2025-09-08T01:08:11,746 Created temporary directory: /tmp/pip-build-tracker-53okysio 2025-09-08T01:08:11,747 Initialized build tracking at /tmp/pip-build-tracker-53okysio 2025-09-08T01:08:11,747 Created build tracker: /tmp/pip-build-tracker-53okysio 2025-09-08T01:08:11,747 Entered build tracker: /tmp/pip-build-tracker-53okysio 2025-09-08T01:08:11,747 Created temporary directory: /tmp/pip-wheel-s93cclxi 2025-09-08T01:08:11,750 Created temporary directory: /tmp/pip-ephem-wheel-cache-iu71l000 2025-09-08T01:08:11,806 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T01:08:11,808 2 location(s) to search for versions of rnacounter: 2025-09-08T01:08:11,808 * https://pypi.org/simple/rnacounter/ 2025-09-08T01:08:11,808 * https://www.piwheels.org/simple/rnacounter/ 2025-09-08T01:08:11,808 Fetching project page and analyzing links: https://pypi.org/simple/rnacounter/ 2025-09-08T01:08:11,809 Getting page https://pypi.org/simple/rnacounter/ 2025-09-08T01:08:11,810 Found index url https://pypi.org/simple/ 2025-09-08T01:08:11,879 Fetched page https://pypi.org/simple/rnacounter/ as application/vnd.pypi.simple.v1+json 2025-09-08T01:08:11,882 Found link https://files.pythonhosted.org/packages/8f/49/762bb78c6a1215e30ccd9702444375015a50b14847266db0c2f11219e78f/rnacounter-1.1.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.2 2025-09-08T01:08:11,882 Found link https://files.pythonhosted.org/packages/04/c4/e2924af98cbf63c98cc5a9d210c3c54d959cf961fba4df5da3972afc84ae/rnacounter-1.1.3.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.1 2025-09-08T01:08:11,882 Found link https://files.pythonhosted.org/packages/39/70/41efc4ca6703ffdbdbab1dcd66976ed9a30c363b6f5ba417501e2dd9fb00/rnacounter-1.1.3.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.2 2025-09-08T01:08:11,883 Found link https://files.pythonhosted.org/packages/b1/1c/9f8deaa78b994019b9024043168567099fe010c79018373e2f6ed60ea646/rnacounter-1.1.3.7.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.7 2025-09-08T01:08:11,883 Found link https://files.pythonhosted.org/packages/14/a1/be9b12f40d130b182ed0d5d01b36f76e6089805a5c945d77941f5eb0928e/rnacounter-1.1.3.10.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.10 2025-09-08T01:08:11,883 Found link https://files.pythonhosted.org/packages/8a/5e/1b112fc6343bf52ace3a9afaa30eabaf4338afadabf1fb97454a7556b835/rnacounter-1.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.2 2025-09-08T01:08:11,883 Found link https://files.pythonhosted.org/packages/05/7d/42ecc29d98f52b77953a55da4836d36d534b317b4d66af971c9008804b61/rnacounter-1.2.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.2.1 2025-09-08T01:08:11,883 Found link https://files.pythonhosted.org/packages/dd/92/d53ee16c942fb78a312c03b22b0ddc08eb00ae4627f9125415a2c650b674/rnacounter-1.3.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.3 2025-09-08T01:08:11,884 Found link https://files.pythonhosted.org/packages/49/18/a50e0e2b164272f6d13f458b43d6851766cf121b5672de12078df2bb953a/rnacounter-1.3.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.3.1 2025-09-08T01:08:11,884 Found link https://files.pythonhosted.org/packages/ab/bf/54a012d6660528530b8404401bf494bda91947e38aae0d45ba4d721de6d4/rnacounter-1.4.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4 2025-09-08T01:08:11,884 Found link https://files.pythonhosted.org/packages/84/c0/8f274da33c177f6a7c6d8632d9e99413c83e6ec688825677acace41cfdb1/rnacounter-1.4.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4.1 2025-09-08T01:08:11,884 Found link https://files.pythonhosted.org/packages/45/3a/3cc530b864e9fbd87542c73df418d091aeaeb7b73863fb206e62494d988e/rnacounter-1.4.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4.2 2025-09-08T01:08:11,884 Found link https://files.pythonhosted.org/packages/46/ee/29eed438b10276db92163dff3d25bcb91f3f9e99d9a629c35ddb97f27f4d/rnacounter-1.5.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.5 2025-09-08T01:08:11,885 Found link https://files.pythonhosted.org/packages/a2/ea/657e7b7aa7d777173695606509933b52d794b7dbb79501a87bfea2fb511f/rnacounter-1.5.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.5.2 2025-09-08T01:08:11,885 Fetching project page and analyzing links: https://www.piwheels.org/simple/rnacounter/ 2025-09-08T01:08:11,885 Getting page https://www.piwheels.org/simple/rnacounter/ 2025-09-08T01:08:11,886 Found index url https://www.piwheels.org/simple/ 2025-09-08T01:08:11,976 Fetched page https://www.piwheels.org/simple/rnacounter/ as text/html 2025-09-08T01:08:11,987 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp35-cp35m-linux_armv7l.whl#sha256=1720939a09d8fbca466729cc4db98be3526fe7a3283ce22ef5c5a21d204a6161 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,988 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp35-cp35m-linux_armv6l.whl#sha256=1720939a09d8fbca466729cc4db98be3526fe7a3283ce22ef5c5a21d204a6161 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,988 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp34-cp34m-linux_armv7l.whl#sha256=e384cbf3852a44dffbf3a6887901acb36b9b30bd5c7e1a3585b2fe39d868d67a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,988 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp34-cp34m-linux_armv6l.whl#sha256=e384cbf3852a44dffbf3a6887901acb36b9b30bd5c7e1a3585b2fe39d868d67a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,988 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp35-cp35m-linux_armv7l.whl#sha256=02c416ec8854b92c815224212889f47dbd376e9797f66a0fb19531508b6bc793 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,988 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp35-cp35m-linux_armv6l.whl#sha256=02c416ec8854b92c815224212889f47dbd376e9797f66a0fb19531508b6bc793 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,988 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp34-cp34m-linux_armv7l.whl#sha256=ee88d3438f69ffa3b1868868fce8191565f303aee8dd3ff0f34c3a62886a495c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,989 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp34-cp34m-linux_armv6l.whl#sha256=ee88d3438f69ffa3b1868868fce8191565f303aee8dd3ff0f34c3a62886a495c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,989 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp34-cp34m-linux_armv7l.whl#sha256=078f497ded7b5492884f2136fa32e9948422bd185ba0345389b2b0d9fa7ab06e (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,989 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp34-cp34m-linux_armv6l.whl#sha256=078f497ded7b5492884f2136fa32e9948422bd185ba0345389b2b0d9fa7ab06e (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,989 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp35-cp35m-linux_armv6l.whl#sha256=8dffc574db1608136d619621a8809fb0e4d5d3f830e30f94cc2567f4b0a72c55 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,989 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp35-cp35m-linux_armv7l.whl#sha256=8dffc574db1608136d619621a8809fb0e4d5d3f830e30f94cc2567f4b0a72c55 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,989 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.1-cp35-cp35m-linux_armv7l.whl#sha256=35acff814eef7a87f368a8ed7c27f0be20add0cd4a9b4aa8ca756d84f216f218 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,989 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.1-cp35-cp35m-linux_armv6l.whl#sha256=35acff814eef7a87f368a8ed7c27f0be20add0cd4a9b4aa8ca756d84f216f218 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,990 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.1-cp34-cp34m-linux_armv7l.whl#sha256=627ec3e6dccdbc30b6697dd277204e300f58ecc971782b1231b09d84a4c1ef94 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,990 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.1-cp34-cp34m-linux_armv6l.whl#sha256=627ec3e6dccdbc30b6697dd277204e300f58ecc971782b1231b09d84a4c1ef94 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,990 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp34-cp34m-linux_armv7l.whl#sha256=9213623d552d14ff1971589aae10e5f886bcfb42045418cc5871a76607eb25b7 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,990 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp34-cp34m-linux_armv6l.whl#sha256=9213623d552d14ff1971589aae10e5f886bcfb42045418cc5871a76607eb25b7 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,990 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp35-cp35m-linux_armv6l.whl#sha256=14bd0bb3f4379d3d334abacfbbbf7ed43ad60736fa69f394c1eda0385dac9193 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,990 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp35-cp35m-linux_armv7l.whl#sha256=14bd0bb3f4379d3d334abacfbbbf7ed43ad60736fa69f394c1eda0385dac9193 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,991 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3.1-cp35-cp35m-linux_armv6l.whl#sha256=a5e2657cda5fa5a9283a186329fadd8db71987a54d71f713970a85b732030278 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,991 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3.1-cp35-cp35m-linux_armv7l.whl#sha256=a5e2657cda5fa5a9283a186329fadd8db71987a54d71f713970a85b732030278 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,991 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp35-cp35m-linux_armv6l.whl#sha256=b0a053ced5ce83115199785a117fc7820b20daffef5c19acafc83d0425aca0e1 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,991 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp35-cp35m-linux_armv7l.whl#sha256=b0a053ced5ce83115199785a117fc7820b20daffef5c19acafc83d0425aca0e1 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,991 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp34-cp34m-linux_armv7l.whl#sha256=7d3a7695b9d615f45d66d1d00f595ec7b65bbc53dc4ef98292fe909a75adf063 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,991 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp34-cp34m-linux_armv6l.whl#sha256=7d3a7695b9d615f45d66d1d00f595ec7b65bbc53dc4ef98292fe909a75adf063 