2025-09-08T00:41:53,741 Created temporary directory: /tmp/pip-build-tracker-824ib2pz 2025-09-08T00:41:53,742 Initialized build tracking at /tmp/pip-build-tracker-824ib2pz 2025-09-08T00:41:53,742 Created build tracker: /tmp/pip-build-tracker-824ib2pz 2025-09-08T00:41:53,742 Entered build tracker: /tmp/pip-build-tracker-824ib2pz 2025-09-08T00:41:53,742 Created temporary directory: /tmp/pip-wheel-_o2i4_xl 2025-09-08T00:41:53,746 Created temporary directory: /tmp/pip-ephem-wheel-cache-l5kl4tsb 2025-09-08T00:41:53,804 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T00:41:53,806 2 location(s) to search for versions of rnacounter: 2025-09-08T00:41:53,806 * https://pypi.org/simple/rnacounter/ 2025-09-08T00:41:53,806 * https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:41:53,806 Fetching project page and analyzing links: https://pypi.org/simple/rnacounter/ 2025-09-08T00:41:53,806 Getting page https://pypi.org/simple/rnacounter/ 2025-09-08T00:41:53,808 Found index url https://pypi.org/simple/ 2025-09-08T00:41:53,877 Fetched page https://pypi.org/simple/rnacounter/ as application/vnd.pypi.simple.v1+json 2025-09-08T00:41:53,879 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 2025-09-08T00:41:53,879 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 2025-09-08T00:41:53,879 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 2025-09-08T00:41:53,880 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 2025-09-08T00:41:53,880 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 2025-09-08T00:41:53,880 Found link https://files.pythonhosted.org/packages/8a/5e/1b112fc6343bf52ace3a9afaa30eabaf4338afadabf1fb97454a7556b835/rnacounter-1.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.2 2025-09-08T00:41:53,880 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 2025-09-08T00:41:53,880 Found link https://files.pythonhosted.org/packages/dd/92/d53ee16c942fb78a312c03b22b0ddc08eb00ae4627f9125415a2c650b674/rnacounter-1.3.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.3 2025-09-08T00:41:53,881 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 2025-09-08T00:41:53,881 Found link https://files.pythonhosted.org/packages/ab/bf/54a012d6660528530b8404401bf494bda91947e38aae0d45ba4d721de6d4/rnacounter-1.4.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4 2025-09-08T00:41:53,881 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 2025-09-08T00:41:53,881 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 2025-09-08T00:41:53,881 Found link https://files.pythonhosted.org/packages/46/ee/29eed438b10276db92163dff3d25bcb91f3f9e99d9a629c35ddb97f27f4d/rnacounter-1.5.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.5 2025-09-08T00:41:53,882 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 2025-09-08T00:41:53,882 Fetching project page and analyzing links: https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:41:53,882 Getting page https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:41:53,883 Found index url https://www.piwheels.org/simple/ 2025-09-08T00:41:53,973 Fetched page https://www.piwheels.org/simple/rnacounter/ as text/html 2025-09-08T00:41:53,982 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/) 2025-09-08T00:41:53,983 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/) 2025-09-08T00:41:53,983 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/) 2025-09-08T00:41:53,983 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/) 2025-09-08T00:41:53,983 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/) 2025-09-08T00:41:53,983 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/) 2025-09-08T00:41:53,983 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/) 2025-09-08T00:41:53,983 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/) 2025-09-08T00:41:53,984 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/) 2025-09-08T00:41:53,984 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/) 2025-09-08T00:41:53,984 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/) 2025-09-08T00:41:53,984 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/) 2025-09-08T00:41:53,984 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/) 2025-09-08T00:41:53,985 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/) 2025-09-08T00:41:53,985 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/) 2025-09-08T00:41:53,985 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/) 2025-09-08T00:41:53,985 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/) 2025-09-08T00:41:53,985 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/) 2025-09-08T00:41:53,985 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/) 2025-09-08T00:41:53,985 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/) 2025-09-08T00:41:53,985 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/) 2025-09-08T00:41:53,985 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/) 2025-09-08T00:41:53,986 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/) 2025-09-08T00:41:53,986 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/) 2025-09-08T00:41:53,986 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/) 2025-09-08T00:41:53,986 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/) 2025-09-08T00:41:53,986 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/) 2025-09-08T00:41:53,986 Skipping link: No binaries permitted for rnacounter: 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https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2-cp35-cp35m-linux_armv6l.whl#sha256=6271c54eb4c54d72f9499294fc50f1644dbd248414d993f053106a876d2e9400 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:41:53,987 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.10-cp34-cp34m-linux_armv7l.whl#sha256=c27c6c537f58aaa7ad6d853e9791f08485abe8fd219501a30647ef13d19a633a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:41:53,987 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.10-cp34-cp34m-linux_armv6l.whl#sha256=c27c6c537f58aaa7ad6d853e9791f08485abe8fd219501a30647ef13d19a633a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:41:53,987 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/) 2025-09-08T00:41:53,987 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/) 2025-09-08T00:41:53,988 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/) 2025-09-08T00:41:53,988 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/) 2025-09-08T00:41:53,988 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/) 2025-09-08T00:41:53,988 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/) 2025-09-08T00:41:53,988 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/) 2025-09-08T00:41:53,988 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/) 2025-09-08T00:41:53,988 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/) 2025-09-08T00:41:53,988 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/) 2025-09-08T00:41:53,989 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/) 2025-09-08T00:41:53,989 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/) 2025-09-08T00:41:53,989 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/) 2025-09-08T00:41:53,989 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/) 2025-09-08T00:41:53,989 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/) 2025-09-08T00:41:53,989 Skipping link: not a file: https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:41:53,989 Skipping link: not a file: https://pypi.org/simple/rnacounter/ 2025-09-08T00:41:54,015 Given no hashes to check 1 links for project 'rnacounter': discarding no candidates 2025-09-08T00:41:54,016 Collecting rnacounter==1.1.3.7 2025-09-08T00:41:54,018 Created temporary directory: /tmp/pip-unpack-4v4i3nvi 2025-09-08T00:41:54,275 Downloading rnacounter-1.1.3.7.tar.gz (289 kB) 2025-09-08T00:41:54,368 Added rnacounter==1.1.3.7 from https://files.pythonhosted.org/packages/b1/1c/9f8deaa78b994019b9024043168567099fe010c79018373e2f6ed60ea646/rnacounter-1.1.3.7.tar.gz to build tracker '/tmp/pip-build-tracker-824ib2pz' 2025-09-08T00:41:54,370 Running setup.py (path:/tmp/pip-wheel-_o2i4_xl/rnacounter_71dbdf9e5f1642f6a29a14bd42447274/setup.py) egg_info for package rnacounter 2025-09-08T00:41:54,370 Created temporary directory: /tmp/pip-pip-egg-info-hzx3o5e6 2025-09-08T00:41:54,370 Preparing metadata (setup.py): started 2025-09-08T00:41:54,371 Running command python setup.py egg_info 2025-09-08T00:41:55,275 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T00:41:55,275 warnings.warn(msg) 2025-09-08T00:41:55,742 running egg_info 2025-09-08T00:41:55,816 creating /tmp/pip-pip-egg-info-hzx3o5e6/rnacounter.egg-info 