2025-09-08T01:20:51,884 Created temporary directory: /tmp/pip-build-tracker-tjt0eref 2025-09-08T01:20:51,885 Initialized build tracking at /tmp/pip-build-tracker-tjt0eref 2025-09-08T01:20:51,885 Created build tracker: /tmp/pip-build-tracker-tjt0eref 2025-09-08T01:20:51,885 Entered build tracker: /tmp/pip-build-tracker-tjt0eref 2025-09-08T01:20:51,885 Created temporary directory: /tmp/pip-wheel-c8oc_1xm 2025-09-08T01:20:51,888 Created temporary directory: /tmp/pip-ephem-wheel-cache-qfotfe_v 2025-09-08T01:20:51,947 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T01:20:51,949 2 location(s) to search for versions of rnacounter: 2025-09-08T01:20:51,949 * https://pypi.org/simple/rnacounter/ 2025-09-08T01:20:51,949 * https://www.piwheels.org/simple/rnacounter/ 2025-09-08T01:20:51,949 Fetching project page and analyzing links: https://pypi.org/simple/rnacounter/ 2025-09-08T01:20:51,950 Getting page https://pypi.org/simple/rnacounter/ 2025-09-08T01:20:51,951 Found index url https://pypi.org/simple/ 2025-09-08T01:20:52,025 Fetched page https://pypi.org/simple/rnacounter/ as application/vnd.pypi.simple.v1+json 2025-09-08T01:20:52,027 Found link https://files.pythonhosted.org/packages/8f/49/762bb78c6a1215e30ccd9702444375015a50b14847266db0c2f11219e78f/rnacounter-1.1.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.2 2025-09-08T01:20:52,027 Found link https://files.pythonhosted.org/packages/04/c4/e2924af98cbf63c98cc5a9d210c3c54d959cf961fba4df5da3972afc84ae/rnacounter-1.1.3.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.1 2025-09-08T01:20:52,027 Found link https://files.pythonhosted.org/packages/39/70/41efc4ca6703ffdbdbab1dcd66976ed9a30c363b6f5ba417501e2dd9fb00/rnacounter-1.1.3.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.2 2025-09-08T01:20:52,027 Found link https://files.pythonhosted.org/packages/b1/1c/9f8deaa78b994019b9024043168567099fe010c79018373e2f6ed60ea646/rnacounter-1.1.3.7.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.7 2025-09-08T01:20:52,027 Found link https://files.pythonhosted.org/packages/14/a1/be9b12f40d130b182ed0d5d01b36f76e6089805a5c945d77941f5eb0928e/rnacounter-1.1.3.10.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.10 2025-09-08T01:20:52,028 Found link https://files.pythonhosted.org/packages/8a/5e/1b112fc6343bf52ace3a9afaa30eabaf4338afadabf1fb97454a7556b835/rnacounter-1.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.2 2025-09-08T01:20:52,028 Found link https://files.pythonhosted.org/packages/05/7d/42ecc29d98f52b77953a55da4836d36d534b317b4d66af971c9008804b61/rnacounter-1.2.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.2.1 2025-09-08T01:20:52,028 Found link https://files.pythonhosted.org/packages/dd/92/d53ee16c942fb78a312c03b22b0ddc08eb00ae4627f9125415a2c650b674/rnacounter-1.3.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.3 2025-09-08T01:20:52,028 Found link https://files.pythonhosted.org/packages/49/18/a50e0e2b164272f6d13f458b43d6851766cf121b5672de12078df2bb953a/rnacounter-1.3.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.3.1 2025-09-08T01:20:52,028 Found link https://files.pythonhosted.org/packages/ab/bf/54a012d6660528530b8404401bf494bda91947e38aae0d45ba4d721de6d4/rnacounter-1.4.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4 2025-09-08T01:20:52,029 Found link https://files.pythonhosted.org/packages/84/c0/8f274da33c177f6a7c6d8632d9e99413c83e6ec688825677acace41cfdb1/rnacounter-1.4.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4.1 2025-09-08T01:20:52,029 Found link https://files.pythonhosted.org/packages/45/3a/3cc530b864e9fbd87542c73df418d091aeaeb7b73863fb206e62494d988e/rnacounter-1.4.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4.2 2025-09-08T01:20:52,029 Found link https://files.pythonhosted.org/packages/46/ee/29eed438b10276db92163dff3d25bcb91f3f9e99d9a629c35ddb97f27f4d/rnacounter-1.5.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.5 2025-09-08T01:20:52,029 Found link https://files.pythonhosted.org/packages/a2/ea/657e7b7aa7d777173695606509933b52d794b7dbb79501a87bfea2fb511f/rnacounter-1.5.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.5.2 2025-09-08T01:20:52,030 Fetching project page and analyzing links: https://www.piwheels.org/simple/rnacounter/ 2025-09-08T01:20:52,030 Getting page https://www.piwheels.org/simple/rnacounter/ 2025-09-08T01:20:52,031 Found index url https://www.piwheels.org/simple/ 2025-09-08T01:20:52,119 Fetched page https://www.piwheels.org/simple/rnacounter/ as text/html 2025-09-08T01:20:52,128 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp35-cp35m-linux_armv7l.whl#sha256=1720939a09d8fbca466729cc4db98be3526fe7a3283ce22ef5c5a21d204a6161 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,128 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp35-cp35m-linux_armv6l.whl#sha256=1720939a09d8fbca466729cc4db98be3526fe7a3283ce22ef5c5a21d204a6161 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,129 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp34-cp34m-linux_armv7l.whl#sha256=e384cbf3852a44dffbf3a6887901acb36b9b30bd5c7e1a3585b2fe39d868d67a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,129 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp34-cp34m-linux_armv6l.whl#sha256=e384cbf3852a44dffbf3a6887901acb36b9b30bd5c7e1a3585b2fe39d868d67a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,129 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp35-cp35m-linux_armv7l.whl#sha256=02c416ec8854b92c815224212889f47dbd376e9797f66a0fb19531508b6bc793 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,129 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp35-cp35m-linux_armv6l.whl#sha256=02c416ec8854b92c815224212889f47dbd376e9797f66a0fb19531508b6bc793 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,129 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp34-cp34m-linux_armv7l.whl#sha256=ee88d3438f69ffa3b1868868fce8191565f303aee8dd3ff0f34c3a62886a495c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,129 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp34-cp34m-linux_armv6l.whl#sha256=ee88d3438f69ffa3b1868868fce8191565f303aee8dd3ff0f34c3a62886a495c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,129 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp34-cp34m-linux_armv7l.whl#sha256=078f497ded7b5492884f2136fa32e9948422bd185ba0345389b2b0d9fa7ab06e (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,129 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp34-cp34m-linux_armv6l.whl#sha256=078f497ded7b5492884f2136fa32e9948422bd185ba0345389b2b0d9fa7ab06e (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,130 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp35-cp35m-linux_armv6l.whl#sha256=8dffc574db1608136d619621a8809fb0e4d5d3f830e30f94cc2567f4b0a72c55 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,130 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp35-cp35m-linux_armv7l.whl#sha256=8dffc574db1608136d619621a8809fb0e4d5d3f830e30f94cc2567f4b0a72c55 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,130 Skipping link: No binaries permitted for rnacounter: 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https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.1-cp34-cp34m-linux_armv6l.whl#sha256=627ec3e6dccdbc30b6697dd277204e300f58ecc971782b1231b09d84a4c1ef94 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,130 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp34-cp34m-linux_armv7l.whl#sha256=9213623d552d14ff1971589aae10e5f886bcfb42045418cc5871a76607eb25b7 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,130 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp34-cp34m-linux_armv6l.whl#sha256=9213623d552d14ff1971589aae10e5f886bcfb42045418cc5871a76607eb25b7 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,131 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp35-cp35m-linux_armv6l.whl#sha256=14bd0bb3f4379d3d334abacfbbbf7ed43ad60736fa69f394c1eda0385dac9193 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,131 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp35-cp35m-linux_armv7l.whl#sha256=14bd0bb3f4379d3d334abacfbbbf7ed43ad60736fa69f394c1eda0385dac9193 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,131 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3.1-cp35-cp35m-linux_armv6l.whl#sha256=a5e2657cda5fa5a9283a186329fadd8db71987a54d71f713970a85b732030278 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,131 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3.1-cp35-cp35m-linux_armv7l.whl#sha256=a5e2657cda5fa5a9283a186329fadd8db71987a54d71f713970a85b732030278 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,131 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp35-cp35m-linux_armv6l.whl#sha256=b0a053ced5ce83115199785a117fc7820b20daffef5c19acafc83d0425aca0e1 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,131 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp35-cp35m-linux_armv7l.whl#sha256=b0a053ced5ce83115199785a117fc7820b20daffef5c19acafc83d0425aca0e1 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,131 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp34-cp34m-linux_armv7l.whl#sha256=7d3a7695b9d615f45d66d1d00f595ec7b65bbc53dc4ef98292fe909a75adf063 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,131 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp34-cp34m-linux_armv6l.whl#sha256=7d3a7695b9d615f45d66d1d00f595ec7b65bbc53dc4ef98292fe909a75adf063 