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{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"test_Align_bigbed.TestAlign_extended_bed.test_writing fails on Biopython 1.87 with Python 3.14","articleBody":"### Setup\n\nI am reporting a test failure with Biopython 1.87.\n\nPython: 3.14.2 \nCompiler: GCC 15.2.0 \nPlatform: Linux x86_64 - RHEL9\nNumPy: 2.4.6\n\nThis was observed while building Biopython 1.87 in an EasyBuild HPC software stack using GCC 15.2.0 / Python 3.14.2. I reproduced the same failure on two different HPC nodes.\n\n### Expected behaviour\n\nThe offline Biopython test suite should pass, or the failing test should be skipped/adjusted if the byte-for-byte comparison is not stable across supported Python/platform/toolchain combinations.\n\n### Actual behaviour\n\nThe offline test suite fails in one test:\n\n```text\ntest_Align_bigbed ... FAIL\n```\n\nThe failing test is:\n\n```text\ntest_Align_bigbed.TestAlign_extended_bed.test_writing\n```\n\nFull failure:\n\n```text\n======================================================================\nFAIL: test_writing (test_Align_bigbed.TestAlign_extended_bed.test_writing)\nTest writing bigbed_extended.bb.\n----------------------------------------------------------------------\nTraceback (most recent call last):\n  File \".../Tests/test_Align_bigbed.py\", line 6920, in test_writing\n    self.assertEqual(correct, data)\n    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^\nAssertionError: b'\\xe[88 chars]00\\xbd\\x05\\x00\\x00\\x00\\x00\\x00\\x00\\x0b\\x00\\t\\x[153227 chars]\\x87' != b'\\xe[88 chars]00\\xbe\\x05\\x00\\x00\\x00\\x00\\x00\\x00\\x0b\\x00\\t\\x[153314 chars]\\x87'\n```\n\nThe test appears to compare the generated `bigbed_extended.bb` binary output byte-for-byte against a reference. The generated output differs slightly from the expected data.\n\n### Steps to reproduce\n\nBuild/install Biopython 1.87 with Python 3.14.2, then run:\n\n```bash\ncd Tests\npython run_tests.py --offline\n```\n\n### Additional context\n\nThere is an older related issue, #4658, where `test_Align_bigbed.TestAlign_extended_bed.test_writing` also failed on s390x due to big-endian/binary-output differences. My case is different: this failure occurs on Linux x86_64/little-endian with Biopython 1.87 and Python 3.14.2.\n\nFor downstream packaging I can skip `test_Align_bigbed.py`, but I wanted to report this because it may indicate either a real bigBed writer regression or an overly strict/non-portable byte-for-byte binary-output test.\n\n*this PR was created with help of ChatGPT5.5","author":{"url":"https://github.com/pavelToman","@type":"Person","name":"pavelToman"},"datePublished":"2026-06-17T14:55:26.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":8},"url":"https://github.com/5239/biopython/issues/5239"}