2025-09-08T00:41:55,816 writing /tmp/pip-pip-egg-info-hzx3o5e6/rnacounter.egg-info/PKG-INFO 2025-09-08T00:41:55,818 writing dependency_links to /tmp/pip-pip-egg-info-hzx3o5e6/rnacounter.egg-info/dependency_links.txt 2025-09-08T00:41:55,818 writing requirements to /tmp/pip-pip-egg-info-hzx3o5e6/rnacounter.egg-info/requires.txt 2025-09-08T00:41:55,818 writing top-level names to /tmp/pip-pip-egg-info-hzx3o5e6/rnacounter.egg-info/top_level.txt 2025-09-08T00:41:55,819 writing manifest file '/tmp/pip-pip-egg-info-hzx3o5e6/rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:41:56,191 reading manifest file '/tmp/pip-pip-egg-info-hzx3o5e6/rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:41:56,192 reading manifest template 'MANIFEST.in' 2025-09-08T00:41:56,196 writing manifest file '/tmp/pip-pip-egg-info-hzx3o5e6/rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:41:56,331 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T00:41:56,336 Source in /tmp/pip-wheel-_o2i4_xl/rnacounter_71dbdf9e5f1642f6a29a14bd42447274 has version 1.1.3.7, which satisfies requirement rnacounter==1.1.3.7 from https://files.pythonhosted.org/packages/b1/1c/9f8deaa78b994019b9024043168567099fe010c79018373e2f6ed60ea646/rnacounter-1.1.3.7.tar.gz 2025-09-08T00:41:56,336 Removed rnacounter==1.1.3.7 from https://files.pythonhosted.org/packages/b1/1c/9f8deaa78b994019b9024043168567099fe010c79018373e2f6ed60ea646/rnacounter-1.1.3.7.tar.gz from build tracker '/tmp/pip-build-tracker-824ib2pz' 2025-09-08T00:41:56,340 Created temporary directory: /tmp/pip-unpack-v5otgsso 2025-09-08T00:41:56,341 Created temporary directory: /tmp/pip-unpack-51642e9e 2025-09-08T00:41:56,341 Building wheels for collected packages: rnacounter 2025-09-08T00:41:56,342 Created temporary directory: /tmp/pip-wheel-mbc41qsg 2025-09-08T00:41:56,343 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 2025-09-08T00:41:56,344 Building wheel for rnacounter (setup.py): started 2025-09-08T00:41:56,344 Destination directory: /tmp/pip-wheel-mbc41qsg 2025-09-08T00:41:56,345 Running command python setup.py bdist_wheel 2025-09-08T00:41:57,238 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T00:41:57,239 warnings.warn(msg) 2025-09-08T00:41:57,632 running bdist_wheel 2025-09-08T00:41:58,000 running build 2025-09-08T00:41:58,000 running build_py 2025-09-08T00:41:58,078 creating build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:41:58,078 copying rnacounter/setup.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:41:58,079 copying rnacounter/main.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:41:58,080 copying rnacounter/__init__.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:41:58,080 running egg_info 2025-09-08T00:41:58,155 writing rnacounter.egg-info/PKG-INFO 2025-09-08T00:41:58,156 writing dependency_links to rnacounter.egg-info/dependency_links.txt 2025-09-08T00:41:58,157 writing requirements to rnacounter.egg-info/requires.txt 2025-09-08T00:41:58,157 writing top-level names to rnacounter.egg-info/top_level.txt 2025-09-08T00:41:58,233 reading manifest file 'rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:41:58,235 reading manifest template 'MANIFEST.in' 2025-09-08T00:41:58,240 writing manifest file 'rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:41:58,241 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'rnacounter.testfiles' is absent from the `packages` configuration. 2025-09-08T00:41:58,242 !! 2025-09-08T00:41:58,242 ******************************************************************************** 2025-09-08T00:41:58,242 ############################ 2025-09-08T00:41:58,242 # Package would be ignored # 2025-09-08T00:41:58,242 ############################ 2025-09-08T00:41:58,242 Python recognizes 'rnacounter.testfiles' as an importable package[^1], 2025-09-08T00:41:58,242 but it is absent from setuptools' `packages` configuration. 2025-09-08T00:41:58,242 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T00:41:58,243 package, please make sure that 'rnacounter.testfiles' is explicitly added 2025-09-08T00:41:58,243 to the `packages` configuration field. 2025-09-08T00:41:58,243 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T00:41:58,243 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T00:41:58,243 instead of `find_packages(...)`/`find:`). 2025-09-08T00:41:58,243 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T00:41:58,243 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T00:41:58,244 If you don't want 'rnacounter.testfiles' to be distributed and are 2025-09-08T00:41:58,244 already explicitly excluding 'rnacounter.testfiles' via 2025-09-08T00:41:58,244 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T00:41:58,244 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T00:41:58,244 combination with a more fine grained `package-data` configuration. 2025-09-08T00:41:58,244 You can read more about "package data files" on setuptools documentation page: 2025-09-08T00:41:58,244 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T00:41:58,244 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T00:41:58,245 even if it does not contain any `.py` files. 2025-09-08T00:41:58,245 On the other hand, currently there is no concept of package data 2025-09-08T00:41:58,245 directory, all directories are treated like packages. 2025-09-08T00:41:58,245 ******************************************************************************** 2025-09-08T00:41:58,245 !! 2025-09-08T00:41:58,245 check.warn(importable) 2025-09-08T00:41:58,245 copying rnacounter/rnacounter.c -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:41:58,249 creating build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:41:58,250 copying rnacounter/testfiles/gapdhKO.bam -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:41:58,251 copying rnacounter/testfiles/gapdhKO.bam.bai -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:41:58,251 copying rnacounter/testfiles/mm9_3genes_renamed.bed -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:41:58,252 copying rnacounter/testfiles/mm9_3genes_renamed.gtf -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:41:58,253 copying rnacounter/testfiles/mm9_Gapdh_renamed.gtf -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:41:58,253 running build_ext 2025-09-08T00:41:58,579 building 'rnacounter/rnacounter' extension 2025-09-08T00:41:58,580 creating build/temp.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:41:58,580 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 2025-09-08T00:41:59,004 rnacounter/rnacounter.c: In function ‘__Pyx_ListComp_Append’: 2025-09-08T00:41:59,004 rnacounter/rnacounter.c:1355:23: error: lvalue required as left operand of assignment 2025-09-08T00:41:59,005 1355 | Py_SIZE(list) = len+1; 2025-09-08T00:41:59,005 | ^ 2025-09-08T00:41:59,005 rnacounter/rnacounter.c: In function ‘__Pyx_PyList_Append’: 2025-09-08T00:41:59,006 rnacounter/rnacounter.c:1422:23: error: lvalue required as left operand of assignment 2025-09-08T00:41:59,006 1422 | Py_SIZE(list) = len+1; 2025-09-08T00:41:59,006 | ^ 2025-09-08T00:41:59,014 rnacounter/rnacounter.c: In function ‘__Pyx_PyList_Extend’: 2025-09-08T00:41:59,015 rnacounter/rnacounter.c:1479:22: error: implicit declaration of function ‘_PyList_Extend’; did you mean ‘PyList_Extend’? [-Wimplicit-function-declaration] 2025-09-08T00:41:59,015 1479 | PyObject* none = _PyList_Extend((PyListObject*)L, v); 2025-09-08T00:41:59,015 | ^~~~~~~~~~~~~~ 2025-09-08T00:41:59,015 | PyList_Extend 2025-09-08T00:41:59,015 rnacounter/rnacounter.c:1479:22: error: initialization of ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:41:59,074 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_2parse_bed’: 2025-09-08T00:41:59,078 rnacounter/rnacounter.c:4156:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:41:59,078 4156 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:41:59,078 | ^~ 2025-09-08T00:41:59,078 In file included from /usr/include/python3.13/Python.h:76, 2025-09-08T00:41:59,078 from rnacounter/rnacounter.c:16: 2025-09-08T00:41:59,078 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:41:59,079 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:41:59,079 | ^~~~~~~~~~~~~~~ 2025-09-08T00:41:59,124 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_4join’: 2025-09-08T00:41:59,129 rnacounter/rnacounter.c:5391:9: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:41:59,129 5391 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:41:59,129 | ^~ 2025-09-08T00:41:59,129 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:41:59,129 