2025-09-08T00:35:41,593 Created temporary directory: /tmp/pip-build-tracker-ujrarugr 2025-09-08T00:35:41,594 Initialized build tracking at /tmp/pip-build-tracker-ujrarugr 2025-09-08T00:35:41,594 Created build tracker: /tmp/pip-build-tracker-ujrarugr 2025-09-08T00:35:41,594 Entered build tracker: /tmp/pip-build-tracker-ujrarugr 2025-09-08T00:35:41,594 Created temporary directory: /tmp/pip-wheel-wjzsk_fj 2025-09-08T00:35:41,597 Created temporary directory: /tmp/pip-ephem-wheel-cache-27g13cy6 2025-09-08T00:35:41,654 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T00:35:41,656 2 location(s) to search for versions of rnacounter: 2025-09-08T00:35:41,656 * https://pypi.org/simple/rnacounter/ 2025-09-08T00:35:41,656 * https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:35:41,657 Fetching project page and analyzing links: https://pypi.org/simple/rnacounter/ 2025-09-08T00:35:41,657 Getting page https://pypi.org/simple/rnacounter/ 2025-09-08T00:35:41,658 Found index url https://pypi.org/simple/ 2025-09-08T00:35:41,807 Fetched page https://pypi.org/simple/rnacounter/ as application/vnd.pypi.simple.v1+json 2025-09-08T00:35:41,812 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 2025-09-08T00:35:41,813 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 2025-09-08T00:35:41,813 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 2025-09-08T00:35:41,814 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 2025-09-08T00:35:41,814 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 2025-09-08T00:35:41,814 Found link https://files.pythonhosted.org/packages/8a/5e/1b112fc6343bf52ace3a9afaa30eabaf4338afadabf1fb97454a7556b835/rnacounter-1.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.2 2025-09-08T00:35:41,815 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 2025-09-08T00:35:41,815 Found link https://files.pythonhosted.org/packages/dd/92/d53ee16c942fb78a312c03b22b0ddc08eb00ae4627f9125415a2c650b674/rnacounter-1.3.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.3 2025-09-08T00:35:41,816 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 2025-09-08T00:35:41,816 Found link https://files.pythonhosted.org/packages/ab/bf/54a012d6660528530b8404401bf494bda91947e38aae0d45ba4d721de6d4/rnacounter-1.4.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4 2025-09-08T00:35:41,817 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 2025-09-08T00:35:41,817 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 2025-09-08T00:35:41,818 Found link https://files.pythonhosted.org/packages/46/ee/29eed438b10276db92163dff3d25bcb91f3f9e99d9a629c35ddb97f27f4d/rnacounter-1.5.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.5 2025-09-08T00:35:41,818 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 2025-09-08T00:35:41,819 Fetching project page and analyzing links: https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:35:41,819 Getting page https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:35:41,821 Found index url https://www.piwheels.org/simple/ 2025-09-08T00:35:41,911 Fetched page https://www.piwheels.org/simple/rnacounter/ as text/html 2025-09-08T00:35:41,923 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/) 2025-09-08T00:35:41,923 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/) 2025-09-08T00:35:41,923 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/) 2025-09-08T00:35:41,923 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/) 2025-09-08T00:35:41,924 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/) 2025-09-08T00:35:41,924 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/) 2025-09-08T00:35:41,924 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/) 2025-09-08T00:35:41,924 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/) 2025-09-08T00:35:41,924 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/) 2025-09-08T00:35:41,924 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/) 2025-09-08T00:35:41,924 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/) 2025-09-08T00:35:41,925 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/) 2025-09-08T00:35:41,925 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/) 2025-09-08T00:35:41,925 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/) 2025-09-08T00:35:41,925 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/) 2025-09-08T00:35:41,926 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/) 2025-09-08T00:35:41,926 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/) 2025-09-08T00:35:41,926 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/) 2025-09-08T00:35:41,926 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/) 2025-09-08T00:35:41,926 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/) 2025-09-08T00:35:41,926 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/) 2025-09-08T00:35:41,926 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/) 2025-09-08T00:35:41,927 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/) 2025-09-08T00:35:41,927 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/) 2025-09-08T00:35:41,927 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/) 2025-09-08T00:35:41,927 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/) 2025-09-08T00:35:41,927 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/) 2025-09-08T00:35:41,927 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2-cp34-cp34m-linux_armv7l.whl#sha256=8ed62342f5d7481f7393010ff34b0286db7f26ea914710a1f81e583b478bb68a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:35:41,928 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2-cp34-cp34m-linux_armv6l.whl#sha256=8ed62342f5d7481f7393010ff34b0286db7f26ea914710a1f81e583b478bb68a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:35:41,928 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2-cp35-cp35m-linux_armv7l.whl#sha256=6271c54eb4c54d72f9499294fc50f1644dbd248414d993f053106a876d2e9400 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:35:41,928 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/) 2025-09-08T00:35:41,929 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/) 2025-09-08T00:35:41,929 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/) 2025-09-08T00:35:41,929 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/) 2025-09-08T00:35:41,929 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/) 2025-09-08T00:35:41,929 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/) 2025-09-08T00:35:41,930 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/) 2025-09-08T00:35:41,930 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/) 2025-09-08T00:35:41,930 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/) 2025-09-08T00:35:41,930 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/) 2025-09-08T00:35:41,930 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/) 2025-09-08T00:35:41,930 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/) 2025-09-08T00:35:41,930 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/) 2025-09-08T00:35:41,931 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/) 2025-09-08T00:35:41,931 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/) 2025-09-08T00:35:41,931 Skipping link: not a file: https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:35:41,931 Skipping link: not a file: https://pypi.org/simple/rnacounter/ 2025-09-08T00:35:41,954 Given no hashes to check 1 links for project 'rnacounter': discarding no candidates 2025-09-08T00:35:41,955 Collecting rnacounter==1.1.2 2025-09-08T00:35:41,957 Created temporary directory: /tmp/pip-unpack-2e5yw2r0 2025-09-08T00:35:42,318 Downloading rnacounter-1.1.2.tar.gz (289 kB) 2025-09-08T00:35:42,403 Added rnacounter==1.1.2 from https://files.pythonhosted.org/packages/8f/49/762bb78c6a1215e30ccd9702444375015a50b14847266db0c2f11219e78f/rnacounter-1.1.2.tar.gz to build tracker '/tmp/pip-build-tracker-ujrarugr' 2025-09-08T00:35:42,404 Running setup.py (path:/tmp/pip-wheel-wjzsk_fj/rnacounter_5b80d0d7437d4dbbbe1e9f393a95544c/setup.py) egg_info for package rnacounter 2025-09-08T00:35:42,405 Created temporary directory: /tmp/pip-pip-egg-info-tlaw66ul 2025-09-08T00:35:42,405 Preparing metadata (setup.py): started 2025-09-08T00:35:42,406 Running command python setup.py egg_info 2025-09-08T00:35:43,381 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T00:35:43,381 warnings.warn(msg) 2025-09-08T00:35:43,853 running egg_info 2025-09-08T00:35:43,925 creating /tmp/pip-pip-egg-info-tlaw66ul/rnacounter.egg-info 2025-09-08T00:35:43,926 writing /tmp/pip-pip-egg-info-tlaw66ul/rnacounter.egg-info/PKG-INFO 2025-09-08T00:35:43,927 writing dependency_links to /tmp/pip-pip-egg-info-tlaw66ul/rnacounter.egg-info/dependency_links.txt 2025-09-08T00:35:43,928 writing requirements to /tmp/pip-pip-egg-info-tlaw66ul/rnacounter.egg-info/requires.txt 2025-09-08T00:35:43,928 writing top-level names to /tmp/pip-pip-egg-info-tlaw66ul/rnacounter.egg-info/top_level.txt 2025-09-08T00:35:43,928 writing