2025-09-08T00:36:25,069 Created temporary directory: /tmp/pip-build-tracker-rh8txr6k 2025-09-08T00:36:25,070 Initialized build tracking at /tmp/pip-build-tracker-rh8txr6k 2025-09-08T00:36:25,070 Created build tracker: /tmp/pip-build-tracker-rh8txr6k 2025-09-08T00:36:25,070 Entered build tracker: /tmp/pip-build-tracker-rh8txr6k 2025-09-08T00:36:25,071 Created temporary directory: /tmp/pip-wheel-e5w_o3ta 2025-09-08T00:36:25,074 Created temporary directory: /tmp/pip-ephem-wheel-cache-ozzuc271 2025-09-08T00:36:25,131 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2025-09-08T00:36:25,133 2 location(s) to search for versions of rnacounter: 2025-09-08T00:36:25,133 * https://pypi.org/simple/rnacounter/ 2025-09-08T00:36:25,133 * https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:36:25,134 Fetching project page and analyzing links: https://pypi.org/simple/rnacounter/ 2025-09-08T00:36:25,134 Getting page https://pypi.org/simple/rnacounter/ 2025-09-08T00:36:25,135 Found index url https://pypi.org/simple/ 2025-09-08T00:36:25,205 Fetched page https://pypi.org/simple/rnacounter/ as application/vnd.pypi.simple.v1+json 2025-09-08T00:36:25,207 Found link https://files.pythonhosted.org/packages/8f/49/762bb78c6a1215e30ccd9702444375015a50b14847266db0c2f11219e78f/rnacounter-1.1.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.2 2025-09-08T00:36:25,207 Found link https://files.pythonhosted.org/packages/04/c4/e2924af98cbf63c98cc5a9d210c3c54d959cf961fba4df5da3972afc84ae/rnacounter-1.1.3.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.1 2025-09-08T00:36:25,207 Found link https://files.pythonhosted.org/packages/39/70/41efc4ca6703ffdbdbab1dcd66976ed9a30c363b6f5ba417501e2dd9fb00/rnacounter-1.1.3.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.2 2025-09-08T00:36:25,208 Found link https://files.pythonhosted.org/packages/b1/1c/9f8deaa78b994019b9024043168567099fe010c79018373e2f6ed60ea646/rnacounter-1.1.3.7.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.7 2025-09-08T00:36:25,208 Found link https://files.pythonhosted.org/packages/14/a1/be9b12f40d130b182ed0d5d01b36f76e6089805a5c945d77941f5eb0928e/rnacounter-1.1.3.10.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.1.3.10 2025-09-08T00:36:25,208 Found link https://files.pythonhosted.org/packages/8a/5e/1b112fc6343bf52ace3a9afaa30eabaf4338afadabf1fb97454a7556b835/rnacounter-1.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.2 2025-09-08T00:36:25,208 Found link https://files.pythonhosted.org/packages/05/7d/42ecc29d98f52b77953a55da4836d36d534b317b4d66af971c9008804b61/rnacounter-1.2.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.2.1 2025-09-08T00:36:25,208 Found link https://files.pythonhosted.org/packages/dd/92/d53ee16c942fb78a312c03b22b0ddc08eb00ae4627f9125415a2c650b674/rnacounter-1.3.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.3 2025-09-08T00:36:25,208 Found link https://files.pythonhosted.org/packages/49/18/a50e0e2b164272f6d13f458b43d6851766cf121b5672de12078df2bb953a/rnacounter-1.3.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.3.1 2025-09-08T00:36:25,209 Found link https://files.pythonhosted.org/packages/ab/bf/54a012d6660528530b8404401bf494bda91947e38aae0d45ba4d721de6d4/rnacounter-1.4.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4 2025-09-08T00:36:25,209 Found link https://files.pythonhosted.org/packages/84/c0/8f274da33c177f6a7c6d8632d9e99413c83e6ec688825677acace41cfdb1/rnacounter-1.4.1.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4.1 2025-09-08T00:36:25,209 Found link https://files.pythonhosted.org/packages/45/3a/3cc530b864e9fbd87542c73df418d091aeaeb7b73863fb206e62494d988e/rnacounter-1.4.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.4.2 2025-09-08T00:36:25,209 Found link https://files.pythonhosted.org/packages/46/ee/29eed438b10276db92163dff3d25bcb91f3f9e99d9a629c35ddb97f27f4d/rnacounter-1.5.