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:41:59,130 | ^~~~~~~~~~~~~~~ 2025-09-08T00:41:59,165 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_13GenomicObject_2__and__’: 2025-09-08T00:41:59,171 rnacounter/rnacounter.c:6551:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:41:59,171 6551 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:41:59,171 | ^~ 2025-09-08T00:41:59,171 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:41:59,172 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:41:59,172 | ^~~~~~~~~~~~~~~ 2025-09-08T00:42:00,067 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_14parse_args’: 2025-09-08T00:42:00,092 rnacounter/rnacounter.c:22043:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:00,092 22043 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:42:00,092 | ^~ 2025-09-08T00:42:00,092 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:42:00,092 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:42:00,092 | ^~~~~~~~~~~~~~~ 2025-09-08T00:42:00,119 rnacounter/rnacounter.c:22097:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:00,119 22097 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:42:00,119 | ^~ 2025-09-08T00:42:00,119 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:42:00,119 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:42:00,119 | ^~~~~~~~~~~~~~~ 2025-09-08T00:42:00,146 rnacounter/rnacounter.c:22192:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:00,147 22192 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:42:00,147 | ^~ 2025-09-08T00:42:00,147 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:42:00,147 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:42:00,147 | ^~~~~~~~~~~~~~~ 2025-09-08T00:42:00,173 rnacounter/rnacounter.c:22241:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:00,173 22241 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:42:00,173 | ^~ 2025-09-08T00:42:00,173 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:42:00,173 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:42:00,174 | ^~~~~~~~~~~~~~~ 2025-09-08T00:42:00,214 rnacounter/rnacounter.c:22377:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:00,215 22377 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:42:00,215 | ^~ 2025-09-08T00:42:00,215 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:42:00,215 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:42:00,215 | ^~~~~~~~~~~~~~~ 2025-09-08T00:42:00,270 rnacounter/rnacounter.c:22579:5: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:00,270 22579 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:42:00,270 | ^~ 2025-09-08T00:42:00,270 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:42:00,270 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:42:00,270 | ^~~~~~~~~~~~~~~ 2025-09-08T00:42:00,297 rnacounter/rnacounter.c:22644:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:00,297 22644 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:42:00,298 | ^~ 2025-09-08T00:42:00,298 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:42:00,298 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:42:00,298 | ^~~~~~~~~~~~~~~ 2025-09-08T00:42:00,342 rnacounter/rnacounter.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-08T00:42:00,380 rnacounter/rnacounter.c:23199:50: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-08T00:42:00,380 23199 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); 2025-09-08T00:42:00,380 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:00,380 | PyBUF_C_CONTIGUOUS 2025-09-08T00:42:00,382 rnacounter/rnacounter.c:23199:50: note: each undeclared identifier is reported only once for each function it appears in 2025-09-08T00:42:00,442 rnacounter/rnacounter.c:23239:50: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-08T00:42:00,442 23239 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); 2025-09-08T00:42:00,442 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:00,442 | PyBUF_F_CONTIGUOUS 2025-09-08T00:42:00,449 rnacounter/rnacounter.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-08T00:42:00,476 rnacounter/rnacounter.c:24245:29: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T00:42:00,477 24245 | if (unlikely(__pyx_v_descr->names == Py_None)) { 2025-09-08T00:42:00,477 | ^~ 2025-09-08T00:42:00,477 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:42:00,477 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:42:00,477 | ^ 2025-09-08T00:42:00,508 rnacounter/rnacounter.c:24249:28: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T00:42:00,508 24249 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; 2025-09-08T00:42:00,508 | ^~ 2025-09-08T00:42:00,542 rnacounter/rnacounter.c:24267:47: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-08T00:42:00,542 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;}; 2025-09-08T00:42:00,542 | ^~ 2025-09-08T00:42:00,591 rnacounter/rnacounter.c:24448:79: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’ 2025-09-08T00:42:00,591 24448 | (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); 2025-09-08T00:42:00,591 | ^~ 2025-09-08T00:42:00,639 rnacounter/rnacounter.c: In function ‘__pyx_tp_dealloc_10rnacounter_10rnacounter_Counter’: 2025-09-08T00:42:00,667 rnacounter/rnacounter.c:25069:75: error: implicit declaration of function ‘_PyGC_FINALIZED’ [-Wimplicit-function-declaration] 2025-09-08T00:42:00,667 25069 | if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { 2025-09-08T00:42:00,667 | ^~~~~~~~~~~~~~~ 2025-09-08T00:42:00,775 rnacounter/rnacounter.c: In function ‘__Pyx_InitCachedConstants’: 2025-09-08T00:42:00,808 rnacounter/rnacounter.c:28836:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:00,808 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;} 2025-09-08T00:42:00,808 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:00,808 In file included from /usr/include/python3.13/Python.h:101: 2025-09-08T00:42:00,808 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:00,808 213 | PyCode_New( 2025-09-08T00:42:00,809 | ^~~~~~~~~~ 2025-09-08T00:42:00,844 rnacounter/rnacounter.c:28836:243: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:42:00,844 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;} 2025-09-08T00:42:00,845 | ^~ 2025-09-08T00:42:00,845 | | 2025-09-08T00:42:00,845 | int 2025-09-08T00:42:00,845 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:00,845 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:00,845 | ^~~~~ 2025-09-08T00:42:00,845 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:42:00,845 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:00,845 | ~~~~~~~~~~^ 2025-09-08T00:42:00,880 rnacounter/rnacounter.c:28836:247: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:42:00,881 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;} 2025-09-08T00:42:00,881 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:00,881 | | 2025-09-08T00:42:00,881 | PyObject * {aka struct _object *} 2025-09-08T00:42:00,881 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:00,881 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:00,881 | ^~~~ 2025-09-08T00:42:00,881 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:42:00,881 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:00,882 | ~~~~^ 2025-09-08T00:42:00,916 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:42:00,917 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:00,917 | ^~~~~~~~~~ 2025-09-08T00:42:00,917 rnacounter/rnacounter.c:28836:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:00,917 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;} 2025-09-08T00:42:00,917 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:00,917 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:00,917 213 | PyCode_New( 2025-09-08T00:42:00,917 | ^~~~~~~~~~ 2025-09-08T00:42:00,949 rnacounter/rnacounter.c:28848:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:00,949 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;} 2025-09-08T00:42:00,949 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:00,950 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:00,950 213 | PyCode_New( 2025-09-08T00:42:00,950 | ^~~~~~~~~~ 2025-09-08T00:42:00,985 rnacounter/rnacounter.c:28848:244: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:42:00,985 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;} 2025-09-08T00:42:00,985 | ^~ 2025-09-08T00:42:00,986 | | 2025-09-08T00:42:00,986 | int 2025-09-08T00:42:00,986 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:00,986 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:00,986 | ^~~~~ 