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,991 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp35-cp35m-linux_armv7l.whl#sha256=b963649459fb2ab742b717d9b68c590d8ce6333d770e20648104b1e30b3ea97c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,992 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp35-cp35m-linux_armv6l.whl#sha256=b963649459fb2ab742b717d9b68c590d8ce6333d770e20648104b1e30b3ea97c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,992 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp34-cp34m-linux_armv7l.whl#sha256=2179418dc1805676ef1838a927c0bbcc2a131b63bd87636aecec3fa865b161d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,992 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp34-cp34m-linux_armv6l.whl#sha256=2179418dc1805676ef1838a927c0bbcc2a131b63bd87636aecec3fa865b161d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,992 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2-cp34-cp34m-linux_armv7l.whl#sha256=8ed62342f5d7481f7393010ff34b0286db7f26ea914710a1f81e583b478bb68a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,992 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2-cp34-cp34m-linux_armv6l.whl#sha256=8ed62342f5d7481f7393010ff34b0286db7f26ea914710a1f81e583b478bb68a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,992 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2-cp35-cp35m-linux_armv7l.whl#sha256=6271c54eb4c54d72f9499294fc50f1644dbd248414d993f053106a876d2e9400 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,992 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2-cp35-cp35m-linux_armv6l.whl#sha256=6271c54eb4c54d72f9499294fc50f1644dbd248414d993f053106a876d2e9400 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,993 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/) 2025-09-08T01:08:11,993 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/) 2025-09-08T01:08:11,993 Skipping link: No binaries permitted for rnacounter: 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https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.7-cp35-cp35m-linux_armv6l.whl#sha256=8863095125d87f061f7651061bc503fbb2c1c613417b578294b555b7bcbdeeba (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,993 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.7-cp34-cp34m-linux_armv7l.whl#sha256=368b4bcbb3bbab49c3600537626272135f936e694d4d17911afd7d83cdb31ee6 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,994 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.7-cp34-cp34m-linux_armv6l.whl#sha256=368b4bcbb3bbab49c3600537626272135f936e694d4d17911afd7d83cdb31ee6 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,994 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp34-cp34m-linux_armv7l.whl#sha256=fb039ca19afdc360ee5843812cf53fbca3ac952fe26a759e4c3700f3b460fc48 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,994 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp34-cp34m-linux_armv6l.whl#sha256=fb039ca19afdc360ee5843812cf53fbca3ac952fe26a759e4c3700f3b460fc48 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,994 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp35-cp35m-linux_armv7l.whl#sha256=51ed8c80ea67e82dc8bdaf5636d930011f8ce97bd9cc30432eedabb4dc8c9c95 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,994 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp35-cp35m-linux_armv6l.whl#sha256=51ed8c80ea67e82dc8bdaf5636d930011f8ce97bd9cc30432eedabb4dc8c9c95 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,994 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp35-cp35m-linux_armv7l.whl#sha256=534e0f91ccc8a7b74d0e8966764195b4b7e008408e132f2714d3790552ffae89 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,994 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp35-cp35m-linux_armv6l.whl#sha256=534e0f91ccc8a7b74d0e8966764195b4b7e008408e132f2714d3790552ffae89 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,995 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp34-cp34m-linux_armv7l.whl#sha256=699103109ceb69845e93941543cff532f3d26934d4a5ceb71af07f8f0c972407 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,995 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp34-cp34m-linux_armv6l.whl#sha256=699103109ceb69845e93941543cff532f3d26934d4a5ceb71af07f8f0c972407 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,995 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp34-cp34m-linux_armv7l.whl#sha256=e9936c67b8b3ee724e15ef197fef27eb2f5516ba9e9681ca399c5914b4fa01d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,995 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp34-cp34m-linux_armv6l.whl#sha256=e9936c67b8b3ee724e15ef197fef27eb2f5516ba9e9681ca399c5914b4fa01d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,995 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp35-cp35m-linux_armv6l.whl#sha256=edb76e1344212be1373b20323904b92e0429f1b336a75b9b74a852152217fbab (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,995 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp35-cp35m-linux_armv7l.whl#sha256=edb76e1344212be1373b20323904b92e0429f1b336a75b9b74a852152217fbab (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T01:08:11,996 Skipping link: not a file: https://www.piwheels.org/simple/rnacounter/ 2025-09-08T01:08:11,996 Skipping link: not a file: https://pypi.org/simple/rnacounter/ 2025-09-08T01:08:12,019 Given no hashes to check 1 links for project 'rnacounter': discarding no candidates 2025-09-08T01:08:12,020 Collecting rnacounter==1.4 2025-09-08T01:08:12,021 Created temporary directory: /tmp/pip-unpack-4gwk4vmn 2025-09-08T01:08:12,163 Downloading rnacounter-1.4.tar.gz (301 kB) 2025-09-08T01:08:12,250 Added rnacounter==1.4 from https://files.pythonhosted.org/packages/ab/bf/54a012d6660528530b8404401bf494bda91947e38aae0d45ba4d721de6d4/rnacounter-1.4.tar.gz to build tracker '/tmp/pip-build-tracker-53okysio' 2025-09-08T01:08:12,251 Running setup.py (path:/tmp/pip-wheel-s93cclxi/rnacounter_51c7292e391d4cec9b1f8d0e7b39126e/setup.py) egg_info for package rnacounter 2025-09-08T01:08:12,251 Created temporary directory: /tmp/pip-pip-egg-info-qfwj97j4 2025-09-08T01:08:12,251 Preparing metadata (setup.py): started 2025-09-08T01:08:12,252 Running command python setup.py egg_info 2025-09-08T01:08:13,149 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T01:08:13,149 warnings.warn(msg) 2025-09-08T01:08:13,605 running egg_info 2025-09-08T01:08:13,678 creating /tmp/pip-pip-egg-info-qfwj97j4/rnacounter.egg-info 2025-09-08T01:08:13,679 writing /tmp/pip-pip-egg-info-qfwj97j4/rnacounter.egg-info/PKG-INFO 2025-09-08T01:08:13,680 writing dependency_links to /tmp/pip-pip-egg-info-qfwj97j4/rnacounter.egg-info/dependency_links.txt 2025-09-08T01:08:13,681 writing requirements to /tmp/pip-pip-egg-info-qfwj97j4/rnacounter.egg-info/requires.txt 2025-09-08T01:08:13,681 writing top-level names to /tmp/pip-pip-egg-info-qfwj97j4/rnacounter.egg-info/top_level.txt 2025-09-08T01:08:13,681 writing manifest file '/tmp/pip-pip-egg-info-qfwj97j4/rnacounter.egg-info/SOURCES.txt' 2025-09-08T01:08:14,042 reading manifest file '/tmp/pip-pip-egg-info-qfwj97j4/rnacounter.egg-info/SOURCES.txt' 2025-09-08T01:08:14,043 reading manifest template 'MANIFEST.in' 2025-09-08T01:08:14,047 writing manifest file '/tmp/pip-pip-egg-info-qfwj97j4/rnacounter.egg-info/SOURCES.txt' 2025-09-08T01:08:14,183 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T01:08:14,188 Source in /tmp/pip-wheel-s93cclxi/rnacounter_51c7292e391d4cec9b1f8d0e7b39126e has version 1.4, which satisfies requirement rnacounter==1.4 from https://files.pythonhosted.org/packages/ab/bf/54a012d6660528530b8404401bf494bda91947e38aae0d45ba4d721de6d4/rnacounter-1.4.tar.gz 2025-09-08T01:08:14,188 Removed rnacounter==1.4 from https://files.pythonhosted.org/packages/ab/bf/54a012d6660528530b8404401bf494bda91947e38aae0d45ba4d721de6d4/rnacounter-1.4.tar.gz from build tracker '/tmp/pip-build-tracker-53okysio' 2025-09-08T01:08:14,192 Created temporary directory: /tmp/pip-unpack-led2rx67 2025-09-08T01:08:14,193 Created temporary directory: /tmp/pip-unpack-3882b4tk 2025-09-08T01:08:14,193 Building wheels for collected packages: rnacounter 2025-09-08T01:08:14,194 Created temporary directory: /tmp/pip-wheel-aqq8y3oz 2025-09-08T01:08:14,195 DEPRECATION: Building 'rnacounter' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'rnacounter'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T01:08:14,196 Building wheel for rnacounter (setup.py): started 2025-09-08T01:08:14,196 Destination directory: /tmp/pip-wheel-aqq8y3oz 2025-09-08T01:08:14,196 Running command python setup.py bdist_wheel 2025-09-08T01:08:15,068 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T01:08:15,068 warnings.warn(msg) 2025-09-08T01:08:15,456 running bdist_wheel 2025-09-08T01:08:15,817 running build 2025-09-08T01:08:15,817 running build_py 2025-09-08T01:08:15,892 creating build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:08:15,893 copying rnacounter/setup.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:08:15,893 copying rnacounter/main.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:08:15,894 copying rnacounter/draft_nocython.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:08:15,895 copying rnacounter/__init__.