.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,924   copying build/scripts-3.11/adaptor-distances.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,926   copying build/scripts-3.11/fasta-split-by-length.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,928   copying build/scripts-3.11/translate.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,930   copying build/scripts-3.11/fasta-lengths.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,932   copying build/scripts-3.11/fasta-find.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,934   copying build/scripts-3.11/sam-reference-read-counts.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,936   copying build/scripts-3.11/fasta-sort.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,938   copying build/scripts-3.11/ncbi-fetch-id.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,941   copying build/scripts-3.11/get-reads.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,943   copying build/scripts-3.11/fasta-sequences.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,945   copying build/scripts-3.11/fasta-translate.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,947   copying build/scripts-3.11/filter-sam.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,949   copying build/scripts-3.11/fasta-identity-table.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,953   copying build/scripts-3.11/filter-hits-to-fasta.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,955   copying build/scripts-3.11/plot-windowed-identity.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,958   copying build/scripts-3.11/fasta-variable-sites.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,960   copying build/scripts-3.11/aa-to-dna.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
2025-06-03T12:42:49,962   copying build/scripts-3.11/sam-coverage.py -> build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts
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2025-06-03T12:42:50,102   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/noninteractive-alignment-panel.py to 755
2025-06-03T12:42:50,102   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/graph-evalues.py to 755
2025-06-03T12:42:50,103   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/genbank-grep.py to 755
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2025-06-03T12:42:50,104   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/dna-to-aa.py to 755
2025-06-03T12:42:50,104   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/fasta-match-offsets.py to 755
2025-06-03T12:42:50,105   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/bit-score-to-e-value.py to 755
2025-06-03T12:42:50,105   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/fasta-coverage.py to 755
2025-06-03T12:42:50,106   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/aa-info.py to 755
2025-06-03T12:42:50,107   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/fasta-count-chars.py to 755
2025-06-03T12:42:50,107   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/sam-to-fasta-alignment.py to 755
2025-06-03T12:42:50,108   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/fastq-set-quality.py to 755
2025-06-03T12:42:50,108   changing mode of build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.data/scripts/get-hosts.py to 755
2025-06-03T12:42:50,111   creating build/bdist.linux-armv7l/wheel/dark_matter-5.0.33.dist-info/WHEEL