2025-09-08T00:42:00,986 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:42:00,986 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:00,986 | ~~~~~~~~~~^ 2025-09-08T00:42:01,021 rnacounter/rnacounter.c:28848:248: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:42:01,022 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;} 2025-09-08T00:42:01,022 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,022 | | 2025-09-08T00:42:01,022 | PyObject * {aka struct _object *} 2025-09-08T00:42:01,022 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,022 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,022 | ^~~~ 2025-09-08T00:42:01,022 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:42:01,022 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,022 | ~~~~^ 2025-09-08T00:42:01,057 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:42:01,058 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,058 | ^~~~~~~~~~ 2025-09-08T00:42:01,058 rnacounter/rnacounter.c:28848:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,058 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;} 2025-09-08T00:42:01,058 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,058 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,058 213 | PyCode_New( 2025-09-08T00:42:01,058 | ^~~~~~~~~~ 2025-09-08T00:42:01,090 rnacounter/rnacounter.c:28860:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:01,090 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;} 2025-09-08T00:42:01,090 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,091 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,091 213 | PyCode_New( 2025-09-08T00:42:01,091 | ^~~~~~~~~~ 2025-09-08T00:42:01,127 rnacounter/rnacounter.c:28860:239: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:42:01,127 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;} 2025-09-08T00:42:01,127 | ^~~ 2025-09-08T00:42:01,127 | | 2025-09-08T00:42:01,127 | int 2025-09-08T00:42:01,127 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,127 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,127 | ^~~~~ 2025-09-08T00:42:01,127 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:42:01,127 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,128 | ~~~~~~~~~~^ 2025-09-08T00:42:01,165 rnacounter/rnacounter.c:28860:244: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:42:01,165 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;} 2025-09-08T00:42:01,165 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,166 | | 2025-09-08T00:42:01,166 | PyObject * {aka struct _object *} 2025-09-08T00:42:01,166 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,166 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,166 | ^~~~ 2025-09-08T00:42:01,166 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:42:01,166 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,166 | ~~~~^ 2025-09-08T00:42:01,205 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:42:01,205 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,205 | ^~~~~~~~~~ 2025-09-08T00:42:01,205 rnacounter/rnacounter.c:28860:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,205 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;} 2025-09-08T00:42:01,205 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,206 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,206 213 | PyCode_New( 2025-09-08T00:42:01,206 | ^~~~~~~~~~ 2025-09-08T00:42:01,241 rnacounter/rnacounter.c:28872:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:01,241 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;} 2025-09-08T00:42:01,241 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,241 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,241 213 | PyCode_New( 2025-09-08T00:42:01,241 | ^~~~~~~~~~ 2025-09-08T00:42:01,277 rnacounter/rnacounter.c:28872:248: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:42:01,277 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;} 2025-09-08T00:42:01,277 | ^~~ 2025-09-08T00:42:01,277 | | 2025-09-08T00:42:01,277 | int 2025-09-08T00:42:01,278 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,278 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,278 | ^~~~~ 2025-09-08T00:42:01,278 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:42:01,278 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,278 | ~~~~~~~~~~^ 2025-09-08T00:42:01,313 rnacounter/rnacounter.c:28872:253: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:42:01,313 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;} 2025-09-08T00:42:01,314 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,314 | | 2025-09-08T00:42:01,314 | PyObject * {aka struct _object *} 2025-09-08T00:42:01,314 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,314 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,314 | ^~~~ 2025-09-08T00:42:01,314 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:42:01,314 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,314 | ~~~~^ 2025-09-08T00:42:01,349 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:42:01,349 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,350 | ^~~~~~~~~~ 2025-09-08T00:42:01,350 rnacounter/rnacounter.c:28872:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,350 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;} 2025-09-08T00:42:01,350 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,350 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,350 213 | PyCode_New( 2025-09-08T00:42:01,350 | ^~~~~~~~~~ 2025-09-08T00:42:01,382 rnacounter/rnacounter.c:28884:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:01,382 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;} 2025-09-08T00:42:01,382 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,382 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,383 213 | PyCode_New( 2025-09-08T00:42:01,383 | ^~~~~~~~~~ 2025-09-08T00:42:01,418 rnacounter/rnacounter.c:28884:247: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:42:01,418 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;} 2025-09-08T00:42:01,419 | ^~~ 2025-09-08T00:42:01,419 | | 2025-09-08T00:42:01,419 | int 2025-09-08T00:42:01,419 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,419 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,419 | ^~~~~ 2025-09-08T00:42:01,419 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:42:01,419 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,419 | ~~~~~~~~~~^ 2025-09-08T00:42:01,454 rnacounter/rnacounter.c:28884:252: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:42:01,455 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;} 2025-09-08T00:42:01,455 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,455 | | 2025-09-08T00:42:01,455 | PyObject * {aka struct _object *} 2025-09-08T00:42:01,455 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,455 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,455 | ^~~~ 2025-09-08T00:42:01,455 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:42:01,455 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,455 | ~~~~^ 2025-09-08T00:42:01,491 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:42:01,491 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,491 | ^~~~~~~~~~ 2025-09-08T00:42:01,491 rnacounter/rnacounter.c:28884:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,491 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;} 2025-09-08T00:42:01,491 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,491 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,491 213 | PyCode_New( 2025-09-08T00:42:01,491 | ^~~~~~~~~~ 2025-09-08T00:42:01,523 rnacounter/rnacounter.c:28896:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:01,524 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;} 2025-09-08T00:42:01,524 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,524 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,524 213 | PyCode_New( 2025-09-08T00:42:01,524 | ^~~~~~~~~~ 2025-09-08T00:42:01,560 rnacounter/rnacounter.c:28896:250: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:42:01,560 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;} 2025-09-08T00:42:01,560 | ^~~ 2025-09-08T00:42:01,560 | | 2025-09-08T00:42:01,560 | int 2025-09-08T00:42:01,560 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,560 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,560 | ^~~~~ 2025-09-08T00:42:01,560 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:42:01,560 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,561 | ~~~~~~~~~~^ 2025-09-08T00:42:01,596 rnacounter/rnacounter.c:28896:255: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:42:01,596 