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,131 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp35-cp35m-linux_armv7l.whl#sha256=b963649459fb2ab742b717d9b68c590d8ce6333d770e20648104b1e30b3ea97c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,132 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp35-cp35m-linux_armv6l.whl#sha256=b963649459fb2ab742b717d9b68c590d8ce6333d770e20648104b1e30b3ea97c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,132 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp34-cp34m-linux_armv7l.whl#sha256=2179418dc1805676ef1838a927c0bbcc2a131b63bd87636aecec3fa865b161d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,132 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp34-cp34m-linux_armv6l.whl#sha256=2179418dc1805676ef1838a927c0bbcc2a131b63bd87636aecec3fa865b161d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,132 Skipping link: No binaries permitted for rnacounter: 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https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.7-cp35-cp35m-linux_armv6l.whl#sha256=8863095125d87f061f7651061bc503fbb2c1c613417b578294b555b7bcbdeeba (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,133 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.7-cp34-cp34m-linux_armv7l.whl#sha256=368b4bcbb3bbab49c3600537626272135f936e694d4d17911afd7d83cdb31ee6 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,133 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.7-cp34-cp34m-linux_armv6l.whl#sha256=368b4bcbb3bbab49c3600537626272135f936e694d4d17911afd7d83cdb31ee6 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,133 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp34-cp34m-linux_armv7l.whl#sha256=fb039ca19afdc360ee5843812cf53fbca3ac952fe26a759e4c3700f3b460fc48 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,133 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp34-cp34m-linux_armv6l.whl#sha256=fb039ca19afdc360ee5843812cf53fbca3ac952fe26a759e4c3700f3b460fc48 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,134 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp35-cp35m-linux_armv7l.whl#sha256=51ed8c80ea67e82dc8bdaf5636d930011f8ce97bd9cc30432eedabb4dc8c9c95 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,134 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp35-cp35m-linux_armv6l.whl#sha256=51ed8c80ea67e82dc8bdaf5636d930011f8ce97bd9cc30432eedabb4dc8c9c95 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,134 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp35-cp35m-linux_armv7l.whl#sha256=534e0f91ccc8a7b74d0e8966764195b4b7e008408e132f2714d3790552ffae89 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,134 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp35-cp35m-linux_armv6l.whl#sha256=534e0f91ccc8a7b74d0e8966764195b4b7e008408e132f2714d3790552ffae89 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,134 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp34-cp34m-linux_armv7l.whl#sha256=699103109ceb69845e93941543cff532f3d26934d4a5ceb71af07f8f0c972407 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,134 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp34-cp34m-linux_armv6l.whl#sha256=699103109ceb69845e93941543cff532f3d26934d4a5ceb71af07f8f0c972407 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,134 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp34-cp34m-linux_armv7l.whl#sha256=e9936c67b8b3ee724e15ef197fef27eb2f5516ba9e9681ca399c5914b4fa01d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,134 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp34-cp34m-linux_armv6l.whl#sha256=e9936c67b8b3ee724e15ef197fef27eb2f5516ba9e9681ca399c5914b4fa01d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,135 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp35-cp35m-linux_armv6l.whl#sha256=edb76e1344212be1373b20323904b92e0429f1b336a75b9b74a852152217fbab (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,135 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp35-cp35m-linux_armv7l.whl#sha256=edb76e1344212be1373b20323904b92e0429f1b336a75b9b74a852152217fbab (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:20:52,135 Skipping link: not a file: https://www.piwheels.org/simple/rnacounter/ 2025-09-08T01:20:52,135 Skipping link: not a file: https://pypi.org/simple/rnacounter/ 2025-09-08T01:20:52,159 Given no hashes to check 1 links for project 'rnacounter': discarding no candidates 2025-09-08T01:20:52,161 Collecting rnacounter==1.5.2 2025-09-08T01:20:52,162 Created temporary directory: /tmp/pip-unpack-ir7llver 2025-09-08T01:20:52,455 Downloading rnacounter-1.5.2.tar.gz (302 kB) 2025-09-08T01:20:52,542 Added rnacounter==1.5.2 from https://files.pythonhosted.org/packages/a2/ea/657e7b7aa7d777173695606509933b52d794b7dbb79501a87bfea2fb511f/rnacounter-1.5.2.tar.gz to build tracker '/tmp/pip-build-tracker-tjt0eref' 2025-09-08T01:20:52,543 Running setup.py (path:/tmp/pip-wheel-c8oc_1xm/rnacounter_b8e2bb631e394de4945d62e2c57f44d4/setup.py) egg_info for package rnacounter 2025-09-08T01:20:52,543 Created temporary directory: /tmp/pip-pip-egg-info-62hzeyh8 2025-09-08T01:20:52,543 Preparing metadata (setup.py): started 2025-09-08T01:20:52,544 Running command python setup.py egg_info 2025-09-08T01:20:53,453 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T01:20:53,453 warnings.warn(msg) 2025-09-08T01:20:53,912 running egg_info 2025-09-08T01:20:53,985 creating /tmp/pip-pip-egg-info-62hzeyh8/rnacounter.egg-info 2025-09-08T01:20:53,986 writing /tmp/pip-pip-egg-info-62hzeyh8/rnacounter.egg-info/PKG-INFO 2025-09-08T01:20:53,987 writing dependency_links to /tmp/pip-pip-egg-info-62hzeyh8/rnacounter.egg-info/dependency_links.txt 2025-09-08T01:20:53,988 writing requirements to /tmp/pip-pip-egg-info-62hzeyh8/rnacounter.egg-info/requires.txt 2025-09-08T01:20:53,988 writing top-level names to /tmp/pip-pip-egg-info-62hzeyh8/rnacounter.egg-info/top_level.txt 2025-09-08T01:20:53,988 writing manifest file '/tmp/pip-pip-egg-info-62hzeyh8/rnacounter.egg-info/SOURCES.txt' 2025-09-08T01:20:54,360 reading manifest file '/tmp/pip-pip-egg-info-62hzeyh8/rnacounter.egg-info/SOURCES.txt' 2025-09-08T01:20:54,361 reading manifest template 'MANIFEST.in' 2025-09-08T01:20:54,365 writing manifest file '/tmp/pip-pip-egg-info-62hzeyh8/rnacounter.egg-info/SOURCES.txt' 2025-09-08T01:20:54,503 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T01:20:54,508 Source in /tmp/pip-wheel-c8oc_1xm/rnacounter_b8e2bb631e394de4945d62e2c57f44d4 has version 1.5.2, which satisfies requirement rnacounter==1.5.2 from https://files.pythonhosted.org/packages/a2/ea/657e7b7aa7d777173695606509933b52d794b7dbb79501a87bfea2fb511f/rnacounter-1.5.2.tar.gz 2025-09-08T01:20:54,508 Removed rnacounter==1.5.2 from https://files.pythonhosted.org/packages/a2/ea/657e7b7aa7d777173695606509933b52d794b7dbb79501a87bfea2fb511f/rnacounter-1.5.2.tar.gz from build tracker '/tmp/pip-build-tracker-tjt0eref' 2025-09-08T01:20:54,512 Created temporary directory: /tmp/pip-unpack-kixtd1wv 2025-09-08T01:20:54,513 Created temporary directory: /tmp/pip-unpack-rm7sh01z 2025-09-08T01:20:54,513 Building wheels for collected packages: rnacounter 2025-09-08T01:20:54,514 Created temporary directory: /tmp/pip-wheel-zyd2khfd 2025-09-08T01:20:54,514 DEPRECATION: Building 'rnacounter' 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 'rnacounter'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T01:20:54,515 Building wheel for rnacounter (setup.py): started 2025-09-08T01:20:54,516 Destination directory: /tmp/pip-wheel-zyd2khfd 2025-09-08T01:20:54,516 Running command python setup.py bdist_wheel 2025-09-08T01:20:55,408 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T01:20:55,408 warnings.warn(msg) 2025-09-08T01:20:55,798 running bdist_wheel 2025-09-08T01:20:56,166 running build 2025-09-08T01:20:56,166 running build_py 2025-09-08T01:20:56,243 creating build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:20:56,243 copying rnacounter/setup.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:20:56,244 copying rnacounter/main.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:20:56,244 copying rnacounter/draft_nocython.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:20:56,245 copying rnacounter/__init__.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:20:56,246 creating build/lib.linux-armv7l-cpython-313/testfiles 2025-09-08T01:20:56,246 copying testfiles/__init__.py -> build/lib.linux-armv7l-cpython-313/testfiles 2025-09-08T01:20:56,246 running egg_info 2025-09-08T01:20:56,321 writing rnacounter.egg-info/PKG-INFO 2025-09-08T01:20:56,323 writing dependency_links to rnacounter.egg-info/dependency_links.txt 2025-09-08T01:20:56,323 writing requirements to rnacounter.egg-info/requires.txt 2025-09-08T01:20:56,323 writing top-level names to rnacounter.egg-info/top_level.txt 2025-09-08T01:20:56,401 reading manifest file 'rnacounter.egg-info/SOURCES.txt' 2025-09-08T01:20:56,402 reading manifest template 'MANIFEST.in' 2025-09-08T01:20:56,407 writing manifest file 'rnacounter.egg-info/SOURCES.txt' 2025-09-08T01:20:56,409 copying rnacounter/rnacounter.c -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:20:56,415 copying testfiles/gapdhKO.bam -> build/lib.linux-armv7l-cpython-313/testfiles 2025-09-08T01:20:56,416 copying testfiles/gapdhKO.bam.bai -> build/lib.linux-armv7l-cpython-313/testfiles 2025-09-08T01:20:56,417 copying testfiles/mm9_3genes_renamed.gtf -> build/lib.linux-armv7l-cpython-313/testfiles 2025-09-08T01:20:56,418 running build_ext 2025-09-08T01:20:56,739 building 'rnacounter/rnacounter' extension 2025-09-08T01:20:56,739 creating build/temp.