manifest file '/tmp/pip-pip-egg-info-tlaw66ul/rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:35:44,299 reading manifest file '/tmp/pip-pip-egg-info-tlaw66ul/rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:35:44,300 reading manifest template 'MANIFEST.in' 2025-09-08T00:35:44,304 writing manifest file '/tmp/pip-pip-egg-info-tlaw66ul/rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:35:44,441 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T00:35:44,448 Source in /tmp/pip-wheel-wjzsk_fj/rnacounter_5b80d0d7437d4dbbbe1e9f393a95544c has version 1.1.2, which satisfies requirement rnacounter==1.1.2 from https://files.pythonhosted.org/packages/8f/49/762bb78c6a1215e30ccd9702444375015a50b14847266db0c2f11219e78f/rnacounter-1.1.2.tar.gz 2025-09-08T00:35:44,448 Removed rnacounter==1.1.2 from https://files.pythonhosted.org/packages/8f/49/762bb78c6a1215e30ccd9702444375015a50b14847266db0c2f11219e78f/rnacounter-1.1.2.tar.gz from build tracker '/tmp/pip-build-tracker-ujrarugr' 2025-09-08T00:35:44,452 Created temporary directory: /tmp/pip-unpack-3xmbafe8 2025-09-08T00:35:44,452 Created temporary directory: /tmp/pip-unpack-10ashm7a 2025-09-08T00:35:44,452 Building wheels for collected packages: rnacounter 2025-09-08T00:35:44,454 Created temporary directory: /tmp/pip-wheel-6odnfmcu 2025-09-08T00:35:44,454 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 2025-09-08T00:35:44,455 Building wheel for rnacounter (setup.py): started 2025-09-08T00:35:44,456 Destination directory: /tmp/pip-wheel-6odnfmcu 2025-09-08T00:35:44,456 Running command python setup.py bdist_wheel 2025-09-08T00:35:45,586 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T00:35:45,586 warnings.warn(msg) 2025-09-08T00:35:45,975 running bdist_wheel 2025-09-08T00:35:46,336 running build 2025-09-08T00:35:46,336 running build_py 2025-09-08T00:35:46,412 creating build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:35:46,413 copying rnacounter/setup.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:35:46,413 copying rnacounter/__init__.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:35:46,414 running egg_info 2025-09-08T00:35:46,488 writing rnacounter.egg-info/PKG-INFO 2025-09-08T00:35:46,489 writing dependency_links to rnacounter.egg-info/dependency_links.txt 2025-09-08T00:35:46,490 writing requirements to rnacounter.egg-info/requires.txt 2025-09-08T00:35:46,490 writing top-level names to rnacounter.egg-info/top_level.txt 2025-09-08T00:35:46,566 reading manifest file 'rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:35:46,568 reading manifest template 'MANIFEST.in' 2025-09-08T00:35:46,572 writing manifest file 'rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:35:46,574 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'rnacounter.testfiles' is absent from the `packages` configuration. 2025-09-08T00:35:46,574 !! 2025-09-08T00:35:46,574 ******************************************************************************** 2025-09-08T00:35:46,574 ############################ 2025-09-08T00:35:46,574 # Package would be ignored # 2025-09-08T00:35:46,574 ############################ 2025-09-08T00:35:46,575 Python recognizes 'rnacounter.testfiles' as an importable package[^1], 2025-09-08T00:35:46,575 but it is absent from setuptools' `packages` configuration. 2025-09-08T00:35:46,575 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T00:35:46,575 package, please make sure that 'rnacounter.testfiles' is explicitly added 2025-09-08T00:35:46,575 to the `packages` configuration field. 2025-09-08T00:35:46,575 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T00:35:46,575 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T00:35:46,575 instead of `find_packages(...)`/`find:`). 2025-09-08T00:35:46,576 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T00:35:46,576 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T00:35:46,576 If you don't want 'rnacounter.testfiles' to be distributed and are 2025-09-08T00:35:46,576 already explicitly excluding 'rnacounter.testfiles' via 2025-09-08T00:35:46,576 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T00:35:46,576 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T00:35:46,576 combination with a more fine grained `package-data` configuration. 2025-09-08T00:35:46,576 You can read more about "package data files" on setuptools documentation page: 2025-09-08T00:35:46,577 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T00:35:46,577 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T00:35:46,577 even if it does not contain any `.py` files. 2025-09-08T00:35:46,577 On the other hand, currently there is no concept of package data 2025-09-08T00:35:46,577 directory, all directories are treated like packages. 2025-09-08T00:35:46,577 ******************************************************************************** 2025-09-08T00:35:46,577 !! 2025-09-08T00:35:46,577 check.warn(importable) 2025-09-08T00:35:46,578 copying rnacounter/rnacounter -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:35:46,578 copying rnacounter/rnacounter.c -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:35:46,583 copying rnacounter/rnacounter3 -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:35:46,583 creating build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:35:46,583 copying rnacounter/testfiles/gapdhKO.bam -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:35:46,584 copying rnacounter/testfiles/gapdhKO.bam.bai -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:35:46,585 copying rnacounter/testfiles/mm9_3genes_renamed.bed -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:35:46,586 copying rnacounter/testfiles/mm9_3genes_renamed.gtf -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:35:46,586 copying rnacounter/testfiles/mm9_Gapdh_renamed.gtf -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:35:46,587 running build_ext 2025-09-08T00:35:46,945 building 'rnacounter/rnacounter' extension 2025-09-08T00:35:46,945 creating build/temp.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:35:46,946 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 2025-09-08T00:35:47,372 rnacounter/rnacounter.c: In function ‘__Pyx_ListComp_Append’: 2025-09-08T00:35:47,373 rnacounter/rnacounter.c:1355:23: error: lvalue required as left operand of assignment 2025-09-08T00:35:47,373 1355 | Py_SIZE(list) = len+1; 2025-09-08T00:35:47,373 | ^ 2025-09-08T00:35:47,373 rnacounter/rnacounter.c: In function ‘__Pyx_PyList_Append’: 2025-09-08T00:35:47,374 rnacounter/rnacounter.c:1422:23: error: lvalue required as left operand of assignment 2025-09-08T00:35:47,374 1422 | Py_SIZE(list) = len+1; 2025-09-08T00:35:47,374 | ^ 2025-09-08T00:35:47,382 rnacounter/rnacounter.c: In function ‘__Pyx_PyList_Extend’: 2025-09-08T00:35:47,383 rnacounter/rnacounter.c:1479:22: error: implicit declaration of function ‘_PyList_Extend’; did you mean ‘PyList_Extend’? [-Wimplicit-function-declaration] 2025-09-08T00:35:47,383 1479 | PyObject* none = _PyList_Extend((PyListObject*)L, v); 2025-09-08T00:35:47,383 | ^~~~~~~~~~~~~~ 2025-09-08T00:35:47,383 | PyList_Extend 2025-09-08T00:35:47,383 rnacounter/rnacounter.c:1479:22: error: initialization of ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:47,442 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_2parse_bed’: 2025-09-08T00:35:47,446 rnacounter/rnacounter.c:4156:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:47,446 4156 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:35:47,446 | ^~ 2025-09-08T00:35:47,446 In file included from /usr/include/python3.13/Python.h:76, 2025-09-08T00:35:47,446 from rnacounter/rnacounter.c:16: 2025-09-08T00:35:47,446 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:35:47,447 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:35:47,447 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:47,492 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_4join’: 2025-09-08T00:35:47,497 rnacounter/rnacounter.c:5391:9: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:47,497 5391 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:35:47,497 | ^~ 2025-09-08T00:35:47,497 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:35:47,497 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:35:47,497 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:47,533 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_13GenomicObject_2__and__’: 2025-09-08T00:35:47,539 rnacounter/rnacounter.c:6551:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:47,539 6551 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:35:47,539 | ^~ 2025-09-08T00:35:47,539 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:35:47,540 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:35:47,540 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:48,432 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_14parse_args’: 2025-09-08T00:35:48,457 rnacounter/rnacounter.c:22043:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:48,457 