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;} 2025-09-08T00:42:01,596 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,596 | | 2025-09-08T00:42:01,596 | PyObject * {aka struct _object *} 2025-09-08T00:42:01,596 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,596 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,596 | ^~~~ 2025-09-08T00:42:01,597 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:42:01,597 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,597 | ~~~~^ 2025-09-08T00:42:01,632 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:42:01,632 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,632 | ^~~~~~~~~~ 2025-09-08T00:42:01,632 rnacounter/rnacounter.c:28896:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,632 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;} 2025-09-08T00:42:01,633 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,633 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,633 213 | PyCode_New( 2025-09-08T00:42:01,633 | ^~~~~~~~~~ 2025-09-08T00:42:01,665 rnacounter/rnacounter.c:28905:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:01,665 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;} 2025-09-08T00:42:01,665 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,665 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,665 213 | PyCode_New( 2025-09-08T00:42:01,665 | ^~~~~~~~~~ 2025-09-08T00:42:01,701 rnacounter/rnacounter.c:28905:248: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:42:01,701 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;} 2025-09-08T00:42:01,701 | ^~~ 2025-09-08T00:42:01,701 | | 2025-09-08T00:42:01,701 | int 2025-09-08T00:42:01,701 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,701 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,701 | ^~~~~ 2025-09-08T00:42:01,702 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:42:01,702 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,702 | ~~~~~~~~~~^ 2025-09-08T00:42:01,737 rnacounter/rnacounter.c:28905:253: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:42:01,737 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;} 2025-09-08T00:42:01,737 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,737 | | 2025-09-08T00:42:01,737 | PyObject * {aka struct _object *} 2025-09-08T00:42:01,737 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,738 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,738 | ^~~~ 2025-09-08T00:42:01,738 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:42:01,738 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,738 | ~~~~^ 2025-09-08T00:42:01,773 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:42:01,773 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,773 | ^~~~~~~~~~ 2025-09-08T00:42:01,774 rnacounter/rnacounter.c:28905:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,774 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;} 2025-09-08T00:42:01,774 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,774 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,774 213 | PyCode_New( 2025-09-08T00:42:01,774 | ^~~~~~~~~~ 2025-09-08T00:42:01,806 rnacounter/rnacounter.c:28917:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:01,806 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;} 2025-09-08T00:42:01,806 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,806 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,806 213 | PyCode_New( 2025-09-08T00:42:01,806 | ^~~~~~~~~~ 2025-09-08T00:42:01,842 rnacounter/rnacounter.c:28917:245: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:42:01,842 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;} 2025-09-08T00:42:01,842 | ^~~ 2025-09-08T00:42:01,843 | | 2025-09-08T00:42:01,843 | int 2025-09-08T00:42:01,843 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,843 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,843 | ^~~~~ 2025-09-08T00:42:01,843 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:42:01,843 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,843 | ~~~~~~~~~~^ 2025-09-08T00:42:01,878 rnacounter/rnacounter.c:28917:250: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:42:01,879 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;} 2025-09-08T00:42:01,879 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,879 | | 2025-09-08T00:42:01,879 | PyObject * {aka struct _object *} 2025-09-08T00:42:01,879 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,879 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,879 | ^~~~ 2025-09-08T00:42:01,879 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:42:01,879 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:01,879 | ~~~~^ 2025-09-08T00:42:01,915 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:42:01,915 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:01,915 | ^~~~~~~~~~ 2025-09-08T00:42:01,915 rnacounter/rnacounter.c:28917:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:01,915 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;} 2025-09-08T00:42:01,915 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:01,915 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:01,915 213 | PyCode_New( 2025-09-08T00:42:01,916 | ^~~~~~~~~~ 2025-09-08T00:42:01,918 rnacounter/rnacounter.c: In function ‘PyInit_rnacounter’: 2025-09-08T00:42:01,951 rnacounter/rnacounter.c:29020:47: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:01,951 29020 | __pyx_type_10rnacounter_10rnacounter_Counter.tp_print = 0; 2025-09-08T00:42:01,951 | ^ 2025-09-08T00:42:01,983 rnacounter/rnacounter.c:29024:53: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:01,984 29024 | __pyx_type_10rnacounter_10rnacounter_GenomicObject.tp_print = 0; 2025-09-08T00:42:01,984 | ^ 2025-09-08T00:42:02,017 rnacounter/rnacounter.c:29041:44: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,017 29041 | __pyx_type_10rnacounter_10rnacounter_Exon.tp_print = 0; 2025-09-08T00:42:02,017 | ^ 2025-09-08T00:42:02,050 rnacounter/rnacounter.c:29047:50: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,050 29047 | __pyx_type_10rnacounter_10rnacounter_Transcript.tp_print = 0; 2025-09-08T00:42:02,050 | ^ 2025-09-08T00:42:02,083 rnacounter/rnacounter.c:29052:44: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,083 29052 | __pyx_type_10rnacounter_10rnacounter_Gene.tp_print = 0; 2025-09-08T00:42:02,083 | ^ 2025-09-08T00:42:02,116 rnacounter/rnacounter.c:29056:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,116 29056 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct__parse_gtf.tp_print = 0; 2025-09-08T00:42:02,116 | ^ 2025-09-08T00:42:02,149 rnacounter/rnacounter.c:29059:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,149 29059 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_1_genexpr.tp_print = 0; 2025-09-08T00:42:02,149 | ^ 2025-09-08T00:42:02,181 rnacounter/rnacounter.c:29062:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,182 29062 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_2_genexpr.tp_print = 0; 2025-09-08T00:42:02,182 | ^ 2025-09-08T00:42:02,215 rnacounter/rnacounter.c:29065:65: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,215 29065 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_3_join.tp_print = 0; 2025-09-08T00:42:02,215 | ^ 2025-09-08T00:42:02,247 rnacounter/rnacounter.c:29068:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,248 29068 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_4_genexpr.tp_print = 0; 2025-09-08T00:42:02,248 | ^ 2025-09-08T00:42:02,280 rnacounter/rnacounter.c:29071:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,281 29071 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_5_genexpr.tp_print = 0; 2025-09-08T00:42:02,281 | ^ 2025-09-08T00:42:02,313 rnacounter/rnacounter.c:29074:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,314 29074 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_6_genexpr.tp_print = 0; 2025-09-08T00:42:02,314 | ^ 2025-09-08T00:42:02,348 rnacounter/rnacounter.c:29077:74: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,348 29077 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk.tp_print = 0; 2025-09-08T00:42:02,349 | ^ 2025-09-08T00:42:02,382 rnacounter/rnacounter.c:29080:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,382 29080 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr.tp_print = 0; 2025-09-08T00:42:02,382 | ^ 2025-09-08T00:42:02,417 rnacounter/rnacounter.c:29083:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,417 29083 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr.tp_print = 0; 