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:20:56,740 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c rnacounter/rnacounter.c -o build/temp.linux-armv7l-cpython-313/rnacounter/rnacounter.o 2025-09-08T01:20:57,161 rnacounter/rnacounter.c: In function ‘__Pyx_ListComp_Append’: 2025-09-08T01:20:57,161 rnacounter/rnacounter.c:1280:23: error: lvalue required as left operand of assignment 2025-09-08T01:20:57,161 1280 | Py_SIZE(list) = len+1; 2025-09-08T01:20:57,162 | ^ 2025-09-08T01:20:57,162 rnacounter/rnacounter.c: In function ‘__Pyx_PyList_Append’: 2025-09-08T01:20:57,163 rnacounter/rnacounter.c:1328:23: error: lvalue required as left operand of assignment 2025-09-08T01:20:57,163 1328 | Py_SIZE(list) = len+1; 2025-09-08T01:20:57,163 | ^ 2025-09-08T01:20:57,172 rnacounter/rnacounter.c: In function ‘__Pyx_PyList_Extend’: 2025-09-08T01:20:57,173 rnacounter/rnacounter.c:1385:22: error: implicit declaration of function ‘_PyList_Extend’; did you mean ‘PyList_Extend’? [-Wimplicit-function-declaration] 2025-09-08T01:20:57,173 1385 | PyObject* none = _PyList_Extend((PyListObject*)L, v); 2025-09-08T01:20:57,173 | ^~~~~~~~~~~~~~ 2025-09-08T01:20:57,173 | PyList_Extend 2025-09-08T01:20:57,173 rnacounter/rnacounter.c:1385:22: error: initialization of ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:20:57,232 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_2parse_bed’: 2025-09-08T01:20:57,236 rnacounter/rnacounter.c:4112:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:20:57,236 4112 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T01:20:57,236 | ^~ 2025-09-08T01:20:57,237 In file included from /usr/include/python3.13/Python.h:76, 2025-09-08T01:20:57,237 from rnacounter/rnacounter.c:16: 2025-09-08T01:20:57,237 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T01:20:57,237 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T01:20:57,237 | ^~~~~~~~~~~~~~~ 2025-09-08T01:20:57,288 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_4join’: 2025-09-08T01:20:57,293 rnacounter/rnacounter.c:5441:9: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:20:57,293 5441 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T01:20:57,293 | ^~ 2025-09-08T01:20:57,294 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T01:20:57,294 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T01:20:57,294 | ^~~~~~~~~~~~~~~ 2025-09-08T01:20:58,460 rnacounter/rnacounter.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-08T01:20:58,500 rnacounter/rnacounter.c:23827:50: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-08T01:20:58,500 23827 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); 2025-09-08T01:20:58,500 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:20:58,501 | PyBUF_C_CONTIGUOUS 2025-09-08T01:20:58,504 rnacounter/rnacounter.c:23827:50: note: each undeclared identifier is reported only once for each function it appears in 2025-09-08T01:20:58,566 rnacounter/rnacounter.c:23867:50: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-08T01:20:58,566 23867 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); 2025-09-08T01:20:58,566 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:20:58,566 | PyBUF_F_CONTIGUOUS 2025-09-08T01:20:58,574 rnacounter/rnacounter.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-08T01:20:58,603 rnacounter/rnacounter.c:24873:29: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T01:20:58,603 24873 | if (unlikely(__pyx_v_descr->names == Py_None)) { 2025-09-08T01:20:58,603 | ^~ 2025-09-08T01:20:58,603 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T01:20:58,603 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T01:20:58,603 | ^ 2025-09-08T01:20:58,636 rnacounter/rnacounter.c:24877:28: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T01:20:58,636 24877 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; 2025-09-08T01:20:58,636 | ^~ 2025-09-08T01:20:58,672 rnacounter/rnacounter.c:24895:47: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-08T01:20:58,672 24895 | __pyx_t_3 = PyObject_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; 2025-09-08T01:20:58,672 | ^~ 2025-09-08T01:20:58,724 rnacounter/rnacounter.c:25076:79: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’ 2025-09-08T01:20:58,724 25076 | (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); 2025-09-08T01:20:58,724 | ^~ 2025-09-08T01:20:58,773 rnacounter/rnacounter.c: In function ‘__pyx_tp_dealloc_10rnacounter_10rnacounter_GenomicObject’: 2025-09-08T01:20:58,802 rnacounter/rnacounter.c:25708:45: error: implicit declaration of function ‘_PyGC_FINALIZED’ [-Wimplicit-function-declaration] 2025-09-08T01:20:58,802 25708 | if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { 2025-09-08T01:20:58,802 | ^~~~~~~~~~~~~~~ 2025-09-08T01:20:58,858 rnacounter/rnacounter.c: In function ‘__Pyx_InitCachedConstants’: 2025-09-08T01:20:58,891 rnacounter/rnacounter.c:28952:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:20:58,892 28952 | __pyx_codeobj__71 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 68, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:58,892 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:58,892 In file included from /usr/include/python3.13/Python.h:101: 2025-09-08T01:20:58,893 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:58,893 213 | PyCode_New( 2025-09-08T01:20:58,893 | ^~~~~~~~~~ 2025-09-08T01:20:58,930 rnacounter/rnacounter.c:28952:244: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:20:58,930 28952 | __pyx_codeobj__71 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 68, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:58,930 | ^~ 2025-09-08T01:20:58,930 | | 2025-09-08T01:20:58,930 | int 2025-09-08T01:20:58,930 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:58,931 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:58,931 | ^~~~~ 2025-09-08T01:20:58,931 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:20:58,931 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:58,931 | ~~~~~~~~~~^ 2025-09-08T01:20:58,968 rnacounter/rnacounter.c:28952:248: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:20:58,968 28952 | __pyx_codeobj__71 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 68, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:58,968 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:58,969 | | 2025-09-08T01:20:58,969 | PyObject * {aka struct _object *} 2025-09-08T01:20:58,969 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:58,969 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:58,969 | ^~~~ 2025-09-08T01:20:58,969 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:20:58,969 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:58,969 | ~~~~^ 2025-09-08T01:20:59,006 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:20:59,006 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,007 | ^~~~~~~~~~ 2025-09-08T01:20:59,007 rnacounter/rnacounter.c:28952:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,007 28952 | __pyx_codeobj__71 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 68, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,007 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,007 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,007 213 | PyCode_New( 2025-09-08T01:20:59,007 | ^~~~~~~~~~ 2025-09-08T01:20:59,041 rnacounter/rnacounter.c:28964:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:20:59,041 28964 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 90, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,041 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,041 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,041 213 | PyCode_New( 2025-09-08T01:20:59,041 | ^~~~~~~~~~ 2025-09-08T01:20:59,079 rnacounter/rnacounter.c:28964:244: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:20:59,079 28964 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 90, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,079 | ^~ 2025-09-08T01:20:59,079 | | 2025-09-08T01:20:59,079 | int 2025-09-08T01:20:59,079 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,079 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,079 | ^~~~~ 2025-09-08T01:20:59,079 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:20:59,080 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,080 | ~~~~~~~~~~^ 2025-09-08T01:20:59,117 rnacounter/rnacounter.c:28964:248: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:20:59,117 28964 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 90, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,117 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,117 | | 2025-09-08T01:20:59,117 | PyObject * {aka struct _object *} 2025-09-08T01:20:59,117 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,117 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,118 | ^~~~ 2025-09-08T01:20:59,118 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:20:59,118 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,118 | ~~~~^ 2025-09-08T01:20:59,159 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:20:59,159 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,159 | ^~~~~~~~~~ 2025-09-08T01:20:59,159 