22043 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:35:48,457 | ^~ 2025-09-08T00:35:48,457 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:35:48,457 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:35:48,457 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:48,484 rnacounter/rnacounter.c:22097:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:48,484 22097 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:35:48,484 | ^~ 2025-09-08T00:35:48,484 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:35:48,484 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:35:48,484 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:48,511 rnacounter/rnacounter.c:22192:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:48,512 22192 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:35:48,512 | ^~ 2025-09-08T00:35:48,512 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:35:48,512 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:35:48,512 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:48,538 rnacounter/rnacounter.c:22241:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:48,538 22241 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:35:48,538 | ^~ 2025-09-08T00:35:48,538 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:35:48,538 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:35:48,539 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:48,579 rnacounter/rnacounter.c:22377:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:48,579 22377 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:35:48,580 | ^~ 2025-09-08T00:35:48,580 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:35:48,580 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:35:48,580 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:48,634 rnacounter/rnacounter.c:22579:5: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:48,635 22579 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:35:48,635 | ^~ 2025-09-08T00:35:48,635 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:35:48,635 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:35:48,635 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:48,662 rnacounter/rnacounter.c:22644:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:48,662 22644 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:35:48,662 | ^~ 2025-09-08T00:35:48,662 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:35:48,663 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:35:48,663 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:48,706 rnacounter/rnacounter.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-08T00:35:48,744 rnacounter/rnacounter.c:23199:50: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-08T00:35:48,745 23199 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); 2025-09-08T00:35:48,745 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:48,745 | PyBUF_C_CONTIGUOUS 2025-09-08T00:35:48,747 rnacounter/rnacounter.c:23199:50: note: each undeclared identifier is reported only once for each function it appears in 2025-09-08T00:35:48,808 rnacounter/rnacounter.c:23239:50: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-08T00:35:48,808 23239 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); 2025-09-08T00:35:48,808 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:48,808 | PyBUF_F_CONTIGUOUS 2025-09-08T00:35:48,816 rnacounter/rnacounter.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-08T00:35:48,844 rnacounter/rnacounter.c:24245:29: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T00:35:48,845 24245 | if (unlikely(__pyx_v_descr->names == Py_None)) { 2025-09-08T00:35:48,845 | ^~ 2025-09-08T00:35:48,845 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:35:48,845 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:35:48,845 | ^ 2025-09-08T00:35:48,878 rnacounter/rnacounter.c:24249:28: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T00:35:48,878 24249 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; 2025-09-08T00:35:48,878 | ^~ 2025-09-08T00:35:48,911 rnacounter/rnacounter.c:24267:47: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-08T00:35:48,912 24267 | __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;}; 2025-09-08T00:35:48,912 | ^~ 2025-09-08T00:35:48,961 rnacounter/rnacounter.c:24448:79: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’ 2025-09-08T00:35:48,961 24448 | (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); 2025-09-08T00:35:48,961 | ^~ 2025-09-08T00:35:49,009 rnacounter/rnacounter.c: In function ‘__pyx_tp_dealloc_10rnacounter_10rnacounter_Counter’: 2025-09-08T00:35:49,037 rnacounter/rnacounter.c:25069:75: error: implicit declaration of function ‘_PyGC_FINALIZED’ [-Wimplicit-function-declaration] 2025-09-08T00:35:49,037 25069 | if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { 2025-09-08T00:35:49,037 | ^~~~~~~~~~~~~~~ 2025-09-08T00:35:49,146 rnacounter/rnacounter.c: In function ‘__Pyx_InitCachedConstants’: 2025-09-08T00:35:49,178 rnacounter/rnacounter.c:28836:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:49,179 28836 | __pyx_codeobj__62 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__61, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 64, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,179 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,179 In file included from /usr/include/python3.13/Python.h:101: 2025-09-08T00:35:49,179 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,179 213 | PyCode_New( 2025-09-08T00:35:49,179 | ^~~~~~~~~~ 2025-09-08T00:35:49,215 rnacounter/rnacounter.c:28836:243: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:49,215 28836 | __pyx_codeobj__62 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__61, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 64, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,215 | ^~ 2025-09-08T00:35:49,215 | | 2025-09-08T00:35:49,215 | int 2025-09-08T00:35:49,215 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,216 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,216 | ^~~~~ 2025-09-08T00:35:49,216 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:35:49,216 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,216 | ~~~~~~~~~~^ 2025-09-08T00:35:49,251 rnacounter/rnacounter.c:28836:247: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:35:49,251 28836 | __pyx_codeobj__62 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__61, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 64, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,251 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,251 | | 2025-09-08T00:35:49,251 | PyObject * {aka struct _object *} 2025-09-08T00:35:49,252 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,252 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,252 | ^~~~ 2025-09-08T00:35:49,252 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:35:49,252 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,252 | ~~~~^ 2025-09-08T00:35:49,287 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:35:49,287 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,287 | ^~~~~~~~~~ 2025-09-08T00:35:49,287 rnacounter/rnacounter.c:28836:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,288 28836 | __pyx_codeobj__62 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__61, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 64, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,288 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,288 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,288 213 | PyCode_New( 2025-09-08T00:35:49,288 | ^~~~~~~~~~ 2025-09-08T00:35:49,320 rnacounter/rnacounter.c:28848:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:49,320 28848 | __pyx_codeobj__64 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 84, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,320 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,320 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,320 213 | PyCode_New( 2025-09-08T00:35:49,320 | ^~~~~~~~~~ 2025-09-08T00:35:49,356 rnacounter/rnacounter.c:28848:244: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:49,356 28848 | __pyx_codeobj__64 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 84, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,356 | ^~ 2025-09-08T00:35:49,356 | | 2025-09-08T00:35:49,356 | int 2025-09-08T00:35:49,356 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,357 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,357 | ^~~~~ 2025-09-08T00:35:49,357 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:35:49,357 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,357 | ~~~~~~~~~~^ 2025-09-08T00:35:49,392 rnacounter/rnacounter.c:28848:248: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:35:49,392 28848 | __pyx_codeobj__64 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 84, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,392 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,392 | | 2025-09-08T00:35:49,392 | PyObject * {aka struct _object *} 2025-09-08T00:35:49,393 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,393 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,393 | ^~~~ 2025-09-08T00:35:49,393 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:35:49,393 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,393 | ~~~~^ 2025-09-08T00:35:49,428 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:35:49,428 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,428 | ^~~~~~~~~~ 2025-09-08T00:35:49,428 rnacounter/rnacounter.c:28848:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,429 28848 | __pyx_codeobj__64 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 84, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,429 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,429 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,429 213 | PyCode_New( 2025-09-08T00:35:49,429 | ^~~~~~~~~~ 2025-09-08T00:35:49,461 rnacounter/rnacounter.c:28860:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:49,461 28860 | __pyx_codeobj__66 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 110, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,461 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,461 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,461 213 | PyCode_New( 2025-09-08T00:35:49,461 | ^~~~~~~~~~ 2025-09-08T00:35:49,497 rnacounter/rnacounter.c:28860:239: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:49,497 28860 | __pyx_codeobj__66 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 110, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,497 | ^~~ 2025-09-08T00:35:49,497 | | 2025-09-08T00:35:49,497 | int 2025-09-08T00:35:49,497 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,497 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,498 | ^~~~~ 2025-09-08T00:35:49,498 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:35:49,498 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,498 | ~~~~~~~~~~^ 2025-09-08T00:35:49,533 rnacounter/rnacounter.c:28860:244: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:35:49,533 28860 | __pyx_codeobj__66 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 110, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,533 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,533 | | 2025-09-08T00:35:49,534 | PyObject * {aka struct _object *} 2025-09-08T00:35:49,534 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,534 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,534 | ^~~~ 2025-09-08T00:35:49,534 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:35:49,534 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,534 | ~~~~^ 2025-09-08T00:35:49,569 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:35:49,569 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,569 | ^~~~~~~~~~ 2025-09-08T00:35:49,570 rnacounter/rnacounter.c:28860:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,570 28860 | __pyx_codeobj__66 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 110, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,570 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,570 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,570 213 | PyCode_New( 2025-09-08T00:35:49,570 | ^~~~~~~~~~ 2025-09-08T00:35:49,602 rnacounter/rnacounter.c:28872:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:49,602 28872 | __pyx_codeobj__68 = (PyObject*)__Pyx_PyCode_New(4, 0, 54, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 589, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,602 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,602 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,603 213 | PyCode_New( 2025-09-08T00:35:49,603 | ^~~~~~~~~~ 2025-09-08T00:35:49,638 rnacounter/rnacounter.c:28872:248: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:49,638 28872 | __pyx_codeobj__68 = (PyObject*)__Pyx_PyCode_New(4, 0, 54, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 589, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,638 | ^~~ 2025-09-08T00:35:49,639 | | 2025-09-08T00:35:49,639 | int 2025-09-08T00:35:49,639 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,639 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,639 | ^~~~~ 2025-09-08T00:35:49,639 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:35:49,639 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,639 | ~~~~~~~~~~^ 2025-09-08T00:35:49,674 rnacounter/rnacounter.c:28872:253: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:35:49,675 28872 | __pyx_codeobj__68 = (PyObject*)__Pyx_PyCode_New(4, 0, 54, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 589, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,675 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,675 | | 2025-09-08T00:35:49,675 | PyObject * {aka struct _object *} 2025-09-08T00:35:49,675 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,675 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,675 | ^~~~ 2025-09-08T00:35:49,675 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:35:49,675 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,675 | ~~~~^ 2025-09-08T00:35:49,710 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:35:49,711 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,711 | ^~~~~~~~~~ 2025-09-08T00:35:49,711 rnacounter/rnacounter.c:28872:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,711 28872 | __pyx_codeobj__68 = (PyObject*)__Pyx_PyCode_New(4, 0, 54, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 589, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,711 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,711 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,711 213 | PyCode_New( 2025-09-08T00:35:49,711 | ^~~~~~~~~~ 2025-09-08T00:35:49,743 rnacounter/rnacounter.c:28884:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:49,743 28884 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 717, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,743 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,744 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,744 213 | PyCode_New( 2025-09-08T00:35:49,744 | ^~~~~~~~~~ 2025-09-08T00:35:49,779 rnacounter/rnacounter.c:28884:247: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:49,780 28884 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 717, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,780 | ^~~ 2025-09-08T00:35:49,780 | | 2025-09-08T00:35:49,780 | int 2025-09-08T00:35:49,780 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,780 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,780 | ^~~~~ 2025-09-08T00:35:49,780 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:35:49,780 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,780 | ~~~~~~~~~~^ 2025-09-08T00:35:49,816 rnacounter/rnacounter.c:28884:252: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:35:49,816 28884 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 717, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,816 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,816 | | 2025-09-08T00:35:49,816 | PyObject * {aka struct _object *} 2025-09-08T00:35:49,816 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,816 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,816 | ^~~~ 2025-09-08T00:35:49,816 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:35:49,817 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,817 | ~~~~^ 2025-09-08T00:35:49,852 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:35:49,852 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,852 | ^~~~~~~~~~ 2025-09-08T00:35:49,852 rnacounter/rnacounter.c:28884:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,852 28884 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 717, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,852 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,852 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,852 213 | PyCode_New( 2025-09-08T00:35:49,853 | ^~~~~~~~~~ 2025-09-08T00:35:49,885 rnacounter/rnacounter.c:28896:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:49,885 28896 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(3, 0, 20, 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_rnacounter_main, 737, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,885 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,885 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,885 213 | PyCode_New( 2025-09-08T00:35:49,885 | ^~~~~~~~~~ 2025-09-08T00:35:49,921 rnacounter/rnacounter.c:28896:250: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:49,921 28896 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(3, 0, 20, 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_rnacounter_main, 737, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,921 | ^~~ 