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:08:15,895 creating build/lib.linux-armv7l-cpython-313/testfiles 2025-09-08T01:08:15,896 copying testfiles/__init__.py -> build/lib.linux-armv7l-cpython-313/testfiles 2025-09-08T01:08:15,896 running egg_info 2025-09-08T01:08:15,971 writing rnacounter.egg-info/PKG-INFO 2025-09-08T01:08:15,972 writing dependency_links to rnacounter.egg-info/dependency_links.txt 2025-09-08T01:08:15,973 writing requirements to rnacounter.egg-info/requires.txt 2025-09-08T01:08:15,973 writing top-level names to rnacounter.egg-info/top_level.txt 2025-09-08T01:08:16,049 reading manifest file 'rnacounter.egg-info/SOURCES.txt' 2025-09-08T01:08:16,051 reading manifest template 'MANIFEST.in' 2025-09-08T01:08:16,055 writing manifest file 'rnacounter.egg-info/SOURCES.txt' 2025-09-08T01:08:16,057 copying rnacounter/rnacounter.c -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:08:16,064 copying testfiles/gapdhKO.bam -> build/lib.linux-armv7l-cpython-313/testfiles 2025-09-08T01:08:16,065 copying testfiles/gapdhKO.bam.bai -> build/lib.linux-armv7l-cpython-313/testfiles 2025-09-08T01:08:16,065 copying testfiles/mm9_3genes_renamed.gtf -> build/lib.linux-armv7l-cpython-313/testfiles 2025-09-08T01:08:16,066 running build_ext 2025-09-08T01:08:16,391 building 'rnacounter/rnacounter' extension 2025-09-08T01:08:16,391 creating build/temp.linux-armv7l-cpython-313/rnacounter 2025-09-08T01:08:16,392 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c rnacounter/rnacounter.c -o build/temp.linux-armv7l-cpython-313/rnacounter/rnacounter.o 2025-09-08T01:08:16,819 rnacounter/rnacounter.c: In function ‘__Pyx_ListComp_Append’: 2025-09-08T01:08:16,820 rnacounter/rnacounter.c:1341:23: error: lvalue required as left operand of assignment 2025-09-08T01:08:16,820 1341 | Py_SIZE(list) = len+1; 2025-09-08T01:08:16,820 | ^ 2025-09-08T01:08:16,821 rnacounter/rnacounter.c: In function ‘__Pyx_PyList_Append’: 2025-09-08T01:08:16,822 rnacounter/rnacounter.c:1406:23: error: lvalue required as left operand of assignment 2025-09-08T01:08:16,822 1406 | Py_SIZE(list) = len+1; 2025-09-08T01:08:16,822 | ^ 2025-09-08T01:08:16,831 rnacounter/rnacounter.c: In function ‘__Pyx_PyList_Extend’: 2025-09-08T01:08:16,831 rnacounter/rnacounter.c:1463:22: error: implicit declaration of function ‘_PyList_Extend’; did you mean ‘PyList_Extend’? [-Wimplicit-function-declaration] 2025-09-08T01:08:16,832 1463 | PyObject* none = _PyList_Extend((PyListObject*)L, v); 2025-09-08T01:08:16,832 | ^~~~~~~~~~~~~~ 2025-09-08T01:08:16,832 | PyList_Extend 2025-09-08T01:08:16,832 rnacounter/rnacounter.c:1463:22: error: initialization of ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:16,892 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_2parse_bed’: 2025-09-08T01:08:16,895 rnacounter/rnacounter.c:4159:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:16,896 4159 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T01:08:16,896 | ^~ 2025-09-08T01:08:16,896 In file included from /usr/include/python3.13/Python.h:76, 2025-09-08T01:08:16,896 from rnacounter/rnacounter.c:16: 2025-09-08T01:08:16,897 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T01:08:16,897 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T01:08:16,897 | ^~~~~~~~~~~~~~~ 2025-09-08T01:08:16,943 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_4join’: 2025-09-08T01:08:16,948 rnacounter/rnacounter.c:5394:9: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:16,948 5394 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T01:08:16,948 | ^~ 2025-09-08T01:08:16,949 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T01:08:16,949 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T01:08:16,949 | ^~~~~~~~~~~~~~~ 2025-09-08T01:08:17,965 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_16parse_args’: 2025-09-08T01:08:17,991 rnacounter/rnacounter.c:22604:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:17,991 22604 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T01:08:17,991 | ^~ 2025-09-08T01:08:17,991 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T01:08:17,991 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T01:08:17,992 | ^~~~~~~~~~~~~~~ 2025-09-08T01:08:18,019 rnacounter/rnacounter.c:22653:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:18,019 22653 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T01:08:18,019 | ^~ 2025-09-08T01:08:18,019 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T01:08:18,019 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T01:08:18,019 | ^~~~~~~~~~~~~~~ 2025-09-08T01:08:18,062 rnacounter/rnacounter.c:22789:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:18,062 22789 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T01:08:18,062 | ^~ 2025-09-08T01:08:18,062 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T01:08:18,062 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T01:08:18,063 | ^~~~~~~~~~~~~~~ 2025-09-08T01:08:18,174 rnacounter/rnacounter.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-08T01:08:18,214 rnacounter/rnacounter.c:23795:50: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-08T01:08:18,214 23795 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); 2025-09-08T01:08:18,214 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:18,214 | PyBUF_C_CONTIGUOUS 2025-09-08T01:08:18,217 rnacounter/rnacounter.c:23795:50: note: each undeclared identifier is reported only once for each function it appears in 2025-09-08T01:08:18,278 rnacounter/rnacounter.c:23835:50: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-08T01:08:18,279 23835 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); 2025-09-08T01:08:18,279 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:18,279 | PyBUF_F_CONTIGUOUS 2025-09-08T01:08:18,287 rnacounter/rnacounter.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-08T01:08:18,315 rnacounter/rnacounter.c:24841:29: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T01:08:18,315 24841 | if (unlikely(__pyx_v_descr->names == Py_None)) { 2025-09-08T01:08:18,315 | ^~ 2025-09-08T01:08:18,315 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T01:08:18,316 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T01:08:18,316 | ^ 2025-09-08T01:08:18,348 rnacounter/rnacounter.c:24845:28: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T01:08:18,349 24845 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; 2025-09-08T01:08:18,349 | ^~ 2025-09-08T01:08:18,384 rnacounter/rnacounter.c:24863:47: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-08T01:08:18,384 24863 | __pyx_t_3 = PyObject_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; 2025-09-08T01:08:18,384 | ^~ 2025-09-08T01:08:18,435 rnacounter/rnacounter.c:25044:79: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’ 2025-09-08T01:08:18,435 25044 | (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); 2025-09-08T01:08:18,435 | ^~ 2025-09-08T01:08:18,484 rnacounter/rnacounter.c: In function ‘__pyx_tp_dealloc_10rnacounter_10rnacounter_GenomicObject’: 2025-09-08T01:08:18,513 rnacounter/rnacounter.c:25672:45: error: implicit declaration of function ‘_PyGC_FINALIZED’ [-Wimplicit-function-declaration] 2025-09-08T01:08:18,513 25672 | if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) { 2025-09-08T01:08:18,513 | ^~~~~~~~~~~~~~~ 2025-09-08T01:08:18,616 rnacounter/rnacounter.c: In function ‘__Pyx_InitCachedConstants’: 2025-09-08T01:08:18,650 rnacounter/rnacounter.c:29392:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:18,650 29392 | __pyx_codeobj__69 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__68, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 68, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:18,650 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:18,651 In file included from /usr/include/python3.13/Python.h:101: 2025-09-08T01:08:18,651 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:18,651 213 | PyCode_New( 2025-09-08T01:08:18,651 | ^~~~~~~~~~ 2025-09-08T01:08:18,689 rnacounter/rnacounter.c:29392:243: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:18,689 29392 | __pyx_codeobj__69 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__68, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 68, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:18,689 | ^~ 2025-09-08T01:08:18,689 | | 2025-09-08T01:08:18,689 | int 2025-09-08T01:08:18,689 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:18,689 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:18,689 | ^~~~~ 2025-09-08T01:08:18,690 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:08:18,690 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:18,690 | ~~~~~~~~~~^ 2025-09-08T01:08:18,727 rnacounter/rnacounter.c:29392:247: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:18,727 29392 | __pyx_codeobj__69 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__68, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 68, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:18,727 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:18,727 | | 2025-09-08T01:08:18,728 | PyObject * {aka struct _object *} 2025-09-08T01:08:18,728 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:18,728 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:18,728 | ^~~~ 2025-09-08T01:08:18,728 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:08:18,728 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:18,728 | ~~~~^ 2025-09-08T01:08:18,765 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:08:18,766 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:18,766 | ^~~~~~~~~~ 2025-09-08T01:08:18,766 rnacounter/rnacounter.c:29392:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:18,766 29392 | __pyx_codeobj__69 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__68, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 68, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__69)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 68; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:18,766 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:18,766 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:18,766 213 | PyCode_New( 2025-09-08T01:08:18,766 | ^~~~~~~~~~ 2025-09-08T01:08:18,800 rnacounter/rnacounter.c:29404:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:18,800 29404 | __pyx_codeobj__71 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 88, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:18,801 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:18,801 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:18,801 213 | PyCode_New( 2025-09-08T01:08:18,801 | ^~~~~~~~~~ 2025-09-08T01:08:18,838 rnacounter/rnacounter.c:29404:244: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:18,838 29404 | __pyx_codeobj__71 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 88, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:18,838 | ^~ 2025-09-08T01:08:18,839 | | 2025-09-08T01:08:18,839 | int 2025-09-08T01:08:18,839 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:18,839 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:18,839 | ^~~~~ 2025-09-08T01:08:18,839 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:08:18,839 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:18,839 | ~~~~~~~~~~^ 2025-09-08T01:08:18,877 rnacounter/rnacounter.c:29404:248: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:18,877 29404 | __pyx_codeobj__71 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 88, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:18,877 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:18,877 | | 2025-09-08T01:08:18,877 | PyObject * {aka struct _object *} 2025-09-08T01:08:18,877 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:18,877 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:18,877 | ^~~~ 2025-09-08T01:08:18,878 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:08:18,878 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:18,878 | ~~~~^ 2025-09-08T01:08:18,915 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:08:18,915 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:18,915 | ^~~~~~~~~~ 2025-09-08T01:08:18,915 rnacounter/rnacounter.c:29404:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:18,916 29404 | __pyx_codeobj__71 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__70, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 88, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__71)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 88; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:18,916 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:18,916 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:18,916 213 | PyCode_New( 2025-09-08T01:08:18,916 | ^~~~~~~~~~ 2025-09-08T01:08:18,950 rnacounter/rnacounter.c:29416:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:18,950 29416 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 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_join, 113, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:18,950 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:18,950 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:18,950 213 | PyCode_New( 2025-09-08T01:08:18,951 | ^~~~~~~~~~ 2025-09-08T01:08:18,988 rnacounter/rnacounter.c:29416:239: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:18,988 29416 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 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_join, 113, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:18,988 | ^~~ 2025-09-08T01:08:18,988 | | 2025-09-08T01:08:18,988 | int 2025-09-08T01:08:18,988 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:18,988 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:18,989 | ^~~~~ 2025-09-08T01:08:18,989 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:08:18,989 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:18,989 | ~~~~~~~~~~^ 2025-09-08T01:08:19,026 rnacounter/rnacounter.c:29416:244: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:19,027 29416 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 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_join, 113, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,027 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,027 | | 2025-09-08T01:08:19,027 | PyObject * {aka struct _object *} 2025-09-08T01:08:19,027 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,027 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,027 | ^~~~ 2025-09-08T01:08:19,027 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:08:19,027 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,027 | ~~~~^ 2025-09-08T01:08:19,065 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:08:19,065 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,065 | ^~~~~~~~~~ 2025-09-08T01:08:19,065 rnacounter/rnacounter.c:29416:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,065 29416 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 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_join, 113, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 113; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,065 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,066 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,066 213 | PyCode_New( 2025-09-08T01:08:19,066 | ^~~~~~~~~~ 2025-09-08T01:08:19,100 rnacounter/rnacounter.c:29428:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:19,100 29428 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 55, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 584, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,100 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,100 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,100 213 | PyCode_New( 2025-09-08T01:08:19,100 | ^~~~~~~~~~ 2025-09-08T01:08:19,138 rnacounter/rnacounter.c:29428:248: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:19,138 29428 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 55, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 584, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,138 | ^~~ 2025-09-08T01:08:19,138 | | 2025-09-08T01:08:19,138 | int 2025-09-08T01:08:19,138 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,138 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,139 | ^~~~~ 2025-09-08T01:08:19,139 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:08:19,139 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,139 | ~~~~~~~~~~^ 2025-09-08T01:08:19,176 rnacounter/rnacounter.c:29428:253: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:19,177 29428 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 55, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 584, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,177 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,177 | | 2025-09-08T01:08:19,177 | PyObject * {aka struct _object *} 2025-09-08T01:08:19,177 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,177 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,177 | ^~~~ 2025-09-08T01:08:19,177 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:08:19,177 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,178 | ~~~~^ 2025-09-08T01:08:19,215 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:08:19,215 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,215 | ^~~~~~~~~~ 2025-09-08T01:08:19,215 rnacounter/rnacounter.c:29428:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,215 29428 | __pyx_codeobj__75 = (PyObject*)__Pyx_PyCode_New(4, 0, 55, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__74, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 584, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__75)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 584; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,215 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,216 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,216 213 | PyCode_New( 2025-09-08T01:08:19,216 | ^~~~~~~~~~ 2025-09-08T01:08:19,250 rnacounter/rnacounter.c:29440:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:19,250 29440 | __pyx_codeobj__77 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 719, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,250 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,251 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,251 213 | PyCode_New( 2025-09-08T01:08:19,251 | ^~~~~~~~~~ 2025-09-08T01:08:19,293 rnacounter/rnacounter.c:29440:247: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:19,293 29440 | __pyx_codeobj__77 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 719, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,293 | ^~~ 2025-09-08T01:08:19,294 | | 2025-09-08T01:08:19,294 | int 2025-09-08T01:08:19,294 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,294 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,294 | ^~~~~ 2025-09-08T01:08:19,294 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:08:19,294 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,294 | ~~~~~~~~~~^ 2025-09-08T01:08:19,330 rnacounter/rnacounter.c:29440:252: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:19,331 29440 | __pyx_codeobj__77 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 719, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,331 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,331 | | 2025-09-08T01:08:19,331 | PyObject * {aka struct _object *} 2025-09-08T01:08:19,331 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,331 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,331 | ^~~~ 2025-09-08T01:08:19,331 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:08:19,331 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,331 | ~~~~^ 2025-09-08T01:08:19,367 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:08:19,368 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,368 | ^~~~~~~~~~ 2025-09-08T01:08:19,368 rnacounter/rnacounter.c:29440:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,368 29440 | __pyx_codeobj__77 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__76, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 719, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__77)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 719; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,368 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,368 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,368 213 | PyCode_New( 2025-09-08T01:08:19,368 | ^~~~~~~~~~ 2025-09-08T01:08:19,402 