rnacounter/rnacounter.c:28964:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,159 28964 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 90, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 90; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,159 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,160 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,160 213 | PyCode_New( 2025-09-08T01:20:59,160 | ^~~~~~~~~~ 2025-09-08T01:20:59,192 rnacounter/rnacounter.c:28976:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:20:59,193 28976 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(2, 0, 19, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 116, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,193 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,193 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,193 213 | PyCode_New( 2025-09-08T01:20:59,193 | ^~~~~~~~~~ 2025-09-08T01:20:59,229 rnacounter/rnacounter.c:28976:239: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:20:59,229 28976 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(2, 0, 19, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 116, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,230 | ^~~ 2025-09-08T01:20:59,230 | | 2025-09-08T01:20:59,230 | int 2025-09-08T01:20:59,230 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,230 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,230 | ^~~~~ 2025-09-08T01:20:59,230 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:20:59,230 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,230 | ~~~~~~~~~~^ 2025-09-08T01:20:59,266 rnacounter/rnacounter.c:28976:244: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:20:59,266 28976 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(2, 0, 19, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 116, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,266 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,267 | | 2025-09-08T01:20:59,267 | PyObject * {aka struct _object *} 2025-09-08T01:20:59,267 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,267 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,267 | ^~~~ 2025-09-08T01:20:59,267 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:20:59,267 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,267 | ~~~~^ 2025-09-08T01:20:59,303 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:20:59,303 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,303 | ^~~~~~~~~~ 2025-09-08T01:20:59,303 rnacounter/rnacounter.c:28976:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,303 28976 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(2, 0, 19, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 116, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 116; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,304 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,304 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,304 213 | PyCode_New( 2025-09-08T01:20:59,304 | ^~~~~~~~~~ 2025-09-08T01:20:59,337 rnacounter/rnacounter.c:28988:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:20:59,337 28988 | __pyx_codeobj__77 = (PyObject*)__Pyx_PyCode_New(4, 0, 57, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 573, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,337 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,337 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,337 213 | PyCode_New( 2025-09-08T01:20:59,337 | ^~~~~~~~~~ 2025-09-08T01:20:59,374 rnacounter/rnacounter.c:28988:248: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:20:59,374 28988 | __pyx_codeobj__77 = (PyObject*)__Pyx_PyCode_New(4, 0, 57, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 573, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,374 | ^~~ 2025-09-08T01:20:59,374 | | 2025-09-08T01:20:59,374 | int 2025-09-08T01:20:59,374 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,374 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,374 | ^~~~~ 2025-09-08T01:20:59,375 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:20:59,375 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,375 | ~~~~~~~~~~^ 2025-09-08T01:20:59,411 rnacounter/rnacounter.c:28988:253: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:20:59,411 28988 | __pyx_codeobj__77 = (PyObject*)__Pyx_PyCode_New(4, 0, 57, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 573, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,411 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,411 | | 2025-09-08T01:20:59,411 | PyObject * {aka struct _object *} 2025-09-08T01:20:59,411 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,411 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,411 | ^~~~ 2025-09-08T01:20:59,412 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:20:59,412 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,412 | ~~~~^ 2025-09-08T01:20:59,448 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:20:59,448 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,448 | ^~~~~~~~~~ 2025-09-08T01:20:59,448 rnacounter/rnacounter.c:28988:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,448 28988 | __pyx_codeobj__77 = (PyObject*)__Pyx_PyCode_New(4, 0, 57, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 573, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 573; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,448 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,448 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,448 213 | PyCode_New( 2025-09-08T01:20:59,448 | ^~~~~~~~~~ 2025-09-08T01:20:59,481 rnacounter/rnacounter.c:29000:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:20:59,481 29000 | __pyx_codeobj__79 = (PyObject*)__Pyx_PyCode_New(8, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_write_output, 718, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,481 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,482 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,482 213 | PyCode_New( 2025-09-08T01:20:59,482 | ^~~~~~~~~~ 2025-09-08T01:20:59,518 rnacounter/rnacounter.c:29000:247: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:20:59,518 29000 | __pyx_codeobj__79 = (PyObject*)__Pyx_PyCode_New(8, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_write_output, 718, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,518 | ^~~ 2025-09-08T01:20:59,518 | | 2025-09-08T01:20:59,519 | int 2025-09-08T01:20:59,519 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,519 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,519 | ^~~~~ 2025-09-08T01:20:59,519 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:20:59,519 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,519 | ~~~~~~~~~~^ 2025-09-08T01:20:59,555 rnacounter/rnacounter.c:29000:252: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:20:59,555 29000 | __pyx_codeobj__79 = (PyObject*)__Pyx_PyCode_New(8, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_write_output, 718, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,555 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,555 | | 2025-09-08T01:20:59,556 | PyObject * {aka struct _object *} 2025-09-08T01:20:59,556 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,556 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,556 | ^~~~ 2025-09-08T01:20:59,556 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:20:59,556 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,556 | ~~~~^ 2025-09-08T01:20:59,592 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:20:59,592 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,592 | ^~~~~~~~~~ 2025-09-08T01:20:59,592 rnacounter/rnacounter.c:29000:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,593 29000 | __pyx_codeobj__79 = (PyObject*)__Pyx_PyCode_New(8, 0, 16, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__78, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_write_output, 718, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__79)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 718; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,593 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,593 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,593 213 | PyCode_New( 2025-09-08T01:20:59,593 | ^~~~~~~~~~ 2025-09-08T01:20:59,626 rnacounter/rnacounter.c:29012:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:20:59,626 29012 | __pyx_codeobj__82 = (PyObject*)__Pyx_PyCode_New(3, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__81, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 739, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,626 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,626 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,626 213 | PyCode_New( 2025-09-08T01:20:59,626 | ^~~~~~~~~~ 2025-09-08T01:20:59,663 rnacounter/rnacounter.c:29012:250: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:20:59,663 29012 | __pyx_codeobj__82 = (PyObject*)__Pyx_PyCode_New(3, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__81, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 739, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,663 | ^~~ 2025-09-08T01:20:59,663 | | 2025-09-08T01:20:59,663 | int 2025-09-08T01:20:59,663 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,663 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,663 | ^~~~~ 2025-09-08T01:20:59,664 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:20:59,664 