2025-09-08T00:35:49,921 | | 2025-09-08T00:35:49,921 | int 2025-09-08T00:35:49,921 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,921 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,921 | ^~~~~ 2025-09-08T00:35:49,922 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:35:49,922 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,922 | ~~~~~~~~~~^ 2025-09-08T00:35:49,958 rnacounter/rnacounter.c:28896:255: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:35:49,958 28896 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(3, 0, 20, 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_rnacounter_main, 737, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,958 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,958 | | 2025-09-08T00:35:49,958 | PyObject * {aka struct _object *} 2025-09-08T00:35:49,958 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,958 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,959 | ^~~~ 2025-09-08T00:35:49,959 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:35:49,959 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:49,959 | ~~~~^ 2025-09-08T00:35:49,996 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:35:49,997 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:49,997 | ^~~~~~~~~~ 2025-09-08T00:35:49,997 rnacounter/rnacounter.c:28896:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:49,997 28896 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(3, 0, 20, 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_rnacounter_main, 737, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:49,997 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:49,997 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:49,997 213 | PyCode_New( 2025-09-08T00:35:49,997 | ^~~~~~~~~~ 2025-09-08T00:35:50,031 rnacounter/rnacounter.c:28905:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:50,031 28905 | __pyx_codeobj__74 = (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, 823, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:50,031 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:50,031 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:50,031 213 | PyCode_New( 2025-09-08T00:35:50,031 | ^~~~~~~~~~ 2025-09-08T00:35:50,069 rnacounter/rnacounter.c:28905:248: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:50,069 28905 | __pyx_codeobj__74 = (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, 823, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:50,069 | ^~~ 2025-09-08T00:35:50,069 | | 2025-09-08T00:35:50,069 | int 2025-09-08T00:35:50,069 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:50,070 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:50,070 | ^~~~~ 2025-09-08T00:35:50,070 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:35:50,070 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:50,070 | ~~~~~~~~~~^ 2025-09-08T00:35:50,105 rnacounter/rnacounter.c:28905:253: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:35:50,105 28905 | __pyx_codeobj__74 = (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, 823, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:50,105 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:50,105 | | 2025-09-08T00:35:50,106 | PyObject * {aka struct _object *} 2025-09-08T00:35:50,106 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:50,106 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:50,106 | ^~~~ 2025-09-08T00:35:50,106 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:35:50,106 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:50,106 | ~~~~^ 2025-09-08T00:35:50,141 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:35:50,141 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:50,142 | ^~~~~~~~~~ 2025-09-08T00:35:50,142 rnacounter/rnacounter.c:28905:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:50,142 28905 | __pyx_codeobj__74 = (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, 823, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:50,142 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:50,142 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:50,142 213 | PyCode_New( 2025-09-08T00:35:50,142 | ^~~~~~~~~~ 2025-09-08T00:35:50,174 rnacounter/rnacounter.c:28917:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:50,174 28917 | __pyx_codeobj__76 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 826, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:50,174 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:50,174 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:50,175 213 | PyCode_New( 2025-09-08T00:35:50,175 | ^~~~~~~~~~ 2025-09-08T00:35:50,210 rnacounter/rnacounter.c:28917:245: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:50,211 28917 | __pyx_codeobj__76 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 826, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:50,211 | ^~~ 2025-09-08T00:35:50,211 | | 2025-09-08T00:35:50,211 | int 2025-09-08T00:35:50,211 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:50,211 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:50,211 | ^~~~~ 2025-09-08T00:35:50,211 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:35:50,211 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:50,211 | ~~~~~~~~~~^ 2025-09-08T00:35:50,247 rnacounter/rnacounter.c:28917:250: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:35:50,247 28917 | __pyx_codeobj__76 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 826, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:50,247 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:50,247 | | 2025-09-08T00:35:50,247 | PyObject * {aka struct _object *} 2025-09-08T00:35:50,247 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:50,247 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:50,247 | ^~~~ 2025-09-08T00:35:50,247 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:35:50,247 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:50,248 | ~~~~^ 2025-09-08T00:35:50,283 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:35:50,283 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:50,283 | ^~~~~~~~~~ 2025-09-08T00:35:50,283 rnacounter/rnacounter.c:28917:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:50,283 28917 | __pyx_codeobj__76 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 826, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:35:50,283 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:50,283 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:50,284 213 | PyCode_New( 2025-09-08T00:35:50,284 | ^~~~~~~~~~ 2025-09-08T00:35:50,286 rnacounter/rnacounter.c: In function ‘PyInit_rnacounter’: 2025-09-08T00:35:50,319 rnacounter/rnacounter.c:29020:47: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,319 29020 | __pyx_type_10rnacounter_10rnacounter_Counter.tp_print = 0; 2025-09-08T00:35:50,319 | ^ 2025-09-08T00:35:50,352 rnacounter/rnacounter.c:29024:53: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,352 29024 | __pyx_type_10rnacounter_10rnacounter_GenomicObject.tp_print = 0; 2025-09-08T00:35:50,352 | ^ 2025-09-08T00:35:50,385 rnacounter/rnacounter.c:29041:44: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,385 29041 | __pyx_type_10rnacounter_10rnacounter_Exon.tp_print = 0; 2025-09-08T00:35:50,385 | ^ 2025-09-08T00:35:50,418 rnacounter/rnacounter.c:29047:50: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,418 29047 | __pyx_type_10rnacounter_10rnacounter_Transcript.tp_print = 0; 2025-09-08T00:35:50,418 | ^ 2025-09-08T00:35:50,451 rnacounter/rnacounter.c:29052:44: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,451 29052 | __pyx_type_10rnacounter_10rnacounter_Gene.tp_print = 0; 2025-09-08T00:35:50,451 | ^ 2025-09-08T00:35:50,484 rnacounter/rnacounter.c:29056:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,484 29056 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct__parse_gtf.tp_print = 0; 2025-09-08T00:35:50,484 | ^ 2025-09-08T00:35:50,517 rnacounter/rnacounter.c:29059:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,517 29059 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_1_genexpr.tp_print = 0; 2025-09-08T00:35:50,517 | ^ 2025-09-08T00:35:50,550 rnacounter/rnacounter.c:29062:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,550 29062 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_2_genexpr.tp_print = 0; 2025-09-08T00:35:50,550 | ^ 2025-09-08T00:35:50,582 rnacounter/rnacounter.c:29065:65: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,583 29065 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_3_join.tp_print = 0; 2025-09-08T00:35:50,583 | ^ 2025-09-08T00:35:50,615 rnacounter/rnacounter.c:29068:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,616 29068 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_4_genexpr.tp_print = 0; 2025-09-08T00:35:50,616 | ^ 2025-09-08T00:35:50,648 rnacounter/rnacounter.c:29071:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,648 29071 