rnacounter/rnacounter.c:29452:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:19,403 29452 | __pyx_codeobj__80 = (PyObject*)__Pyx_PyCode_New(3, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__79, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 739, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,403 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,403 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,403 213 | PyCode_New( 2025-09-08T01:08:19,403 | ^~~~~~~~~~ 2025-09-08T01:08:19,440 rnacounter/rnacounter.c:29452:250: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:19,440 29452 | __pyx_codeobj__80 = (PyObject*)__Pyx_PyCode_New(3, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__79, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 739, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,441 | ^~~ 2025-09-08T01:08:19,441 | | 2025-09-08T01:08:19,441 | int 2025-09-08T01:08:19,441 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,441 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,441 | ^~~~~ 2025-09-08T01:08:19,441 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:08:19,441 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,441 | ~~~~~~~~~~^ 2025-09-08T01:08:19,479 rnacounter/rnacounter.c:29452:255: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:19,479 29452 | __pyx_codeobj__80 = (PyObject*)__Pyx_PyCode_New(3, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__79, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 739, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,479 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,479 | | 2025-09-08T01:08:19,479 | PyObject * {aka struct _object *} 2025-09-08T01:08:19,479 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,479 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,480 | ^~~~ 2025-09-08T01:08:19,480 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:08:19,480 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,480 | ~~~~^ 2025-09-08T01:08:19,517 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:08:19,517 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,518 | ^~~~~~~~~~ 2025-09-08T01:08:19,518 rnacounter/rnacounter.c:29452:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,518 29452 | __pyx_codeobj__80 = (PyObject*)__Pyx_PyCode_New(3, 0, 25, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__79, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 739, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__80)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 739; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,518 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,518 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,518 213 | PyCode_New( 2025-09-08T01:08:19,518 | ^~~~~~~~~~ 2025-09-08T01:08:19,552 rnacounter/rnacounter.c:29461:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:19,552 29461 | __pyx_codeobj__81 = (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, 833, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,552 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,552 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,553 213 | PyCode_New( 2025-09-08T01:08:19,553 | ^~~~~~~~~~ 2025-09-08T01:08:19,590 rnacounter/rnacounter.c:29461:248: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:19,590 29461 | __pyx_codeobj__81 = (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, 833, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,590 | ^~~ 2025-09-08T01:08:19,590 | | 2025-09-08T01:08:19,590 | int 2025-09-08T01:08:19,591 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,591 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,591 | ^~~~~ 2025-09-08T01:08:19,591 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:08:19,591 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,591 | ~~~~~~~~~~^ 2025-09-08T01:08:19,628 rnacounter/rnacounter.c:29461:253: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:19,628 29461 | __pyx_codeobj__81 = (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, 833, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,628 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,628 | | 2025-09-08T01:08:19,628 | PyObject * {aka struct _object *} 2025-09-08T01:08:19,628 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,628 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,628 | ^~~~ 2025-09-08T01:08:19,628 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:08:19,628 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,629 | ~~~~^ 2025-09-08T01:08:19,665 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:08:19,665 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,665 | ^~~~~~~~~~ 2025-09-08T01:08:19,665 rnacounter/rnacounter.c:29461:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,665 29461 | __pyx_codeobj__81 = (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, 833, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__81)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 833; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,665 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,665 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,665 213 | PyCode_New( 2025-09-08T01:08:19,666 | ^~~~~~~~~~ 2025-09-08T01:08:19,698 rnacounter/rnacounter.c:29473:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:19,699 29473 | __pyx_codeobj__83 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__82, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_errmsg, 836, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,699 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,699 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,699 213 | PyCode_New( 2025-09-08T01:08:19,699 | ^~~~~~~~~~ 2025-09-08T01:08:19,735 rnacounter/rnacounter.c:29473:240: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:19,736 29473 | __pyx_codeobj__83 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__82, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_errmsg, 836, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,736 | ^~~ 2025-09-08T01:08:19,736 | | 2025-09-08T01:08:19,736 | int 2025-09-08T01:08:19,736 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,736 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,736 | ^~~~~ 2025-09-08T01:08:19,736 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:08:19,736 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,737 | ~~~~~~~~~~^ 2025-09-08T01:08:19,773 rnacounter/rnacounter.c:29473:245: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:19,773 29473 | __pyx_codeobj__83 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__82, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_errmsg, 836, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,773 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,773 | | 2025-09-08T01:08:19,773 | PyObject * {aka struct _object *} 2025-09-08T01:08:19,773 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,773 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,773 | ^~~~ 2025-09-08T01:08:19,774 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:08:19,774 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,774 | ~~~~^ 2025-09-08T01:08:19,810 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:08:19,810 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,810 | ^~~~~~~~~~ 2025-09-08T01:08:19,810 rnacounter/rnacounter.c:29473:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,810 29473 | __pyx_codeobj__83 = (PyObject*)__Pyx_PyCode_New(1, 0, 1, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__82, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_errmsg, 836, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__83)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 836; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,811 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,811 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,811 213 | PyCode_New( 2025-09-08T01:08:19,811 | ^~~~~~~~~~ 2025-09-08T01:08:19,844 rnacounter/rnacounter.c:29485:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:19,844 29485 | __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__84, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 840, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,844 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,844 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,844 213 | PyCode_New( 2025-09-08T01:08:19,844 | ^~~~~~~~~~ 2025-09-08T01:08:19,881 rnacounter/rnacounter.c:29485:245: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:19,881 29485 | __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__84, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 840, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,881 | ^~~ 2025-09-08T01:08:19,881 | | 2025-09-08T01:08:19,881 | int 2025-09-08T01:08:19,882 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,882 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,882 | ^~~~~ 2025-09-08T01:08:19,882 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:08:19,882 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,882 | ~~~~~~~~~~^ 2025-09-08T01:08:19,921 rnacounter/rnacounter.c:29485:250: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:19,921 29485 | __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__84, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 840, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,921 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,921 | | 2025-09-08T01:08:19,921 | PyObject * {aka struct _object *} 2025-09-08T01:08:19,921 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,921 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,921 | ^~~~ 2025-09-08T01:08:19,921 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:08:19,921 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:19,922 | ~~~~^ 2025-09-08T01:08:19,960 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:08:19,960 