2025-06-03T12:42:50,113   creating '/tmp/pip-wheel-ttmzyw_y/dark_matter-5.0.33-py3-none-any.whl' and adding 'build/bdist.linux-armv7l/wheel' to it
2025-06-03T12:42:50,116   adding 'dark/__init__.py'
2025-06-03T12:42:50,119   adding 'dark/aa.py'
2025-06-03T12:42:50,122   adding 'dark/aaVars.py'
2025-06-03T12:42:50,124   adding 'dark/aligners.py'
2025-06-03T12:42:50,128   adding 'dark/alignments.py'
2025-06-03T12:42:50,129   adding 'dark/analyze_reads.py'
2025-06-03T12:42:50,131   adding 'dark/baseimage.py'
2025-06-03T12:42:50,133   adding 'dark/bowtie2.py'
2025-06-03T12:42:50,134   adding 'dark/btop.py'
2025-06-03T12:42:50,136   adding 'dark/cigar.py'
2025-06-03T12:42:50,138   adding 'dark/codonDistance.py'
2025-06-03T12:42:50,139   adding 'dark/colors.py'
2025-06-03T12:42:50,143   adding 'dark/consensus-with-debugging.py'
2025-06-03T12:42:50,147   adding 'dark/consensus.py'
2025-06-03T12:42:50,149   adding 'dark/database.py'
2025-06-03T12:42:50,150   adding 'dark/dimension.py'
2025-06-03T12:42:50,151   adding 'dark/distance.py'
2025-06-03T12:42:50,155   adding 'dark/dna.py'
2025-06-03T12:42:50,156   adding 'dark/entrez.py'
2025-06-03T12:42:50,158   adding 'dark/errors.py'
2025-06-03T12:42:50,160   adding 'dark/fasta.py'
2025-06-03T12:42:50,162   adding 'dark/fasta_ss.py'
2025-06-03T12:42:50,163   adding 'dark/fastq.py'
2025-06-03T12:42:50,165   adding 'dark/features.py'
2025-06-03T12:42:50,168   adding 'dark/filter.py'
2025-06-03T12:42:50,169   adding 'dark/fpcache.py'
2025-06-03T12:42:50,172   adding 'dark/genbank.py'
2025-06-03T12:42:50,174   adding 'dark/genomes.py'
2025-06-03T12:42:50,178   adding 'dark/graphics.py'
2025-06-03T12:42:50,180   adding 'dark/hsp.py'
2025-06-03T12:42:50,182   adding 'dark/html.py'
2025-06-03T12:42:50,184   adding 'dark/idutils.py'
2025-06-03T12:42:50,185   adding 'dark/intervals.py'
2025-06-03T12:42:50,187   adding 'dark/ipynb.py'
2025-06-03T12:42:50,189   adding 'dark/local_align.py'
2025-06-03T12:42:50,191   adding 'dark/mutations.py'
2025-06-03T12:42:50,193   adding 'dark/ncbidb.py'
2025-06-03T12:42:50,194   adding 'dark/orfs.py'
2025-06-03T12:42:50,196   adding 'dark/process.py'
2025-06-03T12:42:50,197   adding 'dark/progress.py'
2025-06-03T12:42:50,203   adding 'dark/proteins.py'
2025-06-03T12:42:50,214   adding 'dark/reads.py'
2025-06-03T12:42:50,222   adding 'dark/sam.py'
2025-06-03T12:42:50,223   adding 'dark/score.py'
2025-06-03T12:42:50,225   adding 'dark/sequence.py'
2025-06-03T12:42:50,226   adding 'dark/simplify.py'
2025-06-03T12:42:50,227   adding 'dark/sqlite3.py'
2025-06-03T12:42:50,229   adding 'dark/summarize.py'
2025-06-03T12:42:50,232   adding 'dark/taxonomy.py'
2025-06-03T12:42:50,235   adding 'dark/titles.py'
2025-06-03T12:42:50,237   adding 'dark/trees.py'
2025-06-03T12:42:50,239   adding 'dark/utils.py'
2025-06-03T12:42:50,241   adding 'dark/windowedIdentity.py'
2025-06-03T12:42:50,243   adding 'dark/blast/__init__.py'
2025-06-03T12:42:50,245   adding 'dark/blast/alignments.py'
2025-06-03T12:42:50,247   adding 'dark/blast/conversion.py'
2025-06-03T12:42:50,248   adding 'dark/blast/hacks.py'
2025-06-03T12:42:50,250   adding 'dark/blast/hsp.py'
2025-06-03T12:42:50,252   adding 'dark/blast/params.py'
2025-06-03T12:42:50,253   adding 'dark/blast/records.py'
2025-06-03T12:42:50,254   adding 'dark/blast/score.py'
2025-06-03T12:42:50,256   adding 'dark/civ/__init__.py'
2025-06-03T12:42:50,259   adding 'dark/civ/graphics.py'
2025-06-03T12:42:50,261   adding 'dark/civ/html.py'
2025-06-03T12:42:50,272   adding 'dark/civ/proteins.py'
2025-06-03T12:42:50,274   adding 'dark/diamond/__init__.py'