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_5_genexpr.tp_print = 0; 2025-09-08T00:35:50,648 | ^ 2025-09-08T00:35:50,681 rnacounter/rnacounter.c:29074:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,681 29074 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_6_genexpr.tp_print = 0; 2025-09-08T00:35:50,681 | ^ 2025-09-08T00:35:50,714 rnacounter/rnacounter.c:29077:74: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,714 29077 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk.tp_print = 0; 2025-09-08T00:35:50,714 | ^ 2025-09-08T00:35:50,747 rnacounter/rnacounter.c:29080:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,747 29080 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr.tp_print = 0; 2025-09-08T00:35:50,747 | ^ 2025-09-08T00:35:50,780 rnacounter/rnacounter.c:29083:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,780 29083 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr.tp_print = 0; 2025-09-08T00:35:50,780 | ^ 2025-09-08T00:35:50,813 rnacounter/rnacounter.c:29086:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,813 29086 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr.tp_print = 0; 2025-09-08T00:35:50,813 | ^ 2025-09-08T00:35:50,845 rnacounter/rnacounter.c:29089:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,846 29089 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_11_genexpr.tp_print = 0; 2025-09-08T00:35:50,846 | ^ 2025-09-08T00:35:50,878 rnacounter/rnacounter.c:29092:74: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,879 29092 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_12_print_output.tp_print = 0; 2025-09-08T00:35:50,879 | ^ 2025-09-08T00:35:50,911 rnacounter/rnacounter.c:29095:72: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,912 29095 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_13_parse_args.tp_print = 0; 2025-09-08T00:35:50,912 | ^ 2025-09-08T00:35:50,944 rnacounter/rnacounter.c:29098:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,944 29098 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr.tp_print = 0; 2025-09-08T00:35:50,945 | ^ 2025-09-08T00:35:50,977 rnacounter/rnacounter.c:29101:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:50,977 29101 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_15_genexpr.tp_print = 0; 2025-09-08T00:35:50,977 | ^ 2025-09-08T00:35:51,010 rnacounter/rnacounter.c:29104:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:35:51,011 29104 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_16_genexpr.tp_print = 0; 2025-09-08T00:35:51,011 | ^ 2025-09-08T00:35:51,065 rnacounter/rnacounter.c: In function ‘__Pyx_PyUnicode_Equals’: 2025-09-08T00:35:51,102 rnacounter/rnacounter.c:84:51: error: implicit declaration of function ‘_PyUnicode_Ready’; did you mean ‘PyUnicode_READY’? [-Wimplicit-function-declaration] 2025-09-08T00:35:51,102 84 | 0 : _PyUnicode_Ready((PyObject *)(op))) 2025-09-08T00:35:51,103 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:51,103 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:35:51,103 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:35:51,103 | ^ 2025-09-08T00:35:51,103 rnacounter/rnacounter.c:29616:22: note: in expansion of macro ‘__Pyx_PyUnicode_READY’ 2025-09-08T00:35:51,103 29616 | if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) 2025-09-08T00:35:51,103 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-08T00:35:51,151 rnacounter/rnacounter.c: In function ‘__Pyx_ErrRestore’: 2025-09-08T00:35:51,186 rnacounter/rnacounter.c:29708:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:35:51,186 29708 | tmp_type = tstate->curexc_type; 2025-09-08T00:35:51,186 | ^~ 2025-09-08T00:35:51,221 rnacounter/rnacounter.c:29709:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:35:51,221 29709 | tmp_value = tstate->curexc_value; 2025-09-08T00:35:51,221 | ^~ 2025-09-08T00:35:51,255 rnacounter/rnacounter.c:29710:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:35:51,255 29710 | tmp_tb = tstate->curexc_traceback; 2025-09-08T00:35:51,255 | ^~ 2025-09-08T00:35:51,290 rnacounter/rnacounter.c:29711:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:35:51,290 29711 | tstate->curexc_type = type; 2025-09-08T00:35:51,290 | ^~ 2025-09-08T00:35:51,323 rnacounter/rnacounter.c:29712:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:35:51,324 29712 | tstate->curexc_value = value; 2025-09-08T00:35:51,324 | ^~ 2025-09-08T00:35:51,357 rnacounter/rnacounter.c:29713:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:35:51,357 29713 | tstate->curexc_traceback = tb; 2025-09-08T00:35:51,357 | ^~ 2025-09-08T00:35:51,357 rnacounter/rnacounter.c: In function ‘__Pyx_ErrFetch’: 2025-09-08T00:35:51,391 rnacounter/rnacounter.c:29724:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:35:51,391 29724 | *type = tstate->curexc_type; 2025-09-08T00:35:51,391 | ^~ 2025-09-08T00:35:51,424 rnacounter/rnacounter.c:29725:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:35:51,425 29725 | *value = tstate->curexc_value; 2025-09-08T00:35:51,425 | ^~ 2025-09-08T00:35:51,458 rnacounter/rnacounter.c:29726:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:35:51,458 29726 | *tb = tstate->curexc_traceback; 2025-09-08T00:35:51,458 | ^~ 2025-09-08T00:35:51,491 rnacounter/rnacounter.c:29727:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:35:51,492 29727 | tstate->curexc_type = 0; 2025-09-08T00:35:51,492 | ^~ 2025-09-08T00:35:51,525 rnacounter/rnacounter.c:29728:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:35:51,525 29728 | tstate->curexc_value = 0; 2025-09-08T00:35:51,525 | ^~ 2025-09-08T00:35:51,559 rnacounter/rnacounter.c:29729:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:35:51,559 29729 | tstate->curexc_traceback = 0; 2025-09-08T00:35:51,559 | ^~ 2025-09-08T00:35:51,625 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionSave’: 2025-09-08T00:35:51,674 rnacounter/rnacounter.c:29926:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:35:51,675 29926 | *type = tstate->exc_type; 2025-09-08T00:35:51,675 | ^~~~~~~~ 2025-09-08T00:35:51,675 | exc_state 2025-09-08T00:35:51,708 rnacounter/rnacounter.c:29927:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:35:51,708 29927 | *value = tstate->exc_value; 2025-09-08T00:35:51,708 | ^~ 2025-09-08T00:35:51,742 rnacounter/rnacounter.c:29928:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:35:51,742 29928 | *tb = tstate->exc_traceback; 2025-09-08T00:35:51,742 | ^~ 2025-09-08T00:35:51,742 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionReset’: 2025-09-08T00:35:51,791 rnacounter/rnacounter.c:29940:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:35:51,791 29940 | tmp_type = tstate->exc_type; 2025-09-08T00:35:51,791 | ^~~~~~~~ 2025-09-08T00:35:51,791 | exc_state 2025-09-08T00:35:51,825 rnacounter/rnacounter.c:29941:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:35:51,825 29941 | tmp_value = tstate->exc_value; 2025-09-08T00:35:51,825 | ^~ 2025-09-08T00:35:51,858 rnacounter/rnacounter.c:29942:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:35:51,858 29942 | tmp_tb = tstate->exc_traceback; 2025-09-08T00:35:51,859 | ^~ 2025-09-08T00:35:51,907 rnacounter/rnacounter.c:29943:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:35:51,907 29943 | tstate->exc_type = type; 2025-09-08T00:35:51,907 | ^~~~~~~~ 2025-09-08T00:35:51,907 | exc_state 2025-09-08T00:35:51,941 rnacounter/rnacounter.c:29944:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:35:51,941 29944 | tstate->exc_value = value; 2025-09-08T00:35:51,941 | ^~ 2025-09-08T00:35:51,974 rnacounter/rnacounter.c:29945:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:35:51,975 29945 | tstate->exc_traceback = tb; 2025-09-08T00:35:51,975 | ^~ 2025-09-08T00:35:51,975 rnacounter/rnacounter.c: In function ‘__Pyx_GetException’: 2025-09-08T00:35:52,009 rnacounter/rnacounter.c:29959:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:35:52,009 29959 | local_type = tstate->curexc_type; 2025-09-08T00:35:52,009 | ^~ 2025-09-08T00:35:52,043 rnacounter/rnacounter.c:29960:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:35:52,043 29960 | local_value = tstate->curexc_value; 2025-09-08T00:35:52,043 | ^~ 2025-09-08T00:35:52,076 rnacounter/rnacounter.c:29961:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:35:52,077 29961 | local_tb = tstate->curexc_traceback; 2025-09-08T00:35:52,077 | ^~ 2025-09-08T00:35:52,110 rnacounter/rnacounter.c:29962:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:35:52,110 29962 | tstate->curexc_type = 0; 2025-09-08T00:35:52,110 | ^~ 2025-09-08T00:35:52,144 rnacounter/rnacounter.c:29963:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:35:52,144 29963 | tstate->curexc_value = 0; 2025-09-08T00:35:52,144 | ^~ 2025-09-08T00:35:52,178 rnacounter/rnacounter.c:29964:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:35:52,178 29964 | tstate->curexc_traceback = 0; 2025-09-08T00:35:52,178 | ^~ 2025-09-08T00:35:52,212 