2025-09-08T00:42:02,417 | ^ 2025-09-08T00:42:02,452 rnacounter/rnacounter.c:29086:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,452 29086 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr.tp_print = 0; 2025-09-08T00:42:02,453 | ^ 2025-09-08T00:42:02,485 rnacounter/rnacounter.c:29089:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,485 29089 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_11_genexpr.tp_print = 0; 2025-09-08T00:42:02,485 | ^ 2025-09-08T00:42:02,518 rnacounter/rnacounter.c:29092:74: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,518 29092 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_12_print_output.tp_print = 0; 2025-09-08T00:42:02,518 | ^ 2025-09-08T00:42:02,551 rnacounter/rnacounter.c:29095:72: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,551 29095 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_13_parse_args.tp_print = 0; 2025-09-08T00:42:02,551 | ^ 2025-09-08T00:42:02,584 rnacounter/rnacounter.c:29098:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,584 29098 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr.tp_print = 0; 2025-09-08T00:42:02,584 | ^ 2025-09-08T00:42:02,617 rnacounter/rnacounter.c:29101:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,617 29101 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_15_genexpr.tp_print = 0; 2025-09-08T00:42:02,617 | ^ 2025-09-08T00:42:02,650 rnacounter/rnacounter.c:29104:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:42:02,650 29104 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_16_genexpr.tp_print = 0; 2025-09-08T00:42:02,650 | ^ 2025-09-08T00:42:02,704 rnacounter/rnacounter.c: In function ‘__Pyx_PyUnicode_Equals’: 2025-09-08T00:42:02,741 rnacounter/rnacounter.c:84:51: error: implicit declaration of function ‘_PyUnicode_Ready’; did you mean ‘PyUnicode_READY’? [-Wimplicit-function-declaration] 2025-09-08T00:42:02,742 84 | 0 : _PyUnicode_Ready((PyObject *)(op))) 2025-09-08T00:42:02,742 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:02,742 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:42:02,742 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:42:02,742 | ^ 2025-09-08T00:42:02,742 rnacounter/rnacounter.c:29616:22: note: in expansion of macro ‘__Pyx_PyUnicode_READY’ 2025-09-08T00:42:02,742 29616 | if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) 2025-09-08T00:42:02,742 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-08T00:42:02,790 rnacounter/rnacounter.c: In function ‘__Pyx_ErrRestore’: 2025-09-08T00:42:02,824 rnacounter/rnacounter.c:29708:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:42:02,824 29708 | tmp_type = tstate->curexc_type; 2025-09-08T00:42:02,824 | ^~ 2025-09-08T00:42:02,858 rnacounter/rnacounter.c:29709:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:42:02,858 29709 | tmp_value = tstate->curexc_value; 2025-09-08T00:42:02,858 | ^~ 2025-09-08T00:42:02,892 rnacounter/rnacounter.c:29710:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:42:02,892 29710 | tmp_tb = tstate->curexc_traceback; 2025-09-08T00:42:02,892 | ^~ 2025-09-08T00:42:02,926 rnacounter/rnacounter.c:29711:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:42:02,926 29711 | tstate->curexc_type = type; 2025-09-08T00:42:02,926 | ^~ 2025-09-08T00:42:02,960 rnacounter/rnacounter.c:29712:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:42:02,960 29712 | tstate->curexc_value = value; 2025-09-08T00:42:02,960 | ^~ 2025-09-08T00:42:02,994 rnacounter/rnacounter.c:29713:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:42:02,994 29713 | tstate->curexc_traceback = tb; 2025-09-08T00:42:02,994 | ^~ 2025-09-08T00:42:02,994 rnacounter/rnacounter.c: In function ‘__Pyx_ErrFetch’: 2025-09-08T00:42:03,028 rnacounter/rnacounter.c:29724:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:42:03,028 29724 | *type = tstate->curexc_type; 2025-09-08T00:42:03,028 | ^~ 2025-09-08T00:42:03,062 rnacounter/rnacounter.c:29725:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:42:03,062 29725 | *value = tstate->curexc_value; 2025-09-08T00:42:03,062 | ^~ 2025-09-08T00:42:03,096 rnacounter/rnacounter.c:29726:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:42:03,096 29726 | *tb = tstate->curexc_traceback; 2025-09-08T00:42:03,096 | ^~ 2025-09-08T00:42:03,130 rnacounter/rnacounter.c:29727:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:42:03,130 29727 | tstate->curexc_type = 0; 2025-09-08T00:42:03,130 | ^~ 2025-09-08T00:42:03,164 rnacounter/rnacounter.c:29728:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:42:03,164 29728 | tstate->curexc_value = 0; 2025-09-08T00:42:03,164 | ^~ 2025-09-08T00:42:03,198 rnacounter/rnacounter.c:29729:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:42:03,198 29729 | tstate->curexc_traceback = 0; 2025-09-08T00:42:03,198 | ^~ 2025-09-08T00:42:03,265 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionSave’: 2025-09-08T00:42:03,314 rnacounter/rnacounter.c:29926:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:42:03,314 29926 | *type = tstate->exc_type; 2025-09-08T00:42:03,314 | ^~~~~~~~ 2025-09-08T00:42:03,314 | exc_state 2025-09-08T00:42:03,347 rnacounter/rnacounter.c:29927:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:42:03,348 29927 | *value = tstate->exc_value; 2025-09-08T00:42:03,348 | ^~ 2025-09-08T00:42:03,381 rnacounter/rnacounter.c:29928:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:42:03,381 29928 | *tb = tstate->exc_traceback; 2025-09-08T00:42:03,381 | ^~ 2025-09-08T00:42:03,382 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionReset’: 2025-09-08T00:42:03,430 rnacounter/rnacounter.c:29940:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:42:03,430 29940 | tmp_type = tstate->exc_type; 2025-09-08T00:42:03,430 | ^~~~~~~~ 2025-09-08T00:42:03,430 | exc_state 2025-09-08T00:42:03,464 rnacounter/rnacounter.c:29941:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:42:03,464 29941 | tmp_value = tstate->exc_value; 2025-09-08T00:42:03,464 | ^~ 2025-09-08T00:42:03,497 rnacounter/rnacounter.c:29942:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:42:03,497 29942 | tmp_tb = tstate->exc_traceback; 2025-09-08T00:42:03,498 | ^~ 2025-09-08T00:42:03,546 rnacounter/rnacounter.c:29943:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:42:03,546 29943 | tstate->exc_type = type; 2025-09-08T00:42:03,546 | ^~~~~~~~ 2025-09-08T00:42:03,546 | exc_state 2025-09-08T00:42:03,579 rnacounter/rnacounter.c:29944:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:42:03,580 29944 | tstate->exc_value = value; 2025-09-08T00:42:03,580 | ^~ 2025-09-08T00:42:03,613 rnacounter/rnacounter.c:29945:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:42:03,613 29945 | tstate->exc_traceback = tb; 2025-09-08T00:42:03,613 | ^~ 2025-09-08T00:42:03,614 rnacounter/rnacounter.c: In function ‘__Pyx_GetException’: 2025-09-08T00:42:03,647 rnacounter/rnacounter.c:29959:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:42:03,647 29959 | local_type = tstate->curexc_type; 2025-09-08T00:42:03,647 | ^~ 2025-09-08T00:42:03,681 rnacounter/rnacounter.c:29960:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:42:03,681 29960 | local_value = tstate->curexc_value; 2025-09-08T00:42:03,681 | ^~ 2025-09-08T00:42:03,715 rnacounter/rnacounter.c:29961:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:42:03,715 29961 | local_tb = tstate->curexc_traceback; 2025-09-08T00:42:03,715 | ^~ 2025-09-08T00:42:03,748 rnacounter/rnacounter.c:29962:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:42:03,749 29962 | tstate->curexc_type = 0; 2025-09-08T00:42:03,749 | ^~ 2025-09-08T00:42:03,782 rnacounter/rnacounter.c:29963:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:42:03,782 29963 | tstate->curexc_value = 0; 2025-09-08T00:42:03,782 | ^~ 2025-09-08T00:42:03,816 rnacounter/rnacounter.c:29964:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:42:03,816 29964 | tstate->curexc_traceback = 0; 2025-09-08T00:42:03,816 | ^~ 2025-09-08T00:42:03,850 rnacounter/rnacounter.c:29970:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:42:03,850 29970 | if (unlikely(tstate->curexc_type)) 2025-09-08T00:42:03,850 | ^~ 2025-09-08T00:42:03,850 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:42:03,850 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:42:03,850 | ^ 2025-09-08T00:42:03,910 rnacounter/rnacounter.c:29988:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:42:03,911 29988 | tmp_type = tstate->exc_type; 2025-09-08T00:42:03,911 | ^~~~~~~~ 2025-09-08T00:42:03,911 | exc_state 2025-09-08T00:42:03,944 