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:19,961 | ^~~~~~~~~~ 2025-09-08T01:08:19,961 rnacounter/rnacounter.c:29485:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:19,961 29485 | __pyx_codeobj__85 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__84, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 840, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__85)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 840; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T01:08:19,961 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:19,961 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:19,961 213 | PyCode_New( 2025-09-08T01:08:19,961 | ^~~~~~~~~~ 2025-09-08T01:08:19,964 rnacounter/rnacounter.c: In function ‘PyInit_rnacounter’: 2025-09-08T01:08:19,998 rnacounter/rnacounter.c:29589:53: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:19,999 29589 | __pyx_type_10rnacounter_10rnacounter_GenomicObject.tp_print = 0; 2025-09-08T01:08:19,999 | ^ 2025-09-08T01:08:20,034 rnacounter/rnacounter.c:29606:44: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,034 29606 | __pyx_type_10rnacounter_10rnacounter_Exon.tp_print = 0; 2025-09-08T01:08:20,034 | ^ 2025-09-08T01:08:20,068 rnacounter/rnacounter.c:29612:50: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,068 29612 | __pyx_type_10rnacounter_10rnacounter_Transcript.tp_print = 0; 2025-09-08T01:08:20,068 | ^ 2025-09-08T01:08:20,101 rnacounter/rnacounter.c:29617:44: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,102 29617 | __pyx_type_10rnacounter_10rnacounter_Gene.tp_print = 0; 2025-09-08T01:08:20,102 | ^ 2025-09-08T01:08:20,135 rnacounter/rnacounter.c:29621:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,135 29621 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct__parse_gtf.tp_print = 0; 2025-09-08T01:08:20,135 | ^ 2025-09-08T01:08:20,169 rnacounter/rnacounter.c:29624:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,169 29624 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_1_genexpr.tp_print = 0; 2025-09-08T01:08:20,169 | ^ 2025-09-08T01:08:20,203 rnacounter/rnacounter.c:29627:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,203 29627 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_2_genexpr.tp_print = 0; 2025-09-08T01:08:20,203 | ^ 2025-09-08T01:08:20,237 rnacounter/rnacounter.c:29630:65: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,237 29630 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_3_join.tp_print = 0; 2025-09-08T01:08:20,237 | ^ 2025-09-08T01:08:20,271 rnacounter/rnacounter.c:29633:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,271 29633 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_4_genexpr.tp_print = 0; 2025-09-08T01:08:20,271 | ^ 2025-09-08T01:08:20,304 rnacounter/rnacounter.c:29636:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,304 29636 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_5_genexpr.tp_print = 0; 2025-09-08T01:08:20,305 | ^ 2025-09-08T01:08:20,338 rnacounter/rnacounter.c:29639:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,338 29639 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_6_genexpr.tp_print = 0; 2025-09-08T01:08:20,338 | ^ 2025-09-08T01:08:20,372 rnacounter/rnacounter.c:29642:74: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,372 29642 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk.tp_print = 0; 2025-09-08T01:08:20,372 | ^ 2025-09-08T01:08:20,406 rnacounter/rnacounter.c:29645:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,406 29645 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr.tp_print = 0; 2025-09-08T01:08:20,406 | ^ 2025-09-08T01:08:20,439 rnacounter/rnacounter.c:29648:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,439 29648 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr.tp_print = 0; 2025-09-08T01:08:20,440 | ^ 2025-09-08T01:08:20,473 rnacounter/rnacounter.c:29651:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,473 29651 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr.tp_print = 0; 2025-09-08T01:08:20,473 | ^ 2025-09-08T01:08:20,507 rnacounter/rnacounter.c:29654:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,507 29654 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_11_genexpr.tp_print = 0; 2025-09-08T01:08:20,507 | ^ 2025-09-08T01:08:20,541 rnacounter/rnacounter.c:29657:74: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,541 29657 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_12_print_output.tp_print = 0; 2025-09-08T01:08:20,541 | ^ 2025-09-08T01:08:20,574 rnacounter/rnacounter.c:29660:72: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,575 29660 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_13_parse_args.tp_print = 0; 2025-09-08T01:08:20,575 | ^ 2025-09-08T01:08:20,608 rnacounter/rnacounter.c:29663:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,608 29663 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr.tp_print = 0; 2025-09-08T01:08:20,609 | ^ 2025-09-08T01:08:20,642 rnacounter/rnacounter.c:29666:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,642 29666 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_15_genexpr.tp_print = 0; 2025-09-08T01:08:20,642 | ^ 2025-09-08T01:08:20,676 rnacounter/rnacounter.c:29669:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T01:08:20,676 29669 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_16_genexpr.tp_print = 0; 2025-09-08T01:08:20,676 | ^ 2025-09-08T01:08:20,731 rnacounter/rnacounter.c: In function ‘__Pyx_PyUnicode_Equals’: 2025-09-08T01:08:20,769 rnacounter/rnacounter.c:84:51: error: implicit declaration of function ‘_PyUnicode_Ready’; did you mean ‘PyUnicode_READY’? [-Wimplicit-function-declaration] 2025-09-08T01:08:20,770 84 | 0 : _PyUnicode_Ready((PyObject *)(op))) 2025-09-08T01:08:20,770 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:20,770 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T01:08:20,770 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T01:08:20,770 | ^ 2025-09-08T01:08:20,770 rnacounter/rnacounter.c:30193:22: note: in expansion of macro ‘__Pyx_PyUnicode_READY’ 2025-09-08T01:08:20,770 30193 | if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) 2025-09-08T01:08:20,770 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-08T01:08:20,819 rnacounter/rnacounter.c: In function ‘__Pyx_ErrRestore’: 2025-09-08T01:08:20,854 rnacounter/rnacounter.c:30285:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:08:20,854 30285 | tmp_type = tstate->curexc_type; 2025-09-08T01:08:20,854 | ^~ 2025-09-08T01:08:20,889 rnacounter/rnacounter.c:30286:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:08:20,889 30286 | tmp_value = tstate->curexc_value; 2025-09-08T01:08:20,889 | ^~ 2025-09-08T01:08:20,924 rnacounter/rnacounter.c:30287:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:08:20,924 30287 | tmp_tb = tstate->curexc_traceback; 2025-09-08T01:08:20,924 | ^~ 2025-09-08T01:08:20,959 rnacounter/rnacounter.c:30288:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:08:20,959 30288 | tstate->curexc_type = type; 2025-09-08T01:08:20,959 | ^~ 2025-09-08T01:08:20,994 rnacounter/rnacounter.c:30289:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:08:20,994 30289 | tstate->curexc_value = value; 2025-09-08T01:08:20,994 | ^~ 2025-09-08T01:08:21,029 rnacounter/rnacounter.c:30290:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:08:21,029 30290 | tstate->curexc_traceback = tb; 2025-09-08T01:08:21,029 | ^~ 2025-09-08T01:08:21,029 rnacounter/rnacounter.c: In function ‘__Pyx_ErrFetch’: 2025-09-08T01:08:21,064 rnacounter/rnacounter.c:30301:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:08:21,064 30301 | *type = tstate->curexc_type; 2025-09-08T01:08:21,064 | ^~ 2025-09-08T01:08:21,100 rnacounter/rnacounter.c:30302:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:08:21,100 30302 | *value = tstate->curexc_value; 2025-09-08T01:08:21,100 | ^~ 2025-09-08T01:08:21,136 rnacounter/rnacounter.c:30303:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:08:21,137 30303 | *tb = tstate->curexc_traceback; 2025-09-08T01:08:21,137 | ^~ 2025-09-08T01:08:21,173 rnacounter/rnacounter.c:30304:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:08:21,174 30304 | tstate->curexc_type = 0; 2025-09-08T01:08:21,174 | ^~ 2025-09-08T01:08:21,211 rnacounter/rnacounter.c:30305:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:08:21,211 30305 | tstate->curexc_value = 0; 2025-09-08T01:08:21,211 | ^~ 2025-09-08T01:08:21,246 rnacounter/rnacounter.c:30306:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:08:21,246 30306 | tstate->curexc_traceback = 0; 2025-09-08T01:08:21,246 | ^~ 2025-09-08T01:08:21,321 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionSave’: 2025-09-08T01:08:21,371 rnacounter/rnacounter.c:30503:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:08:21,371 30503 | *type = tstate->exc_type; 2025-09-08T01:08:21,372 | ^~~~~~~~ 2025-09-08T01:08:21,372 | exc_state 2025-09-08T01:08:21,406 rnacounter/rnacounter.c:30504:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:08:21,406 30504 | *value = tstate->exc_value; 2025-09-08T01:08:21,406 | ^~ 2025-09-08T01:08:21,440 rnacounter/rnacounter.c:30505:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:08:21,441 30505 | *tb = tstate->exc_traceback; 2025-09-08T01:08:21,441 | ^~ 2025-09-08T01:08:21,441 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionReset’: 2025-09-08T01:08:21,491 rnacounter/rnacounter.c:30517:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:08:21,491 30517 | tmp_type = tstate->exc_type; 2025-09-08T01:08:21,491 | ^~~~~~~~ 2025-09-08T01:08:21,491 | exc_state 2025-09-08T01:08:21,525 rnacounter/rnacounter.c:30518:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:08:21,525 30518 | tmp_value = tstate->exc_value; 2025-09-08T01:08:21,526 | ^~ 2025-09-08T01:08:21,560 rnacounter/rnacounter.c:30519:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:08:21,560 