rnacounter/rnacounter.c:29970:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:35:52,212 29970 | if (unlikely(tstate->curexc_type)) 2025-09-08T00:35:52,212 | ^~ 2025-09-08T00:35:52,212 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:35:52,212 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:35:52,212 | ^ 2025-09-08T00:35:52,272 rnacounter/rnacounter.c:29988:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:35:52,273 29988 | tmp_type = tstate->exc_type; 2025-09-08T00:35:52,273 | ^~~~~~~~ 2025-09-08T00:35:52,273 | exc_state 2025-09-08T00:35:52,306 rnacounter/rnacounter.c:29989:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:35:52,306 29989 | tmp_value = tstate->exc_value; 2025-09-08T00:35:52,307 | ^~ 2025-09-08T00:35:52,340 rnacounter/rnacounter.c:29990:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:35:52,340 29990 | tmp_tb = tstate->exc_traceback; 2025-09-08T00:35:52,340 | ^~ 2025-09-08T00:35:52,392 rnacounter/rnacounter.c:29991:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:35:52,392 29991 | tstate->exc_type = local_type; 2025-09-08T00:35:52,392 | ^~~~~~~~ 2025-09-08T00:35:52,392 | exc_state 2025-09-08T00:35:52,428 rnacounter/rnacounter.c:29992:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:35:52,428 29992 | tstate->exc_value = local_value; 2025-09-08T00:35:52,428 | ^~ 2025-09-08T00:35:52,464 rnacounter/rnacounter.c:29993:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:35:52,465 29993 | tstate->exc_traceback = local_tb; 2025-09-08T00:35:52,465 | ^~ 2025-09-08T00:35:52,492 rnacounter/rnacounter.c: In function ‘__Pyx_ParseOptionalKeywords’: 2025-09-08T00:35:52,541 rnacounter/rnacounter.c:30097:22: error: implicit declaration of function ‘PyUnicode_GET_SIZE’; did you mean ‘PyDict_GET_SIZE’? [-Wimplicit-function-declaration] 2025-09-08T00:35:52,541 30097 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-08T00:35:52,541 | ^~~~~~~~~~~~~~~~~~ 2025-09-08T00:35:52,541 | PyDict_GET_SIZE 2025-09-08T00:35:52,653 rnacounter/rnacounter.c: In function ‘__Pyx_Raise’: 2025-09-08T00:35:52,687 rnacounter/rnacounter.c:30323:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:35:52,687 30323 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-08T00:35:52,687 | ^~ 2025-09-08T00:35:52,722 rnacounter/rnacounter.c:30326:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:35:52,722 30326 | tstate->curexc_traceback = tb; 2025-09-08T00:35:52,722 | ^~ 2025-09-08T00:35:52,779 rnacounter/rnacounter.c: In function ‘__Pyx_PyIter_Next2’: 2025-09-08T00:35:52,814 rnacounter/rnacounter.c:30371:31: error: ‘_PyObject_NextNotImplemented’ undeclared (first use in this function); did you mean ‘PyObject_HashNotImplemented’? 2025-09-08T00:35:52,814 30371 | if (unlikely(iternext == &_PyObject_NextNotImplemented)) 2025-09-08T00:35:52,814 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T00:35:52,814 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:35:52,814 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:35:52,814 | ^ 2025-09-08T00:35:52,859 rnacounter/rnacounter.c: In function ‘__Pyx_IterFinish’: 2025-09-08T00:35:52,894 rnacounter/rnacounter.c:30574:32: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:35:52,894 30574 | PyObject* exc_type = tstate->curexc_type; 2025-09-08T00:35:52,894 | ^~ 2025-09-08T00:35:52,929 rnacounter/rnacounter.c:30578:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:35:52,929 30578 | exc_value = tstate->curexc_value; 2025-09-08T00:35:52,929 | ^~ 2025-09-08T00:35:52,964 rnacounter/rnacounter.c:30579:28: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:35:52,964 30579 | exc_tb = tstate->curexc_traceback; 2025-09-08T00:35:52,964 | ^~ 2025-09-08T00:35:52,999 rnacounter/rnacounter.c:30580:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:35:52,999 30580 | tstate->curexc_type = 0; 2025-09-08T00:35:52,999 | ^~ 2025-09-08T00:35:53,034 rnacounter/rnacounter.c:30581:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:35:53,034 30581 | tstate->curexc_value = 0; 2025-09-08T00:35:53,034 | ^~ 2025-09-08T00:35:53,069 rnacounter/rnacounter.c:30582:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:35:53,069 30582 | tstate->curexc_traceback = 0; 2025-09-08T00:35:53,069 | ^~ 2025-09-08T00:35:53,557 rnacounter/rnacounter.c: In function ‘__Pyx_CyFunction_Call’: 2025-09-08T00:35:53,610 rnacounter/rnacounter.c:31926:16: error: implicit declaration of function ‘PyCFunction_Call’; did you mean ‘PyCFunction_New’? [-Wimplicit-function-declaration] 2025-09-08T00:35:53,610 31926 | return PyCFunction_Call(func, arg, kw); 2025-09-08T00:35:53,610 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:53,610 | PyCFunction_New 2025-09-08T00:35:53,650 rnacounter/rnacounter.c:31926:16: error: returning ‘int’ from a function with return type ‘PyObject *’ {aka ‘struct _object *’} makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:53,651 31926 | return PyCFunction_Call(func, arg, kw); 2025-09-08T00:35:53,651 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T00:35:53,672 rnacounter/rnacounter.c: In function ‘__Pyx_CyFunction_init’: 2025-09-08T00:35:53,723 rnacounter/rnacounter.c:31991:41: error: ‘PyCFunction_Call’ undeclared (first use in this function); did you mean ‘PyCFunction_New’? 2025-09-08T00:35:53,723 31991 | __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; 2025-09-08T00:35:53,723 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:53,723 | PyCFunction_New 2025-09-08T00:35:53,767 rnacounter/rnacounter.c: In function ‘__Pyx_CreateCodeObjectForTraceback’: 2025-09-08T00:35:53,803 rnacounter/rnacounter.c:32167:5: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:35:53,804 32167 | py_code = __Pyx_PyCode_New( 2025-09-08T00:35:53,804 | ^~~~~~~ 2025-09-08T00:35:53,804 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:53,804 213 | PyCode_New( 2025-09-08T00:35:53,804 | ^~~~~~~~~~ 2025-09-08T00:35:53,840 rnacounter/rnacounter.c:32181:9: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:35:53,840 32181 | py_line, 2025-09-08T00:35:53,840 | ^~~~~~~ 2025-09-08T00:35:53,840 | | 2025-09-08T00:35:53,840 | int 2025-09-08T00:35:53,840 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:53,840 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:53,841 | ^~~~~ 2025-09-08T00:35:53,841 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:35:53,841 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:53,841 | ~~~~~~~~~~^ 2025-09-08T00:35:53,880 rnacounter/rnacounter.c:32182:9: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:35:53,880 32182 | __pyx_empty_bytes /*PyObject *lnotab*/ 2025-09-08T00:35:53,881 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:35:53,881 | | 2025-09-08T00:35:53,881 | PyObject * {aka struct _object *} 2025-09-08T00:35:53,881 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:53,881 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:53,881 | ^~~~ 2025-09-08T00:35:53,881 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:35:53,881 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:35:53,881 | ~~~~^ 2025-09-08T00:35:53,921 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:35:53,921 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:35:53,921 | ^~~~~~~~~~ 2025-09-08T00:35:53,921 rnacounter/rnacounter.c:32167:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:35:53,921 32167 | py_code = __Pyx_PyCode_New( 2025-09-08T00:35:53,921 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:35:53,921 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:35:53,922 213 | PyCode_New( 2025-09-08T00:35:53,922 | ^~~~~~~~~~ 2025-09-08T00:35:53,938 rnacounter/rnacounter.c: In function ‘__Pyx_AddTraceback’: 2025-09-08T00:35:53,974 rnacounter/rnacounter.c:32210:13: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:35:53,974 32210 | py_frame->f_lineno = py_line; 2025-09-08T00:35:53,974 | ^~ 2025-09-08T00:35:53,976 rnacounter/rnacounter.c: In function ‘__Pyx_PyInt_As_int’: 2025-09-08T00:35:54,012 rnacounter/rnacounter.c:32331:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T00:35:54,012 32331 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T00:35:54,012 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:35:54,012 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-08T00:35:54,013 from /usr/include/python3.13/Python.h:81: 2025-09-08T00:35:54,013 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T00:35:54,013 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T00:35:54,013 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:35:54,058 rnacounter/rnacounter.c: In function ‘__Pyx_PyInt_As_long’: 2025-09-08T00:35:54,094 rnacounter/rnacounter.c:32786:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T00:35:54,094 32786 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T00:35:54,094 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:35:54,094 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T00:35:54,094 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T00:35:54,094 