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.5 2025-09-08T00:36:25,209 Found link https://files.pythonhosted.org/packages/a2/ea/657e7b7aa7d777173695606509933b52d794b7dbb79501a87bfea2fb511f/rnacounter-1.5.2.tar.gz (from https://pypi.org/simple/rnacounter/), version: 1.5.2 2025-09-08T00:36:25,210 Fetching project page and analyzing links: https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:36:25,210 Getting page https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:36:25,211 Found index url https://www.piwheels.org/simple/ 2025-09-08T00:36:25,296 Fetched page https://www.piwheels.org/simple/rnacounter/ as text/html 2025-09-08T00:36:25,308 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp35-cp35m-linux_armv7l.whl#sha256=1720939a09d8fbca466729cc4db98be3526fe7a3283ce22ef5c5a21d204a6161 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,309 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp35-cp35m-linux_armv6l.whl#sha256=1720939a09d8fbca466729cc4db98be3526fe7a3283ce22ef5c5a21d204a6161 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,309 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp34-cp34m-linux_armv7l.whl#sha256=e384cbf3852a44dffbf3a6887901acb36b9b30bd5c7e1a3585b2fe39d868d67a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,309 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5.2-cp34-cp34m-linux_armv6l.whl#sha256=e384cbf3852a44dffbf3a6887901acb36b9b30bd5c7e1a3585b2fe39d868d67a (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,309 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp35-cp35m-linux_armv7l.whl#sha256=02c416ec8854b92c815224212889f47dbd376e9797f66a0fb19531508b6bc793 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,309 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp35-cp35m-linux_armv6l.whl#sha256=02c416ec8854b92c815224212889f47dbd376e9797f66a0fb19531508b6bc793 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,309 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp34-cp34m-linux_armv7l.whl#sha256=ee88d3438f69ffa3b1868868fce8191565f303aee8dd3ff0f34c3a62886a495c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,309 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.5-cp34-cp34m-linux_armv6l.whl#sha256=ee88d3438f69ffa3b1868868fce8191565f303aee8dd3ff0f34c3a62886a495c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,310 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp34-cp34m-linux_armv7l.whl#sha256=078f497ded7b5492884f2136fa32e9948422bd185ba0345389b2b0d9fa7ab06e (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,310 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp34-cp34m-linux_armv6l.whl#sha256=078f497ded7b5492884f2136fa32e9948422bd185ba0345389b2b0d9fa7ab06e (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,310 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp35-cp35m-linux_armv6l.whl#sha256=8dffc574db1608136d619621a8809fb0e4d5d3f830e30f94cc2567f4b0a72c55 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,310 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.2-cp35-cp35m-linux_armv7l.whl#sha256=8dffc574db1608136d619621a8809fb0e4d5d3f830e30f94cc2567f4b0a72c55 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,310 Skipping link: No binaries permitted for rnacounter: 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https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4.1-cp34-cp34m-linux_armv6l.whl#sha256=627ec3e6dccdbc30b6697dd277204e300f58ecc971782b1231b09d84a4c1ef94 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,311 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp34-cp34m-linux_armv7l.whl#sha256=9213623d552d14ff1971589aae10e5f886bcfb42045418cc5871a76607eb25b7 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,311 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp34-cp34m-linux_armv6l.whl#sha256=9213623d552d14ff1971589aae10e5f886bcfb42045418cc5871a76607eb25b7 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,311 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp35-cp35m-linux_armv6l.whl#sha256=14bd0bb3f4379d3d334abacfbbbf7ed43ad60736fa69f394c1eda0385dac9193 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,311 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.4-cp35-cp35m-linux_armv7l.whl#sha256=14bd0bb3f4379d3d334abacfbbbf7ed43ad60736fa69f394c1eda0385dac9193 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,311 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3.1-cp35-cp35m-linux_armv6l.whl#sha256=a5e2657cda5fa5a9283a186329fadd8db71987a54d71f713970a85b732030278 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,311 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3.1-cp35-cp35m-linux_armv7l.whl#sha256=a5e2657cda5fa5a9283a186329fadd8db71987a54d71f713970a85b732030278 