2025-06-03T12:42:50,276   adding 'dark/diamond/alignments.py'
2025-06-03T12:42:50,279   adding 'dark/diamond/conversion.py'
2025-06-03T12:42:50,280   adding 'dark/diamond/hsp.py'
2025-06-03T12:42:50,282   adding 'dark/diamond/run.py'
2025-06-03T12:42:50,284   adding 'dark/diamond/sam.py'
2025-06-03T12:42:50,288   adding 'dark_matter-5.0.33.data/scripts/aa-info.py'
2025-06-03T12:42:50,289   adding 'dark_matter-5.0.33.data/scripts/aa-to-dna.py'
2025-06-03T12:42:50,290   adding 'dark_matter-5.0.33.data/scripts/aa-to-properties.py'
2025-06-03T12:42:50,291   adding 'dark_matter-5.0.33.data/scripts/adaptor-distances.py'
2025-06-03T12:42:50,294   adding 'dark_matter-5.0.33.data/scripts/alignment-panel-civ.py'
2025-06-03T12:42:50,295   adding 'dark_matter-5.0.33.data/scripts/alignments-per-read.py'
2025-06-03T12:42:50,296   adding 'dark_matter-5.0.33.data/scripts/bit-score-to-e-value.py'
2025-06-03T12:42:50,297   adding 'dark_matter-5.0.33.data/scripts/cat-json-blast-records.py'
2025-06-03T12:42:50,299   adding 'dark_matter-5.0.33.data/scripts/check-fasta-json-blast-consistency.py'
2025-06-03T12:42:50,300   adding 'dark_matter-5.0.33.data/scripts/codon-distance.py'
2025-06-03T12:42:50,302   adding 'dark_matter-5.0.33.data/scripts/compare-consensuses.py'
2025-06-03T12:42:50,304   adding 'dark_matter-5.0.33.data/scripts/compare-sequences.py'
2025-06-03T12:42:50,305   adding 'dark_matter-5.0.33.data/scripts/convert-blast-xml-to-json.py'
2025-06-03T12:42:50,307   adding 'dark_matter-5.0.33.data/scripts/convert-diamond-to-json.py'
2025-06-03T12:42:50,308   adding 'dark_matter-5.0.33.data/scripts/convert-diamond-to-sam.py'
2025-06-03T12:42:50,310   adding 'dark_matter-5.0.33.data/scripts/convert-sam-to-fastq.sh'
2025-06-03T12:42:50,311   adding 'dark_matter-5.0.33.data/scripts/create-newick-relabeling-output.py'
2025-06-03T12:42:50,313   adding 'dark_matter-5.0.33.data/scripts/curate-tree-ete3.py'
2025-06-03T12:42:50,315   adding 'dark_matter-5.0.33.data/scripts/curate-trees.py'
2025-06-03T12:42:50,316   adding 'dark_matter-5.0.33.data/scripts/dark-matter-version.py'
2025-06-03T12:42:50,317   adding 'dark_matter-5.0.33.data/scripts/describe-protein-database.py'
2025-06-03T12:42:50,318   adding 'dark_matter-5.0.33.data/scripts/dna-to-aa.py'
2025-06-03T12:42:50,320   adding 'dark_matter-5.0.33.data/scripts/download-genbank.sh'
2025-06-03T12:42:50,321   adding 'dark_matter-5.0.33.data/scripts/download-refseq-viral-fasta.sh'
2025-06-03T12:42:50,323   adding 'dark_matter-5.0.33.data/scripts/download-refseq-viral-gbff.sh'
2025-06-03T12:42:50,324   adding 'dark_matter-5.0.33.data/scripts/e-value-to-bit-score.py'
2025-06-03T12:42:50,326   adding 'dark_matter-5.0.33.data/scripts/extract-ORFs.py'
2025-06-03T12:42:50,327   adding 'dark_matter-5.0.33.data/scripts/fasta-base-indices.py'
2025-06-03T12:42:50,328   adding 'dark_matter-5.0.33.data/scripts/fasta-count-chars.py'
2025-06-03T12:42:50,330   adding 'dark_matter-5.0.33.data/scripts/fasta-count.py'
2025-06-03T12:42:50,331   adding 'dark_matter-5.0.33.data/scripts/fasta-coverage.py'
2025-06-03T12:42:50,333   adding 'dark_matter-5.0.33.data/scripts/fasta-diff.sh'
2025-06-03T12:42:50,335   adding 'dark_matter-5.0.33.data/scripts/fasta-find.py'
2025-06-03T12:42:50,339   adding 'dark_matter-5.0.33.data/scripts/fasta-identity-table.py'
2025-06-03T12:42:50,340   adding 'dark_matter-5.0.33.data/scripts/fasta-ids.py'
2025-06-03T12:42:50,341   adding 'dark_matter-5.0.33.data/scripts/fasta-join.py'