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:35:54,103 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionSwap’: 2025-09-08T00:35:54,157 rnacounter/rnacounter.c:32818:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:35:54,157 32818 | tmp_type = tstate->exc_type; 2025-09-08T00:35:54,158 | ^~~~~~~~ 2025-09-08T00:35:54,158 | exc_state 2025-09-08T00:35:54,195 rnacounter/rnacounter.c:32819:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:35:54,195 32819 | tmp_value = tstate->exc_value; 2025-09-08T00:35:54,195 | ^~ 2025-09-08T00:35:54,232 rnacounter/rnacounter.c:32820:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:35:54,232 32820 | tmp_tb = tstate->exc_traceback; 2025-09-08T00:35:54,233 | ^~ 2025-09-08T00:35:54,286 rnacounter/rnacounter.c:32821:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:35:54,287 32821 | tstate->exc_type = *type; 2025-09-08T00:35:54,287 | ^~~~~~~~ 2025-09-08T00:35:54,287 | exc_state 2025-09-08T00:35:54,324 rnacounter/rnacounter.c:32822:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:35:54,324 32822 | tstate->exc_value = *value; 2025-09-08T00:35:54,324 | ^~ 2025-09-08T00:35:54,361 rnacounter/rnacounter.c:32823:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:35:54,362 32823 | tstate->exc_traceback = *tb; 2025-09-08T00:35:54,362 | ^~ 2025-09-08T00:35:54,364 In file included from /usr/include/python3.13/Python.h:63: 2025-09-08T00:35:54,364 rnacounter/rnacounter.c: In function ‘__Pyx_Generator_SendEx’: 2025-09-08T00:35:54,441 rnacounter/rnacounter.c:32943:30: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T00:35:54,442 32943 | Py_XINCREF(tstate->frame); 2025-09-08T00:35:54,442 | ^~ 2025-09-08T00:35:54,442 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-08T00:35:54,442 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-08T00:35:54,442 | ^~~~ 2025-09-08T00:35:54,442 /usr/include/python3.13/object.h:1041:37: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-08T00:35:54,442 1041 | # define Py_XINCREF(op) Py_XINCREF(_PyObject_CAST(op)) 2025-09-08T00:35:54,442 | ^~~~~~~~~~~~~~ 2025-09-08T00:35:54,442 rnacounter/rnacounter.c:32943:13: note: in expansion of macro ‘Py_XINCREF’ 2025-09-08T00:35:54,442 32943 | Py_XINCREF(tstate->frame); 2025-09-08T00:35:54,442 | ^~~~~~~~~~ 2025-09-08T00:35:54,478 rnacounter/rnacounter.c:32945:14: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:35:54,478 32945 | f->f_back = tstate->frame; 2025-09-08T00:35:54,478 | ^~ 2025-09-08T00:35:54,518 rnacounter/rnacounter.c:32945:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T00:35:54,518 32945 | f->f_back = tstate->frame; 2025-09-08T00:35:54,519 | ^~ 2025-09-08T00:35:54,596 rnacounter/rnacounter.c:32964:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:35:54,596 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:35:54,596 | ^~ 2025-09-08T00:35:54,596 /usr/include/python3.13/pyport.h:558:39: note: in definition of macro ‘_Py_TYPEOF’ 2025-09-08T00:35:54,596 558 | # define _Py_TYPEOF(expr) __typeof__(expr) 2025-09-08T00:35:54,596 | ^~~~ 2025-09-08T00:35:54,596 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:35:54,596 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:35:54,596 | ^~~~~~~~ 2025-09-08T00:35:54,636 In file included from /usr/include/python3.13/Python.h:72: 2025-09-08T00:35:54,636 rnacounter/rnacounter.c:32964:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:35:54,636 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:35:54,636 | ^~ 2025-09-08T00:35:54,637 /usr/include/python3.13/object.h:1012:41: note: in definition of macro ‘Py_CLEAR’ 2025-09-08T00:35:54,637 1012 | _Py_TYPEOF(op)* _tmp_op_ptr = &(op); \ 2025-09-08T00:35:54,637 | ^~ 2025-09-08T00:35:54,717 rnacounter/rnacounter.c:32964:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:35:54,717 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:35:54,717 | ^~ 2025-09-08T00:35:54,717 /usr/include/python3.13/pyport.h:558:39: note: in definition of macro ‘_Py_TYPEOF’ 2025-09-08T00:35:54,717 558 | # define _Py_TYPEOF(expr) __typeof__(expr) 2025-09-08T00:35:54,717 | ^~~~ 2025-09-08T00:35:54,718 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:35:54,718 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:35:54,718 | ^~~~~~~~ 2025-09-08T00:35:54,758 /usr/include/python3.13/object.h:1014:25: warning: comparison between pointer and integer 2025-09-08T00:35:54,758 1014 | if (_tmp_old_op != NULL) { \ 2025-09-08T00:35:54,758 | ^~ 2025-09-08T00:35:54,758 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:35:54,758 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:35:54,758 | ^~~~~~~~ 2025-09-08T00:35:54,800 /usr/include/python3.13/object.h:1015:26: error: assignment to ‘int’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:35:54,800 1015 | *_tmp_op_ptr = _Py_NULL; \ 2025-09-08T00:35:54,800 | ^ 2025-09-08T00:35:54,800 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:35:54,800 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:35:54,800 | ^~~~~~~~ 2025-09-08T00:35:55,392 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T00:35:55,563 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T00:35:55,574 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T00:35:55,574 exec(compile('"'"''"'"''"'"' 2025-09-08T00:35:55,574 # This is -- a caller that pip uses to run setup.py 2025-09-08T00:35:55,574 # 2025-09-08T00:35:55,574 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T00:35:55,574 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T00:35:55,574 # - It provides a clear error message when setuptools is not installed. 2025-09-08T00:35:55,574 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T00:35:55,574 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T00:35:55,574 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T00:35:55,574 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T00:35:55,574 import os, sys, tokenize, traceback 2025-09-08T00:35:55,574 2025-09-08T00:35:55,574 try: 2025-09-08T00:35:55,574 import setuptools 2025-09-08T00:35:55,574 except ImportError: 2025-09-08T00:35:55,574 print( 2025-09-08T00:35:55,574 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T00:35:55,574 "the build environment with exception:", 2025-09-08T00:35:55,574 file=sys.stderr, 2025-09-08T00:35:55,574 ) 2025-09-08T00:35:55,574 traceback.print_exc() 2025-09-08T00:35:55,574 sys.exit(1) 2025-09-08T00:35:55,574 2025-09-08T00:35:55,574 __file__ = %r 2025-09-08T00:35:55,574 sys.argv[0] = __file__ 2025-09-08T00:35:55,574 2025-09-08T00:35:55,574 if os.path.exists(__file__): 2025-09-08T00:35:55,574 filename = __file__ 2025-09-08T00:35:55,574 with tokenize.open(__file__) as f: 2025-09-08T00:35:55,574 setup_py_code = f.read() 2025-09-08T00:35:55,574 else: 2025-09-08T00:35:55,574 filename = "" 2025-09-08T00:35:55,574 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T00:35:55,574 2025-09-08T00:35:55,574 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T00:35:55,574 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-wjzsk_fj/rnacounter_5b80d0d7437d4dbbbe1e9f393a95544c/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-6odnfmcu[/] 2025-09-08T00:35:55,574 [bold magenta]cwd[/]: /tmp/pip-wheel-wjzsk_fj/rnacounter_5b80d0d7437d4dbbbe1e9f393a95544c/ 2025-09-08T00:35:55,575 Building wheel for rnacounter (setup.py): finished with status 'error' 2025-09-08T00:35:55,575 ERROR: Failed building wheel for rnacounter 2025-09-08T00:35:55,576 Running setup.py clean for rnacounter 2025-09-08T00:35:55,577 Running command python setup.py clean 2025-09-08T00:35:56,507 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T00:35:56,507 warnings.warn(msg) 2025-09-08T00:35:56,972 running clean 2025-09-08T00:35:57,118 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T00:35:57,119 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T00:35:57,120 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T00:35:57,120 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T00:35:57,120 removing 'build' 2025-09-08T00:35:57,257 Failed to build rnacounter 2025-09-08T00:35:57,258 ERROR: Failed to build one or more wheels 2025-09-08T00:35:57,259 Exception information: 2025-09-08T00:35:57,259 Traceback (most recent call last): 2025-09-08T00:35:57,259 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T00:35:57,259 status = _inner_run() 2025-09-08T00:35:57,259 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T00:35:57,259 return self.run(options, args) 2025-09-08T00:35:57,259 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T00:35:57,259 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T00:35:57,259 return func(self, options, args) 2025-09-08T00:35:57,259 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T00:35:57,259 raise CommandError("Failed to build one or more wheels") 2025-09-08T00:35:57,259 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T00:35:57,263 Removed build tracker: '/tmp/pip-build-tracker-ujrarugr'