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,664 | ~~~~~~~~~~^ 2025-09-08T01:20:59,700 rnacounter/rnacounter.c:29012:255: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:20:59,700 29012 | __pyx_codeobj__82 = (PyObject*)__Pyx_PyCode_New(3, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__81, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 739, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,700 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,700 | | 2025-09-08T01:20:59,700 | PyObject * {aka struct _object *} 2025-09-08T01:20:59,700 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,700 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,700 | ^~~~ 2025-09-08T01:20:59,701 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:20:59,701 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,701 | ~~~~^ 2025-09-08T01:20:59,737 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:20:59,737 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,737 | ^~~~~~~~~~ 2025-09-08T01:20:59,737 rnacounter/rnacounter.c:29012:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,737 29012 | __pyx_codeobj__82 = (PyObject*)__Pyx_PyCode_New(3, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__81, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 739, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__82)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,737 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,737 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,738 213 | PyCode_New( 2025-09-08T01:20:59,738 | ^~~~~~~~~~ 2025-09-08T01:20:59,770 rnacounter/rnacounter.c:29021:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:20:59,770 29021 | __pyx_codeobj__83 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_usage_string, 836, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,770 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,770 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,771 213 | PyCode_New( 2025-09-08T01:20:59,771 | ^~~~~~~~~~ 2025-09-08T01:20:59,807 rnacounter/rnacounter.c:29021:248: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:20:59,807 29021 | __pyx_codeobj__83 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_usage_string, 836, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,807 | ^~~ 2025-09-08T01:20:59,807 | | 2025-09-08T01:20:59,808 | int 2025-09-08T01:20:59,808 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,808 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,808 | ^~~~~ 2025-09-08T01:20:59,808 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:20:59,808 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,808 | ~~~~~~~~~~^ 2025-09-08T01:20:59,844 rnacounter/rnacounter.c:29021:253: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:20:59,844 29021 | __pyx_codeobj__83 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_usage_string, 836, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,844 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,845 | | 2025-09-08T01:20:59,845 | PyObject * {aka struct _object *} 2025-09-08T01:20:59,845 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,845 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,845 | ^~~~ 2025-09-08T01:20:59,845 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:20:59,845 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,845 | ~~~~^ 2025-09-08T01:20:59,881 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:20:59,881 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,881 | ^~~~~~~~~~ 2025-09-08T01:20:59,881 rnacounter/rnacounter.c:29021:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,882 29021 | __pyx_codeobj__83 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_usage_string, 836, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,882 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,882 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,882 213 | PyCode_New( 2025-09-08T01:20:59,882 | ^~~~~~~~~~ 2025-09-08T01:20:59,915 rnacounter/rnacounter.c:29033:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:20:59,915 29033 | __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__84, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_errmsg, 839, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,915 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,915 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:20:59,915 213 | PyCode_New( 2025-09-08T01:20:59,915 | ^~~~~~~~~~ 2025-09-08T01:20:59,952 rnacounter/rnacounter.c:29033:240: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:20:59,952 29033 | __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__84, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_errmsg, 839, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,952 | ^~~ 2025-09-08T01:20:59,952 | | 2025-09-08T01:20:59,952 | int 2025-09-08T01:20:59,952 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,952 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,952 | ^~~~~ 2025-09-08T01:20:59,953 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:20:59,953 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,953 | ~~~~~~~~~~^ 2025-09-08T01:20:59,989 rnacounter/rnacounter.c:29033:245: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:20:59,989 29033 | __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__84, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_errmsg, 839, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:20:59,989 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:20:59,989 | | 2025-09-08T01:20:59,989 | PyObject * {aka struct _object *} 2025-09-08T01:20:59,989 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:20:59,989 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:20:59,990 | ^~~~ 2025-09-08T01:20:59,990 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:20:59,990 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:20:59,990 | ~~~~^ 2025-09-08T01:21:00,026 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:21:00,026 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:21:00,026 | ^~~~~~~~~~ 2025-09-08T01:21:00,026 rnacounter/rnacounter.c:29033:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:21:00,026 29033 | __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__84, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_errmsg, 839, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 839; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:21:00,026 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:21:00,026 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:21:00,026 213 | PyCode_New( 2025-09-08T01:21:00,027 | ^~~~~~~~~~ 2025-09-08T01:21:00,059 rnacounter/rnacounter.c:29045:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:21:00,059 29045 | __pyx_codeobj__87 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__86, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 843, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:21:00,060 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:21:00,060 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:21:00,060 213 | PyCode_New( 2025-09-08T01:21:00,060 | ^~~~~~~~~~ 2025-09-08T01:21:00,096 rnacounter/rnacounter.c:29045:245: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:21:00,096 29045 | __pyx_codeobj__87 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__86, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 843, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:21:00,097 | ^~~ 2025-09-08T01:21:00,097 | | 2025-09-08T01:21:00,097 | int 2025-09-08T01:21:00,097 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:21:00,097 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:21:00,097 | ^~~~~ 2025-09-08T01:21:00,097 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:21:00,097 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:21:00,097 | ~~~~~~~~~~^ 2025-09-08T01:21:00,133 rnacounter/rnacounter.c:29045:250: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:21:00,134 29045 | __pyx_codeobj__87 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__86, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 843, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:21:00,134 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:21:00,134 | | 2025-09-08T01:21:00,134 | PyObject * {aka struct _object *} 2025-09-08T01:21:00,134 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:21:00,134 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:21:00,134 | ^~~~ 2025-09-08T01:21:00,134 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:21:00,134 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:21:00,134 | ~~~~^ 2025-09-08T01:21:00,170 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:21:00,171 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:21:00,171 | ^~~~~~~~~~ 2025-09-08T01:21:00,171 rnacounter/rnacounter.c:29045:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:21:00,171 29045 | __pyx_codeobj__87 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__86, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 843, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__87)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 843; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:21:00,171 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:21:00,171 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:21:00,171 213 | PyCode_New( 2025-09-08T01:21:00,171 | ^~~~~~~~~~ 