2025-06-03T12:42:50,343   adding 'dark_matter-5.0.33.data/scripts/fasta-lengths.py'
2025-06-03T12:42:50,344   adding 'dark_matter-5.0.33.data/scripts/fasta-match-offsets.py'
2025-06-03T12:42:50,346   adding 'dark_matter-5.0.33.data/scripts/fasta-sequences.py'
2025-06-03T12:42:50,347   adding 'dark_matter-5.0.33.data/scripts/fasta-sort.py'
2025-06-03T12:42:50,349   adding 'dark_matter-5.0.33.data/scripts/fasta-split-by-id.py'
2025-06-03T12:42:50,350   adding 'dark_matter-5.0.33.data/scripts/fasta-split-by-length.py'
2025-06-03T12:42:50,351   adding 'dark_matter-5.0.33.data/scripts/fasta-split.py'
2025-06-03T12:42:50,353   adding 'dark_matter-5.0.33.data/scripts/fasta-subset.py'
2025-06-03T12:42:50,354   adding 'dark_matter-5.0.33.data/scripts/fasta-subtraction.py'
2025-06-03T12:42:50,355   adding 'dark_matter-5.0.33.data/scripts/fasta-to-phylip.py'
2025-06-03T12:42:50,356   adding 'dark_matter-5.0.33.data/scripts/fasta-translate.py'
2025-06-03T12:42:50,358   adding 'dark_matter-5.0.33.data/scripts/fasta-variable-sites.py'
2025-06-03T12:42:50,359   adding 'dark_matter-5.0.33.data/scripts/fastq-set-quality.py'
2025-06-03T12:42:50,360   adding 'dark_matter-5.0.33.data/scripts/filter-fasta-by-complexity.py'
2025-06-03T12:42:50,362   adding 'dark_matter-5.0.33.data/scripts/filter-fasta-by-taxonomy.py'
2025-06-03T12:42:50,363   adding 'dark_matter-5.0.33.data/scripts/filter-fasta.py'
2025-06-03T12:42:50,365   adding 'dark_matter-5.0.33.data/scripts/filter-hits-to-fasta.py'
2025-06-03T12:42:50,367   adding 'dark_matter-5.0.33.data/scripts/filter-reads-alignments.py'
2025-06-03T12:42:50,368   adding 'dark_matter-5.0.33.data/scripts/filter-sam.py'
2025-06-03T12:42:50,370   adding 'dark_matter-5.0.33.data/scripts/format-fasta.py'
2025-06-03T12:42:50,371   adding 'dark_matter-5.0.33.data/scripts/genbank-grep.py'
2025-06-03T12:42:50,373   adding 'dark_matter-5.0.33.data/scripts/genome-protein-summary.py'
2025-06-03T12:42:50,374   adding 'dark_matter-5.0.33.data/scripts/get-features.py'
2025-06-03T12:42:50,376   adding 'dark_matter-5.0.33.data/scripts/get-hosts.py'
2025-06-03T12:42:50,377   adding 'dark_matter-5.0.33.data/scripts/get-reads.py'
2025-06-03T12:42:50,379   adding 'dark_matter-5.0.33.data/scripts/get-taxonomy.py'
2025-06-03T12:42:50,380   adding 'dark_matter-5.0.33.data/scripts/graph-evalues.py'
2025-06-03T12:42:50,382   adding 'dark_matter-5.0.33.data/scripts/ids.py'
2025-06-03T12:42:50,383   adding 'dark_matter-5.0.33.data/scripts/local-align.py'
2025-06-03T12:42:50,385   adding 'dark_matter-5.0.33.data/scripts/make-consensus.py'
2025-06-03T12:42:50,387   adding 'dark_matter-5.0.33.data/scripts/make-fasta-database.py'
2025-06-03T12:42:50,388   adding 'dark_matter-5.0.33.data/scripts/make-protein-database.py'
2025-06-03T12:42:50,390   adding 'dark_matter-5.0.33.data/scripts/ncbi-fetch-id.py'
2025-06-03T12:42:50,391   adding 'dark_matter-5.0.33.data/scripts/newick-to-ascii.py'
2025-06-03T12:42:50,394   adding 'dark_matter-5.0.33.data/scripts/noninteractive-alignment-panel.py'
2025-06-03T12:42:50,396   adding 'dark_matter-5.0.33.data/scripts/parse-genbank-flat-file.py'
2025-06-03T12:42:50,398   adding 'dark_matter-5.0.33.data/scripts/plot-references-by-inter-read-distance.py'
2025-06-03T12:42:50,400   adding 'dark_matter-5.0.33.data/scripts/plot-windowed-identity.py'
2025-06-03T12:42:50,401   adding 'dark_matter-5.0.33.data/scripts/position-summary.py'
2025-06-03T12:42:50,402   adding 'dark_matter-5.0.33.data/scripts/pre-commit.sh'