rnacounter/rnacounter.c:29989:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:42:03,944 29989 | tmp_value = tstate->exc_value; 2025-09-08T00:42:03,944 | ^~ 2025-09-08T00:42:03,978 rnacounter/rnacounter.c:29990:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:42:03,978 29990 | tmp_tb = tstate->exc_traceback; 2025-09-08T00:42:03,978 | ^~ 2025-09-08T00:42:04,026 rnacounter/rnacounter.c:29991:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:42:04,027 29991 | tstate->exc_type = local_type; 2025-09-08T00:42:04,027 | ^~~~~~~~ 2025-09-08T00:42:04,027 | exc_state 2025-09-08T00:42:04,060 rnacounter/rnacounter.c:29992:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:42:04,060 29992 | tstate->exc_value = local_value; 2025-09-08T00:42:04,060 | ^~ 2025-09-08T00:42:04,094 rnacounter/rnacounter.c:29993:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:42:04,094 29993 | tstate->exc_traceback = local_tb; 2025-09-08T00:42:04,094 | ^~ 2025-09-08T00:42:04,121 rnacounter/rnacounter.c: In function ‘__Pyx_ParseOptionalKeywords’: 2025-09-08T00:42:04,170 rnacounter/rnacounter.c:30097:22: error: implicit declaration of function ‘PyUnicode_GET_SIZE’; did you mean ‘PyDict_GET_SIZE’? [-Wimplicit-function-declaration] 2025-09-08T00:42:04,170 30097 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-08T00:42:04,170 | ^~~~~~~~~~~~~~~~~~ 2025-09-08T00:42:04,171 | PyDict_GET_SIZE 2025-09-08T00:42:04,282 rnacounter/rnacounter.c: In function ‘__Pyx_Raise’: 2025-09-08T00:42:04,316 rnacounter/rnacounter.c:30323:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:42:04,316 30323 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-08T00:42:04,316 | ^~ 2025-09-08T00:42:04,351 rnacounter/rnacounter.c:30326:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:42:04,351 30326 | tstate->curexc_traceback = tb; 2025-09-08T00:42:04,351 | ^~ 2025-09-08T00:42:04,408 rnacounter/rnacounter.c: In function ‘__Pyx_PyIter_Next2’: 2025-09-08T00:42:04,443 rnacounter/rnacounter.c:30371:31: error: ‘_PyObject_NextNotImplemented’ undeclared (first use in this function); did you mean ‘PyObject_HashNotImplemented’? 2025-09-08T00:42:04,443 30371 | if (unlikely(iternext == &_PyObject_NextNotImplemented)) 2025-09-08T00:42:04,443 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T00:42:04,443 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:42:04,443 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:42:04,443 | ^ 2025-09-08T00:42:04,488 rnacounter/rnacounter.c: In function ‘__Pyx_IterFinish’: 2025-09-08T00:42:04,523 rnacounter/rnacounter.c:30574:32: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:42:04,523 30574 | PyObject* exc_type = tstate->curexc_type; 2025-09-08T00:42:04,523 | ^~ 2025-09-08T00:42:04,558 rnacounter/rnacounter.c:30578:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:42:04,558 30578 | exc_value = tstate->curexc_value; 2025-09-08T00:42:04,558 | ^~ 2025-09-08T00:42:04,593 rnacounter/rnacounter.c:30579:28: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:42:04,593 30579 | exc_tb = tstate->curexc_traceback; 2025-09-08T00:42:04,593 | ^~ 2025-09-08T00:42:04,627 rnacounter/rnacounter.c:30580:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:42:04,628 30580 | tstate->curexc_type = 0; 2025-09-08T00:42:04,628 | ^~ 2025-09-08T00:42:04,662 rnacounter/rnacounter.c:30581:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:42:04,662 30581 | tstate->curexc_value = 0; 2025-09-08T00:42:04,662 | ^~ 2025-09-08T00:42:04,697 rnacounter/rnacounter.c:30582:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:42:04,697 30582 | tstate->curexc_traceback = 0; 2025-09-08T00:42:04,697 | ^~ 2025-09-08T00:42:05,184 rnacounter/rnacounter.c: In function ‘__Pyx_CyFunction_Call’: 2025-09-08T00:42:05,237 rnacounter/rnacounter.c:31926:16: error: implicit declaration of function ‘PyCFunction_Call’; did you mean ‘PyCFunction_New’? [-Wimplicit-function-declaration] 2025-09-08T00:42:05,237 31926 | return PyCFunction_Call(func, arg, kw); 2025-09-08T00:42:05,237 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:05,237 | PyCFunction_New 2025-09-08T00:42:05,277 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] 2025-09-08T00:42:05,277 31926 | return PyCFunction_Call(func, arg, kw); 2025-09-08T00:42:05,277 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T00:42:05,296 rnacounter/rnacounter.c: In function ‘__Pyx_CyFunction_init’: 2025-09-08T00:42:05,348 rnacounter/rnacounter.c:31991:41: error: ‘PyCFunction_Call’ undeclared (first use in this function); did you mean ‘PyCFunction_New’? 2025-09-08T00:42:05,348 31991 | __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; 2025-09-08T00:42:05,348 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:05,348 | PyCFunction_New 2025-09-08T00:42:05,392 rnacounter/rnacounter.c: In function ‘__Pyx_CreateCodeObjectForTraceback’: 2025-09-08T00:42:05,428 rnacounter/rnacounter.c:32167:5: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:42:05,428 32167 | py_code = __Pyx_PyCode_New( 2025-09-08T00:42:05,428 | ^~~~~~~ 2025-09-08T00:42:05,428 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:05,429 213 | PyCode_New( 2025-09-08T00:42:05,429 | ^~~~~~~~~~ 2025-09-08T00:42:05,464 rnacounter/rnacounter.c:32181:9: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:42:05,464 32181 | py_line, 2025-09-08T00:42:05,465 | ^~~~~~~ 2025-09-08T00:42:05,465 | | 2025-09-08T00:42:05,465 | int 2025-09-08T00:42:05,465 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:05,465 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:05,465 | ^~~~~ 2025-09-08T00:42:05,465 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:42:05,465 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:05,465 | ~~~~~~~~~~^ 2025-09-08T00:42:05,505 rnacounter/rnacounter.c:32182:9: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:42:05,505 32182 | __pyx_empty_bytes /*PyObject *lnotab*/ 2025-09-08T00:42:05,505 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:42:05,505 | | 2025-09-08T00:42:05,505 | PyObject * {aka struct _object *} 2025-09-08T00:42:05,505 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:05,505 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:05,505 | ^~~~ 2025-09-08T00:42:05,506 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:42:05,506 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:42:05,506 | ~~~~^ 2025-09-08T00:42:05,545 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:42:05,545 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:42:05,545 | ^~~~~~~~~~ 2025-09-08T00:42:05,545 rnacounter/rnacounter.c:32167:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:42:05,546 32167 | py_code = __Pyx_PyCode_New( 2025-09-08T00:42:05,546 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:42:05,546 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:42:05,546 213 | PyCode_New( 2025-09-08T00:42:05,546 | ^~~~~~~~~~ 2025-09-08T00:42:05,562 rnacounter/rnacounter.c: In function ‘__Pyx_AddTraceback’: 2025-09-08T00:42:05,598 rnacounter/rnacounter.c:32210:13: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:42:05,598 32210 | py_frame->f_lineno = py_line; 2025-09-08T00:42:05,598 | ^~ 2025-09-08T00:42:05,600 rnacounter/rnacounter.c: In function ‘__Pyx_PyInt_As_int’: 2025-09-08T00:42:05,636 rnacounter/rnacounter.c:32331:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T00:42:05,636 32331 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T00:42:05,636 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:42:05,636 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-08T00:42:05,637 from /usr/include/python3.13/Python.h:81: 2025-09-08T00:42:05,637 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T00:42:05,637 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T00:42:05,637 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:42:05,682 rnacounter/rnacounter.c: In function ‘__Pyx_PyInt_As_long’: 2025-09-08T00:42:05,718 rnacounter/rnacounter.c:32786:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T00:42:05,718 32786 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T00:42:05,718 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:42:05,718 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T00:42:05,718 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T00:42:05,719 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:42:05,727 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionSwap’: 2025-09-08T00:42:05,781 rnacounter/rnacounter.c:32818:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:42:05,781 32818 | tmp_type = tstate->exc_type; 2025-09-08T00:42:05,782 | ^~~~~~~~ 2025-09-08T00:42:05,782 | exc_state 2025-09-08T00:42:05,819 rnacounter/rnacounter.c:32819:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:42:05,819 32819 | tmp_value = tstate->exc_value; 2025-09-08T00:42:05,819 | ^~ 2025-09-08T00:42:05,856 rnacounter/rnacounter.c:32820:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:42:05,856 32820 | tmp_tb = tstate->exc_traceback; 2025-09-08T00:42:05,856 | ^~ 2025-09-08T00:42:05,910 rnacounter/rnacounter.c:32821:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:42:05,910 32821 | tstate->exc_type = *type; 2025-09-08T00:42:05,910 | ^~~~~~~~ 2025-09-08T00:42:05,910 | exc_state 2025-09-08T00:42:05,947 rnacounter/rnacounter.c:32822:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:42:05,948 32822 | tstate->exc_value = *value; 2025-09-08T00:42:05,948 | ^~ 2025-09-08T00:42:05,985 rnacounter/rnacounter.c:32823:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:42:05,985 32823 | tstate->exc_traceback = *tb; 2025-09-08T00:42:05,985 | ^~ 2025-09-08T00:42:05,987 In file included from /usr/include/python3.13/Python.h:63: 2025-09-08T00:42:05,987 rnacounter/rnacounter.c: In function ‘__Pyx_Generator_SendEx’: 2025-09-08T00:42:06,065 rnacounter/rnacounter.c:32943:30: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T00:42:06,065 32943 | Py_XINCREF(tstate->frame); 2025-09-08T00:42:06,065 | ^~ 2025-09-08T00:42:06,065 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-08T00:42:06,065 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-08T00:42:06,065 | ^~~~ 2025-09-08T00:42:06,065 /usr/include/python3.13/object.h:1041:37: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-08T00:42:06,066 1041 | # define Py_XINCREF(op) Py_XINCREF(_PyObject_CAST(op)) 2025-09-08T00:42:06,066 | ^~~~~~~~~~~~~~ 2025-09-08T00:42:06,066 rnacounter/rnacounter.c:32943:13: note: in expansion of macro ‘Py_XINCREF’ 2025-09-08T00:42:06,066 32943 | Py_XINCREF(tstate->frame); 2025-09-08T00:42:06,066 | ^~~~~~~~~~ 2025-09-08T00:42:06,101 rnacounter/rnacounter.c:32945:14: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:42:06,101 32945 | f->f_back = tstate->frame; 2025-09-08T00:42:06,102 | ^~ 2025-09-08T00:42:06,142 rnacounter/rnacounter.c:32945:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T00:42:06,142 32945 | f->f_back = tstate->frame; 2025-09-08T00:42:06,142 | ^~ 2025-09-08T00:42:06,219 rnacounter/rnacounter.c:32964:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:42:06,219 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:42:06,219 | ^~ 2025-09-08T00:42:06,219 /usr/include/python3.13/pyport.h:558:39: note: in definition of macro ‘_Py_TYPEOF’ 2025-09-08T00:42:06,219 558 | # define _Py_TYPEOF(expr) __typeof__(expr) 2025-09-08T00:42:06,219 | ^~~~ 2025-09-08T00:42:06,219 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:42:06,220 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:42:06,220 | ^~~~~~~~ 2025-09-08T00:42:06,259 In file included from /usr/include/python3.13/Python.h:72: 2025-09-08T00:42:06,259 rnacounter/rnacounter.c:32964:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:42:06,260 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:42:06,260 | ^~ 2025-09-08T00:42:06,260 /usr/include/python3.13/object.h:1012:41: note: in definition of macro ‘Py_CLEAR’ 2025-09-08T00:42:06,260 1012 | _Py_TYPEOF(op)* _tmp_op_ptr = &(op); \ 2025-09-08T00:42:06,260 | ^~ 2025-09-08T00:42:06,340 rnacounter/rnacounter.c:32964:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:42:06,340 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:42:06,340 | ^~ 2025-09-08T00:42:06,340 /usr/include/python3.13/pyport.h:558:39: note: in definition of macro ‘_Py_TYPEOF’ 2025-09-08T00:42:06,340 558 | # define _Py_TYPEOF(expr) __typeof__(expr) 2025-09-08T00:42:06,341 | ^~~~ 2025-09-08T00:42:06,341 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:42:06,341 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:42:06,341 | ^~~~~~~~ 2025-09-08T00:42:06,380 /usr/include/python3.13/object.h:1014:25: warning: comparison between pointer and integer 2025-09-08T00:42:06,381 1014 | if (_tmp_old_op != NULL) { \ 2025-09-08T00:42:06,381 | ^~ 2025-09-08T00:42:06,381 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:42:06,381 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:42:06,381 | ^~~~~~~~ 2025-09-08T00:42:06,421 /usr/include/python3.13/object.h:1015:26: error: assignment to ‘int’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:42:06,421 1015 | *_tmp_op_ptr = _Py_NULL; \ 2025-09-08T00:42:06,421 | ^ 2025-09-08T00:42:06,421 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:42:06,421 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:42:06,422 | ^~~~~~~~ 2025-09-08T00:42:07,011 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T00:42:07,180 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T00:42:07,192 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T00:42:07,192 exec(compile('"'"''"'"''"'"' 2025-09-08T00:42:07,192 # This is -- a caller that pip uses to run setup.py 2025-09-08T00:42:07,192 # 2025-09-08T00:42:07,192 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T00:42:07,192 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T00:42:07,192 # - It provides a clear error message when setuptools is not installed. 2025-09-08T00:42:07,192 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T00:42:07,192 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T00:42:07,192 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T00:42:07,192 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T00:42:07,192 import os, sys, tokenize, traceback 2025-09-08T00:42:07,192 2025-09-08T00:42:07,192 try: 2025-09-08T00:42:07,192 import setuptools 2025-09-08T00:42:07,192 except ImportError: 2025-09-08T00:42:07,192 print( 2025-09-08T00:42:07,192 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T00:42:07,192 "the build environment with exception:", 2025-09-08T00:42:07,192 file=sys.stderr, 2025-09-08T00:42:07,192 ) 2025-09-08T00:42:07,192 traceback.print_exc() 2025-09-08T00:42:07,192 sys.exit(1) 2025-09-08T00:42:07,192 2025-09-08T00:42:07,192 __file__ = %r 2025-09-08T00:42:07,192 sys.argv[0] = __file__ 2025-09-08T00:42:07,192 2025-09-08T00:42:07,192 if os.path.exists(__file__): 2025-09-08T00:42:07,192 filename = __file__ 2025-09-08T00:42:07,192 with tokenize.open(__file__) as f: 2025-09-08T00:42:07,192 setup_py_code = f.read() 2025-09-08T00:42:07,192 else: 2025-09-08T00:42:07,192 filename = "" 2025-09-08T00:42:07,192 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T00:42:07,192 2025-09-08T00:42:07,192 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T00:42:07,192 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-_o2i4_xl/rnacounter_71dbdf9e5f1642f6a29a14bd42447274/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-mbc41qsg[/] 2025-09-08T00:42:07,192 [bold magenta]cwd[/]: /tmp/pip-wheel-_o2i4_xl/rnacounter_71dbdf9e5f1642f6a29a14bd42447274/ 2025-09-08T00:42:07,193 Building wheel for rnacounter (setup.py): finished with status 'error' 2025-09-08T00:42:07,193 ERROR: Failed building wheel for rnacounter 2025-09-08T00:42:07,194 Running setup.py clean for rnacounter 2025-09-08T00:42:07,195 Running command python setup.py clean 2025-09-08T00:42:08,076 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T00:42:08,076 warnings.warn(msg) 2025-09-08T00:42:08,551 running clean 2025-09-08T00:42:08,696 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T00:42:08,696 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T00:42:08,698 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T00:42:08,698 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T00:42:08,698 removing 'build' 2025-09-08T00:42:08,833 Failed to build rnacounter 2025-09-08T00:42:08,834 ERROR: Failed to build one or more wheels 2025-09-08T00:42:08,834 Exception information: 2025-09-08T00:42:08,834 Traceback (most recent call last): 2025-09-08T00:42:08,834 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T00:42:08,834 status = _inner_run() 2025-09-08T00:42:08,834 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T00:42:08,834 return self.run(options, args) 2025-09-08T00:42:08,834 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T00:42:08,834 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T00:42:08,834 return func(self, options, args) 2025-09-08T00:42:08,834 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T00:42:08,834 raise CommandError("Failed to build one or more wheels") 2025-09-08T00:42:08,834 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T00:42:08,839 Removed build tracker: '/tmp/pip-build-tracker-824ib2pz'