2025-09-08T01:21:00,174 rnacounter/rnacounter.c: In function ‘PyInit_rnacounter’: 2025-09-08T01:21:00,207 rnacounter/rnacounter.c:29152:53: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,208 29152 | __pyx_type_10rnacounter_10rnacounter_GenomicObject.tp_print = 0; 2025-09-08T01:21:00,208 | ^ 2025-09-08T01:21:00,242 rnacounter/rnacounter.c:29167:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,242 29167 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct__parse_gtf.tp_print = 0; 2025-09-08T01:21:00,242 | ^ 2025-09-08T01:21:00,275 rnacounter/rnacounter.c:29170:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,275 29170 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_1_genexpr.tp_print = 0; 2025-09-08T01:21:00,275 | ^ 2025-09-08T01:21:00,309 rnacounter/rnacounter.c:29173:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,309 29173 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_2_genexpr.tp_print = 0; 2025-09-08T01:21:00,309 | ^ 2025-09-08T01:21:00,342 rnacounter/rnacounter.c:29176:65: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,342 29176 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_3_join.tp_print = 0; 2025-09-08T01:21:00,343 | ^ 2025-09-08T01:21:00,376 rnacounter/rnacounter.c:29179:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,376 29179 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_4_genexpr.tp_print = 0; 2025-09-08T01:21:00,376 | ^ 2025-09-08T01:21:00,409 rnacounter/rnacounter.c:29182:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,410 29182 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_5_genexpr.tp_print = 0; 2025-09-08T01:21:00,410 | ^ 2025-09-08T01:21:00,443 rnacounter/rnacounter.c:29185:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,443 29185 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_6_genexpr.tp_print = 0; 2025-09-08T01:21:00,443 | ^ 2025-09-08T01:21:00,477 rnacounter/rnacounter.c:29188:74: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,477 29188 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk.tp_print = 0; 2025-09-08T01:21:00,477 | ^ 2025-09-08T01:21:00,510 rnacounter/rnacounter.c:29191:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,510 29191 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr.tp_print = 0; 2025-09-08T01:21:00,510 | ^ 2025-09-08T01:21:00,544 rnacounter/rnacounter.c:29194:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,544 29194 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr.tp_print = 0; 2025-09-08T01:21:00,544 | ^ 2025-09-08T01:21:00,577 rnacounter/rnacounter.c:29197:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,578 29197 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr.tp_print = 0; 2025-09-08T01:21:00,578 | ^ 2025-09-08T01:21:00,611 rnacounter/rnacounter.c:29200:74: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,611 29200 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_11_write_output.tp_print = 0; 2025-09-08T01:21:00,611 | ^ 2025-09-08T01:21:00,645 rnacounter/rnacounter.c:29203:72: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,646 29203 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_12_parse_args.tp_print = 0; 2025-09-08T01:21:00,646 | ^ 2025-09-08T01:21:00,679 rnacounter/rnacounter.c:29206:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,679 29206 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_13_genexpr.tp_print = 0; 2025-09-08T01:21:00,679 | ^ 2025-09-08T01:21:00,713 rnacounter/rnacounter.c:29209:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,713 29209 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr.tp_print = 0; 2025-09-08T01:21:00,713 | ^ 2025-09-08T01:21:00,746 rnacounter/rnacounter.c:29212:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:21:00,747 29212 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_15_genexpr.tp_print = 0; 2025-09-08T01:21:00,747 | ^ 2025-09-08T01:21:00,801 rnacounter/rnacounter.c: In function ‘__Pyx_PyUnicode_Equals’: 2025-09-08T01:21:00,839 rnacounter/rnacounter.c:84:51: error: implicit declaration of function ‘_PyUnicode_Ready’; did you mean ‘PyUnicode_READY’? [-Wimplicit-function-declaration] 2025-09-08T01:21:00,839 84 | 0 : _PyUnicode_Ready((PyObject *)(op))) 2025-09-08T01:21:00,839 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:21:00,840 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T01:21:00,840 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T01:21:00,840 | ^ 2025-09-08T01:21:00,840 rnacounter/rnacounter.c:29710:22: note: in expansion of macro ‘__Pyx_PyUnicode_READY’ 2025-09-08T01:21:00,840 29710 | if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) 2025-09-08T01:21:00,840 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-08T01:21:00,895 rnacounter/rnacounter.c: In function ‘__Pyx_ErrRestore’: 2025-09-08T01:21:00,930 rnacounter/rnacounter.c:29802:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:21:00,930 29802 | tmp_type = tstate->curexc_type; 2025-09-08T01:21:00,930 | ^~ 2025-09-08T01:21:00,964 rnacounter/rnacounter.c:29803:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:21:00,964 29803 | tmp_value = tstate->curexc_value; 2025-09-08T01:21:00,965 | ^~ 2025-09-08T01:21:00,999 rnacounter/rnacounter.c:29804:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:21:00,999 29804 | tmp_tb = tstate->curexc_traceback; 2025-09-08T01:21:00,999 | ^~ 2025-09-08T01:21:01,034 rnacounter/rnacounter.c:29805:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:21:01,034 29805 | tstate->curexc_type = type; 2025-09-08T01:21:01,034 | ^~ 2025-09-08T01:21:01,069 rnacounter/rnacounter.c:29806:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:21:01,069 29806 | tstate->curexc_value = value; 2025-09-08T01:21:01,069 | ^~ 2025-09-08T01:21:01,103 rnacounter/rnacounter.c:29807:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:21:01,104 29807 | tstate->curexc_traceback = tb; 2025-09-08T01:21:01,104 | ^~ 2025-09-08T01:21:01,104 rnacounter/rnacounter.c: In function ‘__Pyx_ErrFetch’: 2025-09-08T01:21:01,138 rnacounter/rnacounter.c:29818:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:21:01,139 29818 | *type = tstate->curexc_type; 2025-09-08T01:21:01,139 | ^~ 2025-09-08T01:21:01,173 rnacounter/rnacounter.c:29819:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:21:01,173 29819 | *value = tstate->curexc_value; 2025-09-08T01:21:01,173 | ^~ 2025-09-08T01:21:01,208 rnacounter/rnacounter.c:29820:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:21:01,208 29820 | *tb = tstate->curexc_traceback; 2025-09-08T01:21:01,208 | ^~ 2025-09-08T01:21:01,243 rnacounter/rnacounter.c:29821:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:21:01,243 29821 | tstate->curexc_type = 0; 2025-09-08T01:21:01,243 | ^~ 2025-09-08T01:21:01,277 rnacounter/rnacounter.c:29822:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:21:01,278 29822 | tstate->curexc_value = 0; 2025-09-08T01:21:01,278 | ^~ 2025-09-08T01:21:01,312 rnacounter/rnacounter.c:29823:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:21:01,312 29823 | tstate->curexc_traceback = 0; 2025-09-08T01:21:01,312 | ^~ 2025-09-08T01:21:01,380 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionSave’: 2025-09-08T01:21:01,430 rnacounter/rnacounter.c:30020:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:21:01,430 30020 | *type = tstate->exc_type; 2025-09-08T01:21:01,430 | ^~~~~~~~ 2025-09-08T01:21:01,430 | exc_state 2025-09-08T01:21:01,465 rnacounter/rnacounter.c:30021:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:21:01,465 30021 | *value = tstate->exc_value; 2025-09-08T01:21:01,465 | ^~ 2025-09-08T01:21:01,499 rnacounter/rnacounter.c:30022:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:21:01,499 30022 | *tb = tstate->exc_traceback; 2025-09-08T01:21:01,499 | ^~ 2025-09-08T01:21:01,499 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionReset’: 2025-09-08T01:21:01,549 rnacounter/rnacounter.c:30034:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:21:01,549 30034 | tmp_type = tstate->exc_type; 2025-09-08T01:21:01,549 | ^~~~~~~~ 2025-09-08T01:21:01,549 | exc_state 2025-09-08T01:21:01,583 rnacounter/rnacounter.c:30035:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:21:01,584 30035 | tmp_value = tstate->exc_value; 2025-09-08T01:21:01,584 | ^~ 2025-09-08T01:21:01,618 rnacounter/rnacounter.c:30036:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:21:01,618 30036 | tmp_tb = tstate->exc_traceback; 2025-09-08T01:21:01,618 | ^~ 2025-09-08T01:21:01,667 rnacounter/rnacounter.c:30037:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:21:01,668 30037 | tstate->exc_type = type; 2025-09-08T01:21:01,668 | ^~~~~~~~ 2025-09-08T01:21:01,668 | exc_state 2025-09-08T01:21:01,702 rnacounter/rnacounter.c:30038:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:21:01,702 30038 | tstate->exc_value = value; 2025-09-08T01:21:01,702 | ^~ 2025-09-08T01:21:01,736 rnacounter/rnacounter.c:30039:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:21:01,736 30039 | tstate->exc_traceback = tb; 2025-09-08T01:21:01,737 | ^~ 2025-09-08T01:21:01,737 rnacounter/rnacounter.c: In function ‘__Pyx_GetException’: 2025-09-08T01:21:01,771 rnacounter/rnacounter.c:30053:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:21:01,771 30053 | local_type = tstate->curexc_type; 2025-09-08T01:21:01,771 | ^~ 2025-09-08T01:21:01,805 rnacounter/rnacounter.c:30054:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:21:01,806 