30519 | tmp_tb = tstate->exc_traceback; 2025-09-08T01:08:21,560 | ^~ 2025-09-08T01:08:21,610 rnacounter/rnacounter.c:30520:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:08:21,610 30520 | tstate->exc_type = type; 2025-09-08T01:08:21,610 | ^~~~~~~~ 2025-09-08T01:08:21,610 | exc_state 2025-09-08T01:08:21,644 rnacounter/rnacounter.c:30521:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:08:21,645 30521 | tstate->exc_value = value; 2025-09-08T01:08:21,645 | ^~ 2025-09-08T01:08:21,679 rnacounter/rnacounter.c:30522:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:08:21,679 30522 | tstate->exc_traceback = tb; 2025-09-08T01:08:21,679 | ^~ 2025-09-08T01:08:21,679 rnacounter/rnacounter.c: In function ‘__Pyx_GetException’: 2025-09-08T01:08:21,714 rnacounter/rnacounter.c:30536:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:08:21,714 30536 | local_type = tstate->curexc_type; 2025-09-08T01:08:21,714 | ^~ 2025-09-08T01:08:21,749 rnacounter/rnacounter.c:30537:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:08:21,749 30537 | local_value = tstate->curexc_value; 2025-09-08T01:08:21,749 | ^~ 2025-09-08T01:08:21,783 rnacounter/rnacounter.c:30538:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:08:21,783 30538 | local_tb = tstate->curexc_traceback; 2025-09-08T01:08:21,784 | ^~ 2025-09-08T01:08:21,818 rnacounter/rnacounter.c:30539:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:08:21,818 30539 | tstate->curexc_type = 0; 2025-09-08T01:08:21,818 | ^~ 2025-09-08T01:08:21,853 rnacounter/rnacounter.c:30540:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:08:21,853 30540 | tstate->curexc_value = 0; 2025-09-08T01:08:21,853 | ^~ 2025-09-08T01:08:21,887 rnacounter/rnacounter.c:30541:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:08:21,887 30541 | tstate->curexc_traceback = 0; 2025-09-08T01:08:21,888 | ^~ 2025-09-08T01:08:21,922 rnacounter/rnacounter.c:30547:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:08:21,922 30547 | if (unlikely(tstate->curexc_type)) 2025-09-08T01:08:21,922 | ^~ 2025-09-08T01:08:21,922 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T01:08:21,922 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T01:08:21,923 | ^ 2025-09-08T01:08:21,984 rnacounter/rnacounter.c:30565:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:08:21,985 30565 | tmp_type = tstate->exc_type; 2025-09-08T01:08:21,985 | ^~~~~~~~ 2025-09-08T01:08:21,985 | exc_state 2025-09-08T01:08:22,019 rnacounter/rnacounter.c:30566:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:08:22,019 30566 | tmp_value = tstate->exc_value; 2025-09-08T01:08:22,019 | ^~ 2025-09-08T01:08:22,054 rnacounter/rnacounter.c:30567:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:08:22,054 30567 | tmp_tb = tstate->exc_traceback; 2025-09-08T01:08:22,054 | ^~ 2025-09-08T01:08:22,104 rnacounter/rnacounter.c:30568:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:08:22,104 30568 | tstate->exc_type = local_type; 2025-09-08T01:08:22,104 | ^~~~~~~~ 2025-09-08T01:08:22,104 | exc_state 2025-09-08T01:08:22,138 rnacounter/rnacounter.c:30569:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:08:22,138 30569 | tstate->exc_value = local_value; 2025-09-08T01:08:22,139 | ^~ 2025-09-08T01:08:22,173 rnacounter/rnacounter.c:30570:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:08:22,173 30570 | tstate->exc_traceback = local_tb; 2025-09-08T01:08:22,173 | ^~ 2025-09-08T01:08:22,200 rnacounter/rnacounter.c: In function ‘__Pyx_ParseOptionalKeywords’: 2025-09-08T01:08:22,251 rnacounter/rnacounter.c:30674:22: error: implicit declaration of function ‘PyUnicode_GET_SIZE’; did you mean ‘PyDict_GET_SIZE’? [-Wimplicit-function-declaration] 2025-09-08T01:08:22,251 30674 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-08T01:08:22,252 | ^~~~~~~~~~~~~~~~~~ 2025-09-08T01:08:22,252 | PyDict_GET_SIZE 2025-09-08T01:08:22,366 rnacounter/rnacounter.c: In function ‘__Pyx_Raise’: 2025-09-08T01:08:22,401 rnacounter/rnacounter.c:30900:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:08:22,401 30900 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-08T01:08:22,401 | ^~ 2025-09-08T01:08:22,437 rnacounter/rnacounter.c:30903:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:08:22,437 30903 | tstate->curexc_traceback = tb; 2025-09-08T01:08:22,437 | ^~ 2025-09-08T01:08:22,494 rnacounter/rnacounter.c: In function ‘__Pyx_PyIter_Next2’: 2025-09-08T01:08:22,530 rnacounter/rnacounter.c:30948:31: error: ‘_PyObject_NextNotImplemented’ undeclared (first use in this function); did you mean ‘PyObject_HashNotImplemented’? 2025-09-08T01:08:22,530 30948 | if (unlikely(iternext == &_PyObject_NextNotImplemented)) 2025-09-08T01:08:22,531 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T01:08:22,531 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T01:08:22,531 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T01:08:22,531 | ^ 2025-09-08T01:08:22,569 rnacounter/rnacounter.c: In function ‘__Pyx_IterFinish’: 2025-09-08T01:08:22,605 rnacounter/rnacounter.c:31112:32: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:08:22,605 31112 | PyObject* exc_type = tstate->curexc_type; 2025-09-08T01:08:22,605 | ^~ 2025-09-08T01:08:22,641 rnacounter/rnacounter.c:31116:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:08:22,642 31116 | exc_value = tstate->curexc_value; 2025-09-08T01:08:22,642 | ^~ 2025-09-08T01:08:22,678 rnacounter/rnacounter.c:31117:28: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:08:22,678 31117 | exc_tb = tstate->curexc_traceback; 2025-09-08T01:08:22,678 | ^~ 2025-09-08T01:08:22,714 rnacounter/rnacounter.c:31118:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T01:08:22,714 31118 | tstate->curexc_type = 0; 2025-09-08T01:08:22,714 | ^~ 2025-09-08T01:08:22,750 rnacounter/rnacounter.c:31119:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T01:08:22,750 31119 | tstate->curexc_value = 0; 2025-09-08T01:08:22,750 | ^~ 2025-09-08T01:08:22,786 rnacounter/rnacounter.c:31120:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T01:08:22,786 31120 | tstate->curexc_traceback = 0; 2025-09-08T01:08:22,787 | ^~ 2025-09-08T01:08:23,278 rnacounter/rnacounter.c: In function ‘__Pyx_CyFunction_Call’: 2025-09-08T01:08:23,332 rnacounter/rnacounter.c:32464:16: error: implicit declaration of function ‘PyCFunction_Call’; did you mean ‘PyCFunction_New’? [-Wimplicit-function-declaration] 2025-09-08T01:08:23,332 32464 | return PyCFunction_Call(func, arg, kw); 2025-09-08T01:08:23,333 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:23,333 | PyCFunction_New 2025-09-08T01:08:23,374 rnacounter/rnacounter.c:32464:16: error: returning ‘int’ from a function with return type ‘PyObject *’ {aka ‘struct _object *’} makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:23,375 32464 | return PyCFunction_Call(func, arg, kw); 2025-09-08T01:08:23,375 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T01:08:23,394 rnacounter/rnacounter.c: In function ‘__Pyx_CyFunction_init’: 2025-09-08T01:08:23,446 rnacounter/rnacounter.c:32529:41: error: ‘PyCFunction_Call’ undeclared (first use in this function); did you mean ‘PyCFunction_New’? 2025-09-08T01:08:23,447 32529 | __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; 2025-09-08T01:08:23,447 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:23,447 | PyCFunction_New 2025-09-08T01:08:23,492 rnacounter/rnacounter.c: In function ‘__Pyx_CreateCodeObjectForTraceback’: 2025-09-08T01:08:23,530 rnacounter/rnacounter.c:32705:5: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T01:08:23,530 32705 | py_code = __Pyx_PyCode_New( 2025-09-08T01:08:23,530 | ^~~~~~~ 2025-09-08T01:08:23,530 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:23,530 213 | PyCode_New( 2025-09-08T01:08:23,530 | ^~~~~~~~~~ 2025-09-08T01:08:23,568 rnacounter/rnacounter.c:32719:9: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T01:08:23,568 32719 | py_line, 2025-09-08T01:08:23,568 | ^~~~~~~ 2025-09-08T01:08:23,568 | | 2025-09-08T01:08:23,568 | int 2025-09-08T01:08:23,568 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:23,568 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:23,568 | ^~~~~ 2025-09-08T01:08:23,569 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T01:08:23,569 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:23,569 | ~~~~~~~~~~^ 2025-09-08T01:08:23,610 rnacounter/rnacounter.c:32720:9: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:23,610 32720 | __pyx_empty_bytes /*PyObject *lnotab*/ 2025-09-08T01:08:23,610 | ^~~~~~~~~~~~~~~~~ 2025-09-08T01:08:23,610 | | 2025-09-08T01:08:23,610 | PyObject * {aka struct _object *} 2025-09-08T01:08:23,610 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:23,610 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:23,610 | ^~~~ 2025-09-08T01:08:23,611 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T01:08:23,611 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T01:08:23,611 | ~~~~^ 2025-09-08T01:08:23,650 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T01:08:23,651 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T01:08:23,651 | ^~~~~~~~~~ 2025-09-08T01:08:23,651 rnacounter/rnacounter.c:32705:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T01:08:23,651 32705 | py_code = __Pyx_PyCode_New( 2025-09-08T01:08:23,651 | ^~~~~~~~~~~~~~~~ 2025-09-08T01:08:23,651 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T01:08:23,651 213 | PyCode_New( 2025-09-08T01:08:23,651 | ^~~~~~~~~~ 2025-09-08T01:08:23,668 rnacounter/rnacounter.c: In function ‘__Pyx_AddTraceback’: 2025-09-08T01:08:23,705 rnacounter/rnacounter.c:32748:13: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:08:23,705 32748 | py_frame->f_lineno = py_line; 2025-09-08T01:08:23,705 | ^~ 2025-09-08T01:08:23,707 rnacounter/rnacounter.c: In function ‘__Pyx_PyInt_As_int’: 2025-09-08T01:08:23,744 rnacounter/rnacounter.c:32869:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T01:08:23,744 