2025-06-03T12:42:50,404   adding 'dark_matter-5.0.33.data/scripts/print-read-lengths.py'
2025-06-03T12:42:50,406   adding 'dark_matter-5.0.33.data/scripts/proteins-to-pathogens-civ.py'
2025-06-03T12:42:50,408   adding 'dark_matter-5.0.33.data/scripts/proteins-to-pathogens.py'
2025-06-03T12:42:50,410   adding 'dark_matter-5.0.33.data/scripts/randomize-fasta.py'
2025-06-03T12:42:50,411   adding 'dark_matter-5.0.33.data/scripts/read-blast-json.py'
2025-06-03T12:42:50,412   adding 'dark_matter-5.0.33.data/scripts/read-blast-xml.py'
2025-06-03T12:42:50,414   adding 'dark_matter-5.0.33.data/scripts/reference-read-scores-to-JSON.py'
2025-06-03T12:42:50,415   adding 'dark_matter-5.0.33.data/scripts/relabel-newick-tree.py'
2025-06-03T12:42:50,416   adding 'dark_matter-5.0.33.data/scripts/remove-alrt-from-tree.py'
2025-06-03T12:42:50,418   adding 'dark_matter-5.0.33.data/scripts/reverse-complement.py'
2025-06-03T12:42:50,420   adding 'dark_matter-5.0.33.data/scripts/run-bowtie2.py'
2025-06-03T12:42:50,421   adding 'dark_matter-5.0.33.data/scripts/run-bwa.py'
2025-06-03T12:42:50,425   adding 'dark_matter-5.0.33.data/scripts/sam-coverage-depth.py'
2025-06-03T12:42:50,426   adding 'dark_matter-5.0.33.data/scripts/sam-coverage.py'
2025-06-03T12:42:50,428   adding 'dark_matter-5.0.33.data/scripts/sam-reference-read-counts.py'
2025-06-03T12:42:50,429   adding 'dark_matter-5.0.33.data/scripts/sam-references.py'
2025-06-03T12:42:50,431   adding 'dark_matter-5.0.33.data/scripts/sam-to-fasta-alignment.py'
2025-06-03T12:42:50,432   adding 'dark_matter-5.0.33.data/scripts/sff-to-fastq.py'
2025-06-03T12:42:50,433   adding 'dark_matter-5.0.33.data/scripts/simple-consensus.py'
2025-06-03T12:42:50,435   adding 'dark_matter-5.0.33.data/scripts/split-fasta-by-adaptors.py'
2025-06-03T12:42:50,437   adding 'dark_matter-5.0.33.data/scripts/subset-protein-database.py'
2025-06-03T12:42:50,438   adding 'dark_matter-5.0.33.data/scripts/summarize-fasta-bases.py'
2025-06-03T12:42:50,440   adding 'dark_matter-5.0.33.data/scripts/summarize-reads.py'
2025-06-03T12:42:50,441   adding 'dark_matter-5.0.33.data/scripts/translate.py'
2025-06-03T12:42:50,442   adding 'dark_matter-5.0.33.data/scripts/tree-info.py'
2025-06-03T12:42:50,444   adding 'dark_matter-5.0.33.data/scripts/trim-primers.py'
2025-06-03T12:42:50,445   adding 'dark_matter-5.0.33.data/scripts/trim-reads.py'
2025-06-03T12:42:50,447   adding 'dark_matter-5.0.33.data/scripts/window-split-alignment.py'
2025-06-03T12:42:50,449   adding 'dark_matter-5.0.33.data/scripts/write-htcondor-job-spec.py'
2025-06-03T12:42:50,451   adding 'dark_matter-5.0.33.dist-info/licenses/LICENSE'
2025-06-03T12:42:50,452   adding 'dark_matter-5.0.33.dist-info/METADATA'
2025-06-03T12:42:50,453   adding 'dark_matter-5.0.33.dist-info/WHEEL'
2025-06-03T12:42:50,454   adding 'dark_matter-5.0.33.dist-info/top_level.txt'
2025-06-03T12:42:50,457   adding 'dark_matter-5.0.33.dist-info/RECORD'
2025-06-03T12:42:50,465   removing build/bdist.linux-armv7l/wheel
2025-06-03T12:42:50,615   Building wheel for dark-matter (setup.py): finished with status 'done'
2025-06-03T12:42:50,622   Created wheel for dark-matter: filename=dark_matter-5.0.33-py3-none-any.whl size=403755 sha256=b7fa5784eb462a9b1cba5df67f352a735ccc904f4c4dc918cabde6b597d04e1e
2025-06-03T12:42:50,623   Stored in directory: /tmp/pip-ephem-wheel-cache-atugol6i/wheels/2d/bb/a8/9c26cfb2b0a2b47d95efc5ddac25f59db7d1595a432de620bf
2025-06-03T12:42:50,643 Successfully built dark-matter
2025-06-03T12:42:50,662 Removed build tracker: '/tmp/pip-build-tracker-62owkba9'