30054 | local_value = tstate->curexc_value; 2025-09-08T01:21:01,806 | ^~ 2025-09-08T01:21:01,840 rnacounter/rnacounter.c:30055:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:21:01,840 30055 | local_tb = tstate->curexc_traceback; 2025-09-08T01:21:01,840 | ^~ 2025-09-08T01:21:01,874 rnacounter/rnacounter.c:30056:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:21:01,875 30056 | tstate->curexc_type = 0; 2025-09-08T01:21:01,875 | ^~ 2025-09-08T01:21:01,909 rnacounter/rnacounter.c:30057:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:21:01,909 30057 | tstate->curexc_value = 0; 2025-09-08T01:21:01,909 | ^~ 2025-09-08T01:21:01,944 rnacounter/rnacounter.c:30058:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:21:01,944 30058 | tstate->curexc_traceback = 0; 2025-09-08T01:21:01,944 | ^~ 2025-09-08T01:21:01,978 rnacounter/rnacounter.c:30064:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:21:01,978 30064 | if (unlikely(tstate->curexc_type)) 2025-09-08T01:21:01,978 | ^~ 2025-09-08T01:21:01,979 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T01:21:01,979 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T01:21:01,979 | ^ 2025-09-08T01:21:02,040 rnacounter/rnacounter.c:30082:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:21:02,041 30082 | tmp_type = tstate->exc_type; 2025-09-08T01:21:02,041 | ^~~~~~~~ 2025-09-08T01:21:02,041 | exc_state 2025-09-08T01:21:02,075 rnacounter/rnacounter.c:30083:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:21:02,075 30083 | tmp_value = tstate->exc_value; 2025-09-08T01:21:02,075 | ^~ 2025-09-08T01:21:02,109 rnacounter/rnacounter.c:30084:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:21:02,109 30084 | tmp_tb = tstate->exc_traceback; 2025-09-08T01:21:02,110 | ^~ 2025-09-08T01:21:02,159 rnacounter/rnacounter.c:30085:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:21:02,159 30085 | tstate->exc_type = local_type; 2025-09-08T01:21:02,159 | ^~~~~~~~ 2025-09-08T01:21:02,159 | exc_state 2025-09-08T01:21:02,193 rnacounter/rnacounter.c:30086:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:21:02,194 30086 | tstate->exc_value = local_value; 2025-09-08T01:21:02,194 | ^~ 2025-09-08T01:21:02,228 rnacounter/rnacounter.c:30087:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:21:02,228 30087 | tstate->exc_traceback = local_tb; 2025-09-08T01:21:02,228 | ^~ 2025-09-08T01:21:02,255 rnacounter/rnacounter.c: In function ‘__Pyx_ParseOptionalKeywords’: 2025-09-08T01:21:02,306 rnacounter/rnacounter.c:30191:22: error: implicit declaration of function ‘PyUnicode_GET_SIZE’; did you mean ‘PyDict_GET_SIZE’? [-Wimplicit-function-declaration] 2025-09-08T01:21:02,306 30191 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-08T01:21:02,306 | ^~~~~~~~~~~~~~~~~~ 2025-09-08T01:21:02,306 | PyDict_GET_SIZE 2025-09-08T01:21:02,419 rnacounter/rnacounter.c: In function ‘__Pyx_Raise’: 2025-09-08T01:21:02,455 rnacounter/rnacounter.c:30417:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:21:02,455 30417 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-08T01:21:02,455 | ^~ 2025-09-08T01:21:02,490 rnacounter/rnacounter.c:30420:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:21:02,490 30420 | tstate->curexc_traceback = tb; 2025-09-08T01:21:02,490 | ^~ 2025-09-08T01:21:02,547 rnacounter/rnacounter.c: In function ‘__Pyx_PyIter_Next2’: 2025-09-08T01:21:02,582 rnacounter/rnacounter.c:30465:31: error: ‘_PyObject_NextNotImplemented’ undeclared (first use in this function); did you mean ‘PyObject_HashNotImplemented’? 2025-09-08T01:21:02,582 30465 | if (unlikely(iternext == &_PyObject_NextNotImplemented)) 2025-09-08T01:21:02,582 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T01:21:02,582 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T01:21:02,582 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T01:21:02,583 | ^ 2025-09-08T01:21:02,620 rnacounter/rnacounter.c: In function ‘__Pyx_IterFinish’: 2025-09-08T01:21:02,656 rnacounter/rnacounter.c:30629:32: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:21:02,656 30629 | PyObject* exc_type = tstate->curexc_type; 2025-09-08T01:21:02,656 | ^~ 2025-09-08T01:21:02,692 rnacounter/rnacounter.c:30633:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:21:02,693 30633 | exc_value = tstate->curexc_value; 2025-09-08T01:21:02,693 | ^~ 2025-09-08T01:21:02,728 rnacounter/rnacounter.c:30634:28: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:21:02,729 30634 | exc_tb = tstate->curexc_traceback; 2025-09-08T01:21:02,729 | ^~ 2025-09-08T01:21:02,764 rnacounter/rnacounter.c:30635:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:21:02,765 30635 | tstate->curexc_type = 0; 2025-09-08T01:21:02,765 | ^~ 2025-09-08T01:21:02,800 rnacounter/rnacounter.c:30636:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:21:02,801 30636 | tstate->curexc_value = 0; 2025-09-08T01:21:02,801 | ^~ 2025-09-08T01:21:02,836 rnacounter/rnacounter.c:30637:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:21:02,837 30637 | tstate->curexc_traceback = 0; 2025-09-08T01:21:02,837 | ^~ 2025-09-08T01:21:03,325 rnacounter/rnacounter.c: In function ‘__Pyx_CyFunction_Call’: 2025-09-08T01:21:03,380 rnacounter/rnacounter.c:31981:16: error: implicit declaration of function ‘PyCFunction_Call’; did you mean ‘PyCFunction_New’? [-Wimplicit-function-declaration] 2025-09-08T01:21:03,380 31981 | return PyCFunction_Call(func, arg, kw); 2025-09-08T01:21:03,380 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:21:03,380 | PyCFunction_New 2025-09-08T01:21:03,422 rnacounter/rnacounter.c:31981:16: error: returning ‘int’ from a function with return type ‘PyObject *’ {aka ‘struct _object *’} makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:21:03,422 31981 | return PyCFunction_Call(func, arg, kw); 2025-09-08T01:21:03,422 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T01:21:03,441 rnacounter/rnacounter.c: In function ‘__Pyx_CyFunction_init’: 2025-09-08T01:21:03,493 rnacounter/rnacounter.c:32046:41: error: ‘PyCFunction_Call’ undeclared (first use in this function); did you mean ‘PyCFunction_New’? 2025-09-08T01:21:03,493 32046 | __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; 2025-09-08T01:21:03,493 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:21:03,494 | PyCFunction_New 2025-09-08T01:21:03,539 rnacounter/rnacounter.c: In function ‘__Pyx_CreateCodeObjectForTraceback’: 2025-09-08T01:21:03,576 rnacounter/rnacounter.c:32222:5: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:21:03,577 32222 | py_code = __Pyx_PyCode_New( 2025-09-08T01:21:03,577 | ^~~~~~~ 2025-09-08T01:21:03,577 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:21:03,577 213 | PyCode_New( 2025-09-08T01:21:03,577 | ^~~~~~~~~~ 2025-09-08T01:21:03,614 rnacounter/rnacounter.c:32236:9: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:21:03,614 32236 | py_line, 2025-09-08T01:21:03,615 | ^~~~~~~ 2025-09-08T01:21:03,615 | | 2025-09-08T01:21:03,615 | int 2025-09-08T01:21:03,615 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:21:03,615 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:21:03,615 | ^~~~~ 2025-09-08T01:21:03,615 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:21:03,615 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:21:03,615 | ~~~~~~~~~~^ 2025-09-08T01:21:03,657 rnacounter/rnacounter.c:32237:9: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:21:03,657 32237 | __pyx_empty_bytes /*PyObject *lnotab*/ 2025-09-08T01:21:03,657 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:21:03,657 | | 2025-09-08T01:21:03,657 | PyObject * {aka struct _object *} 2025-09-08T01:21:03,657 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:21:03,657 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:21:03,658 | ^~~~ 2025-09-08T01:21:03,658 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:21:03,658 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:21:03,658 | ~~~~^ 2025-09-08T01:21:03,706 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:21:03,707 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:21:03,707 | ^~~~~~~~~~ 2025-09-08T01:21:03,707 rnacounter/rnacounter.c:32222:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:21:03,707 32222 | py_code = __Pyx_PyCode_New( 2025-09-08T01:21:03,707 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:21:03,707 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:21:03,707 213 | PyCode_New( 2025-09-08T01:21:03,707 | ^~~~~~~~~~ 2025-09-08T01:21:03,724 rnacounter/rnacounter.c: In function ‘__Pyx_AddTraceback’: 2025-09-08T01:21:03,760 rnacounter/rnacounter.c:32265:13: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:21:03,761 32265 | py_frame->f_lineno = py_line; 2025-09-08T01:21:03,761 | ^~ 2025-09-08T01:21:03,763 rnacounter/rnacounter.c: In function ‘__Pyx_PyInt_As_int’: 2025-09-08T01:21:03,799 rnacounter/rnacounter.c:32386:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T01:21:03,799 32386 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T01:21:03,799 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:21:03,799 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-08T01:21:03,800 from /usr/include/python3.13/Python.h:81: 2025-09-08T01:21:03,800 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T01:21:03,800 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T01:21:03,800 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:21:03,846 rnacounter/rnacounter.c: In function ‘__Pyx_PyInt_As_long’: 2025-09-08T01:21:03,882 rnacounter/rnacounter.c:32841:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T01:21:03,883 32841 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T01:21:03,883 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:21:03,883 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T01:21:03,883 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T01:21:03,883 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:21:03,892 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionSwap’: 2025-09-08T01:21:03,947 rnacounter/rnacounter.c:32873:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:21:03,947 32873 | tmp_type = tstate->exc_type; 2025-09-08T01:21:03,947 | ^~~~~~~~ 2025-09-08T01:21:03,947 | exc_state 2025-09-08T01:21:03,985 rnacounter/rnacounter.c:32874:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:21:03,985 32874 | tmp_value = tstate->exc_value; 2025-09-08T01:21:03,985 | ^~ 2025-09-08T01:21:04,023 rnacounter/rnacounter.c:32875:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:21:04,023 32875 | tmp_tb = tstate->exc_traceback; 2025-09-08T01:21:04,024 | ^~ 2025-09-08T01:21:04,078 rnacounter/rnacounter.c:32876:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:21:04,078 32876 | tstate->exc_type = *type; 2025-09-08T01:21:04,079 | ^~~~~~~~ 2025-09-08T01:21:04,079 | exc_state 2025-09-08T01:21:04,116 rnacounter/rnacounter.c:32877:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:21:04,117 32877 | tstate->exc_value = *value; 2025-09-08T01:21:04,117 | ^~ 2025-09-08T01:21:04,155 rnacounter/rnacounter.c:32878:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:21:04,155 32878 | tstate->exc_traceback = *tb; 2025-09-08T01:21:04,155 | ^~ 2025-09-08T01:21:04,157 In file included from /usr/include/python3.13/Python.h:63: 2025-09-08T01:21:04,157 rnacounter/rnacounter.c: In function ‘__Pyx_Generator_SendEx’: 2025-09-08T01:21:04,236 rnacounter/rnacounter.c:32998:30: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T01:21:04,236 32998 | Py_XINCREF(tstate->frame); 2025-09-08T01:21:04,236 | ^~ 2025-09-08T01:21:04,236 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-08T01:21:04,236 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-08T01:21:04,237 | ^~~~ 2025-09-08T01:21:04,237 /usr/include/python3.13/object.h:1041:37: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-08T01:21:04,237 1041 | # define Py_XINCREF(op) Py_XINCREF(_PyObject_CAST(op)) 2025-09-08T01:21:04,237 | ^~~~~~~~~~~~~~ 2025-09-08T01:21:04,237 rnacounter/rnacounter.c:32998:13: note: in expansion of macro ‘Py_XINCREF’ 2025-09-08T01:21:04,237 32998 | Py_XINCREF(tstate->frame); 2025-09-08T01:21:04,237 | ^~~~~~~~~~ 2025-09-08T01:21:04,273 rnacounter/rnacounter.c:33000:14: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:21:04,273 33000 | f->f_back = tstate->frame; 2025-09-08T01:21:04,273 | ^~ 2025-09-08T01:21:04,314 rnacounter/rnacounter.c:33000:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T01:21:04,314 33000 | f->f_back = tstate->frame; 2025-09-08T01:21:04,315 | ^~ 2025-09-08T01:21:04,393 rnacounter/rnacounter.c:33019:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:21:04,393 33019 | Py_CLEAR(f->f_back); 2025-09-08T01:21:04,393 | ^~ 2025-09-08T01:21:04,393 /usr/include/python3.13/pyport.h:558:39: note: in definition of macro ‘_Py_TYPEOF’ 2025-09-08T01:21:04,393 558 | # define _Py_TYPEOF(expr) __typeof__(expr) 2025-09-08T01:21:04,393 | ^~~~ 2025-09-08T01:21:04,393 rnacounter/rnacounter.c:33019:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T01:21:04,394 33019 | Py_CLEAR(f->f_back); 2025-09-08T01:21:04,394 | ^~~~~~~~ 2025-09-08T01:21:04,434 In file included from /usr/include/python3.13/Python.h:72: 2025-09-08T01:21:04,434 rnacounter/rnacounter.c:33019:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:21:04,434 33019 | Py_CLEAR(f->f_back); 2025-09-08T01:21:04,434 | ^~ 2025-09-08T01:21:04,435 /usr/include/python3.13/object.h:1012:41: note: in definition of macro ‘Py_CLEAR’ 2025-09-08T01:21:04,435 1012 | _Py_TYPEOF(op)* _tmp_op_ptr = &(op); \ 2025-09-08T01:21:04,435 | ^~ 2025-09-08T01:21:04,516 rnacounter/rnacounter.c:33019:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:21:04,517 33019 | Py_CLEAR(f->f_back); 2025-09-08T01:21:04,517 | ^~ 2025-09-08T01:21:04,517 /usr/include/python3.13/pyport.h:558:39: note: in definition of macro ‘_Py_TYPEOF’ 2025-09-08T01:21:04,517 558 | # define _Py_TYPEOF(expr) __typeof__(expr) 2025-09-08T01:21:04,517 | ^~~~ 2025-09-08T01:21:04,517 rnacounter/rnacounter.c:33019:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T01:21:04,517 33019 | Py_CLEAR(f->f_back); 2025-09-08T01:21:04,517 | ^~~~~~~~ 2025-09-08T01:21:04,558 /usr/include/python3.13/object.h:1014:25: warning: comparison between pointer and integer 2025-09-08T01:21:04,558 1014 | if (_tmp_old_op != NULL) { \ 2025-09-08T01:21:04,558 | ^~ 2025-09-08T01:21:04,558 rnacounter/rnacounter.c:33019:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T01:21:04,558 33019 | Py_CLEAR(f->f_back); 2025-09-08T01:21:04,558 | ^~~~~~~~ 2025-09-08T01:21:04,599 /usr/include/python3.13/object.h:1015:26: error: assignment to ‘int’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:21:04,599 1015 | *_tmp_op_ptr = _Py_NULL; \ 2025-09-08T01:21:04,599 | ^ 2025-09-08T01:21:04,599 rnacounter/rnacounter.c:33019:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T01:21:04,600 33019 | Py_CLEAR(f->f_back); 2025-09-08T01:21:04,600 | ^~~~~~~~ 2025-09-08T01:21:05,210 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T01:21:05,382 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T01:21:05,393 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T01:21:05,393 exec(compile('"'"''"'"''"'"' 2025-09-08T01:21:05,393 # This is -- a caller that pip uses to run setup.py 2025-09-08T01:21:05,393 # 2025-09-08T01:21:05,393 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T01:21:05,393 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T01:21:05,393 # - It provides a clear error message when setuptools is not installed. 2025-09-08T01:21:05,393 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T01:21:05,393 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T01:21:05,393 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T01:21:05,393 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T01:21:05,393 import os, sys, tokenize, traceback 2025-09-08T01:21:05,393 2025-09-08T01:21:05,393 try: 2025-09-08T01:21:05,393 import setuptools 2025-09-08T01:21:05,393 except ImportError: 2025-09-08T01:21:05,393 print( 2025-09-08T01:21:05,393 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T01:21:05,393 "the build environment with exception:", 2025-09-08T01:21:05,393 file=sys.stderr, 2025-09-08T01:21:05,393 ) 2025-09-08T01:21:05,393 traceback.print_exc() 2025-09-08T01:21:05,393 sys.exit(1) 2025-09-08T01:21:05,393 2025-09-08T01:21:05,393 __file__ = %r 2025-09-08T01:21:05,393 sys.argv[0] = __file__ 2025-09-08T01:21:05,393 2025-09-08T01:21:05,393 if os.path.exists(__file__): 2025-09-08T01:21:05,393 filename = __file__ 2025-09-08T01:21:05,393 with tokenize.open(__file__) as f: 2025-09-08T01:21:05,393 setup_py_code = f.read() 2025-09-08T01:21:05,393 else: 2025-09-08T01:21:05,393 filename = "" 2025-09-08T01:21:05,393 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T01:21:05,393 2025-09-08T01:21:05,393 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T01:21:05,393 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-c8oc_1xm/rnacounter_b8e2bb631e394de4945d62e2c57f44d4/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-zyd2khfd[/] 2025-09-08T01:21:05,394 [bold magenta]cwd[/]: /tmp/pip-wheel-c8oc_1xm/rnacounter_b8e2bb631e394de4945d62e2c57f44d4/ 2025-09-08T01:21:05,394 Building wheel for rnacounter (setup.py): finished with status 'error' 2025-09-08T01:21:05,394 ERROR: Failed building wheel for rnacounter 2025-09-08T01:21:05,395 Running setup.py clean for rnacounter 2025-09-08T01:21:05,396 Running command python setup.py clean 2025-09-08T01:21:06,298 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T01:21:06,298 warnings.warn(msg) 2025-09-08T01:21:06,758 running clean 2025-09-08T01:21:06,906 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T01:21:06,906 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T01:21:06,908 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T01:21:06,908 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T01:21:06,908 removing 'build' 2025-09-08T01:21:07,044 Failed to build rnacounter 2025-09-08T01:21:07,045 ERROR: Failed to build one or more wheels 2025-09-08T01:21:07,046 Exception information: 2025-09-08T01:21:07,046 Traceback (most recent call last): 2025-09-08T01:21:07,046 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T01:21:07,046 status = _inner_run() 2025-09-08T01:21:07,046 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T01:21:07,046 return self.run(options, args) 2025-09-08T01:21:07,046 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T01:21:07,046 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T01:21:07,046 return func(self, options, args) 2025-09-08T01:21:07,046 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T01:21:07,046 raise CommandError("Failed to build one or more wheels") 2025-09-08T01:21:07,046 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T01:21:07,050 Removed build tracker: '/tmp/pip-build-tracker-tjt0eref'