32869 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T01:08:23,744 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:08:23,744 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-08T01:08:23,744 from /usr/include/python3.13/Python.h:81: 2025-09-08T01:08:23,744 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T01:08:23,744 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T01:08:23,744 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:08:23,790 rnacounter/rnacounter.c: In function ‘__Pyx_PyInt_As_long’: 2025-09-08T01:08:23,828 rnacounter/rnacounter.c:33324:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T01:08:23,828 33324 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T01:08:23,828 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:08:23,828 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T01:08:23,828 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T01:08:23,828 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T01:08:23,837 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionSwap’: 2025-09-08T01:08:23,892 rnacounter/rnacounter.c:33356:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:08:23,893 33356 | tmp_type = tstate->exc_type; 2025-09-08T01:08:23,893 | ^~~~~~~~ 2025-09-08T01:08:23,893 | exc_state 2025-09-08T01:08:23,931 rnacounter/rnacounter.c:33357:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:08:23,931 33357 | tmp_value = tstate->exc_value; 2025-09-08T01:08:23,931 | ^~ 2025-09-08T01:08:23,969 rnacounter/rnacounter.c:33358:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:08:23,969 33358 | tmp_tb = tstate->exc_traceback; 2025-09-08T01:08:23,970 | ^~ 2025-09-08T01:08:24,025 rnacounter/rnacounter.c:33359:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T01:08:24,025 33359 | tstate->exc_type = *type; 2025-09-08T01:08:24,025 | ^~~~~~~~ 2025-09-08T01:08:24,025 | exc_state 2025-09-08T01:08:24,063 rnacounter/rnacounter.c:33360:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T01:08:24,063 33360 | tstate->exc_value = *value; 2025-09-08T01:08:24,063 | ^~ 2025-09-08T01:08:24,101 rnacounter/rnacounter.c:33361:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T01:08:24,102 33361 | tstate->exc_traceback = *tb; 2025-09-08T01:08:24,102 | ^~ 2025-09-08T01:08:24,104 In file included from /usr/include/python3.13/Python.h:63: 2025-09-08T01:08:24,104 rnacounter/rnacounter.c: In function ‘__Pyx_Generator_SendEx’: 2025-09-08T01:08:24,183 rnacounter/rnacounter.c:33481:30: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T01:08:24,183 33481 | Py_XINCREF(tstate->frame); 2025-09-08T01:08:24,183 | ^~ 2025-09-08T01:08:24,184 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-08T01:08:24,184 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-08T01:08:24,184 | ^~~~ 2025-09-08T01:08:24,184 /usr/include/python3.13/object.h:1041:37: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-08T01:08:24,184 1041 | # define Py_XINCREF(op) Py_XINCREF(_PyObject_CAST(op)) 2025-09-08T01:08:24,184 | ^~~~~~~~~~~~~~ 2025-09-08T01:08:24,184 rnacounter/rnacounter.c:33481:13: note: in expansion of macro ‘Py_XINCREF’ 2025-09-08T01:08:24,184 33481 | Py_XINCREF(tstate->frame); 2025-09-08T01:08:24,184 | ^~~~~~~~~~ 2025-09-08T01:08:24,220 rnacounter/rnacounter.c:33483:14: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:08:24,221 33483 | f->f_back = tstate->frame; 2025-09-08T01:08:24,221 | ^~ 2025-09-08T01:08:24,262 rnacounter/rnacounter.c:33483:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T01:08:24,262 33483 | f->f_back = tstate->frame; 2025-09-08T01:08:24,262 | ^~ 2025-09-08T01:08:24,341 rnacounter/rnacounter.c:33502:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:08:24,341 33502 | Py_CLEAR(f->f_back); 2025-09-08T01:08:24,341 | ^~ 2025-09-08T01:08:24,341 /usr/include/python3.13/pyport.h:558:39: note: in definition of macro ‘_Py_TYPEOF’ 2025-09-08T01:08:24,341 558 | # define _Py_TYPEOF(expr) __typeof__(expr) 2025-09-08T01:08:24,341 | ^~~~ 2025-09-08T01:08:24,342 rnacounter/rnacounter.c:33502:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T01:08:24,342 33502 | Py_CLEAR(f->f_back); 2025-09-08T01:08:24,342 | ^~~~~~~~ 2025-09-08T01:08:24,383 In file included from /usr/include/python3.13/Python.h:72: 2025-09-08T01:08:24,383 rnacounter/rnacounter.c:33502:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:08:24,383 33502 | Py_CLEAR(f->f_back); 2025-09-08T01:08:24,384 | ^~ 2025-09-08T01:08:24,384 /usr/include/python3.13/object.h:1012:41: note: in definition of macro ‘Py_CLEAR’ 2025-09-08T01:08:24,384 1012 | _Py_TYPEOF(op)* _tmp_op_ptr = &(op); \ 2025-09-08T01:08:24,384 | ^~ 2025-09-08T01:08:24,469 rnacounter/rnacounter.c:33502:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T01:08:24,469 33502 | Py_CLEAR(f->f_back); 2025-09-08T01:08:24,469 | ^~ 2025-09-08T01:08:24,469 /usr/include/python3.13/pyport.h:558:39: note: in definition of macro ‘_Py_TYPEOF’ 2025-09-08T01:08:24,469 558 | # define _Py_TYPEOF(expr) __typeof__(expr) 2025-09-08T01:08:24,469 | ^~~~ 2025-09-08T01:08:24,469 rnacounter/rnacounter.c:33502:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T01:08:24,469 33502 | Py_CLEAR(f->f_back); 2025-09-08T01:08:24,469 | ^~~~~~~~ 2025-09-08T01:08:24,511 /usr/include/python3.13/object.h:1014:25: warning: comparison between pointer and integer 2025-09-08T01:08:24,512 1014 | if (_tmp_old_op != NULL) { \ 2025-09-08T01:08:24,512 | ^~ 2025-09-08T01:08:24,512 rnacounter/rnacounter.c:33502:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T01:08:24,512 33502 | Py_CLEAR(f->f_back); 2025-09-08T01:08:24,512 | ^~~~~~~~ 2025-09-08T01:08:24,554 /usr/include/python3.13/object.h:1015:26: error: assignment to ‘int’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T01:08:24,554 1015 | *_tmp_op_ptr = _Py_NULL; \ 2025-09-08T01:08:24,554 | ^ 2025-09-08T01:08:24,555 rnacounter/rnacounter.c:33502:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T01:08:24,555 33502 | Py_CLEAR(f->f_back); 2025-09-08T01:08:24,555 | ^~~~~~~~ 2025-09-08T01:08:25,170 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T01:08:25,333 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T01:08:25,345 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T01:08:25,345 exec(compile('"'"''"'"''"'"' 2025-09-08T01:08:25,345 # This is -- a caller that pip uses to run setup.py 2025-09-08T01:08:25,345 # 2025-09-08T01:08:25,345 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T01:08:25,345 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T01:08:25,345 # - It provides a clear error message when setuptools is not installed. 2025-09-08T01:08:25,345 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T01:08:25,345 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T01:08:25,345 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T01:08:25,345 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T01:08:25,345 import os, sys, tokenize, traceback 2025-09-08T01:08:25,345 2025-09-08T01:08:25,345 try: 2025-09-08T01:08:25,345 import setuptools 2025-09-08T01:08:25,345 except ImportError: 2025-09-08T01:08:25,345 print( 2025-09-08T01:08:25,345 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T01:08:25,345 "the build environment with exception:", 2025-09-08T01:08:25,345 file=sys.stderr, 2025-09-08T01:08:25,345 ) 2025-09-08T01:08:25,345 traceback.print_exc() 2025-09-08T01:08:25,345 sys.exit(1) 2025-09-08T01:08:25,345 2025-09-08T01:08:25,345 __file__ = %r 2025-09-08T01:08:25,345 sys.argv[0] = __file__ 2025-09-08T01:08:25,345 2025-09-08T01:08:25,345 if os.path.exists(__file__): 2025-09-08T01:08:25,345 filename = __file__ 2025-09-08T01:08:25,345 with tokenize.open(__file__) as f: 2025-09-08T01:08:25,345 setup_py_code = f.read() 2025-09-08T01:08:25,345 else: 2025-09-08T01:08:25,345 filename = "" 2025-09-08T01:08:25,345 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T01:08:25,345 2025-09-08T01:08:25,345 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T01:08:25,345 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-s93cclxi/rnacounter_51c7292e391d4cec9b1f8d0e7b39126e/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-aqq8y3oz[/] 2025-09-08T01:08:25,345 [bold magenta]cwd[/]: /tmp/pip-wheel-s93cclxi/rnacounter_51c7292e391d4cec9b1f8d0e7b39126e/ 2025-09-08T01:08:25,345 Building wheel for rnacounter (setup.py): finished with status 'error' 2025-09-08T01:08:25,346 ERROR: Failed building wheel for rnacounter 2025-09-08T01:08:25,347 Running setup.py clean for rnacounter 2025-09-08T01:08:25,347 Running command python setup.py clean 2025-09-08T01:08:26,242 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T01:08:26,242 warnings.warn(msg) 2025-09-08T01:08:26,708 running clean 2025-09-08T01:08:26,855 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T01:08:26,856 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T01:08:26,857 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T01:08:26,857 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T01:08:26,857 removing 'build' 2025-09-08T01:08:26,992 Failed to build rnacounter 2025-09-08T01:08:26,993 ERROR: Failed to build one or more wheels 2025-09-08T01:08:26,994 Exception information: 2025-09-08T01:08:26,994 Traceback (most recent call last): 2025-09-08T01:08:26,994 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T01:08:26,994 status = _inner_run() 2025-09-08T01:08:26,994 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T01:08:26,994 return self.run(options, args) 2025-09-08T01:08:26,994 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T01:08:26,994 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T01:08:26,994 return func(self, options, args) 2025-09-08T01:08:26,994 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T01:08:26,994 raise CommandError("Failed to build one or more wheels") 2025-09-08T01:08:26,994 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T01:08:26,998 Removed build tracker: '/tmp/pip-build-tracker-53okysio'