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,311 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp35-cp35m-linux_armv6l.whl#sha256=b0a053ced5ce83115199785a117fc7820b20daffef5c19acafc83d0425aca0e1 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,312 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp35-cp35m-linux_armv7l.whl#sha256=b0a053ced5ce83115199785a117fc7820b20daffef5c19acafc83d0425aca0e1 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,312 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp34-cp34m-linux_armv7l.whl#sha256=7d3a7695b9d615f45d66d1d00f595ec7b65bbc53dc4ef98292fe909a75adf063 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,312 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.3-cp34-cp34m-linux_armv6l.whl#sha256=7d3a7695b9d615f45d66d1d00f595ec7b65bbc53dc4ef98292fe909a75adf063 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,312 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp35-cp35m-linux_armv7l.whl#sha256=b963649459fb2ab742b717d9b68c590d8ce6333d770e20648104b1e30b3ea97c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,312 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp35-cp35m-linux_armv6l.whl#sha256=b963649459fb2ab742b717d9b68c590d8ce6333d770e20648104b1e30b3ea97c (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,312 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp34-cp34m-linux_armv7l.whl#sha256=2179418dc1805676ef1838a927c0bbcc2a131b63bd87636aecec3fa865b161d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,312 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.2.1-cp34-cp34m-linux_armv6l.whl#sha256=2179418dc1805676ef1838a927c0bbcc2a131b63bd87636aecec3fa865b161d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,312 Skipping link: No binaries permitted for rnacounter: 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https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.7-cp35-cp35m-linux_armv6l.whl#sha256=8863095125d87f061f7651061bc503fbb2c1c613417b578294b555b7bcbdeeba (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,314 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.7-cp34-cp34m-linux_armv7l.whl#sha256=368b4bcbb3bbab49c3600537626272135f936e694d4d17911afd7d83cdb31ee6 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,314 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.7-cp34-cp34m-linux_armv6l.whl#sha256=368b4bcbb3bbab49c3600537626272135f936e694d4d17911afd7d83cdb31ee6 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,314 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp34-cp34m-linux_armv7l.whl#sha256=fb039ca19afdc360ee5843812cf53fbca3ac952fe26a759e4c3700f3b460fc48 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,314 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp34-cp34m-linux_armv6l.whl#sha256=fb039ca19afdc360ee5843812cf53fbca3ac952fe26a759e4c3700f3b460fc48 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,314 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp35-cp35m-linux_armv7l.whl#sha256=51ed8c80ea67e82dc8bdaf5636d930011f8ce97bd9cc30432eedabb4dc8c9c95 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,314 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.2-cp35-cp35m-linux_armv6l.whl#sha256=51ed8c80ea67e82dc8bdaf5636d930011f8ce97bd9cc30432eedabb4dc8c9c95 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,314 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp35-cp35m-linux_armv7l.whl#sha256=534e0f91ccc8a7b74d0e8966764195b4b7e008408e132f2714d3790552ffae89 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,315 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp35-cp35m-linux_armv6l.whl#sha256=534e0f91ccc8a7b74d0e8966764195b4b7e008408e132f2714d3790552ffae89 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,315 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp34-cp34m-linux_armv7l.whl#sha256=699103109ceb69845e93941543cff532f3d26934d4a5ceb71af07f8f0c972407 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,315 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.3.1-cp34-cp34m-linux_armv6l.whl#sha256=699103109ceb69845e93941543cff532f3d26934d4a5ceb71af07f8f0c972407 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,315 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp34-cp34m-linux_armv7l.whl#sha256=e9936c67b8b3ee724e15ef197fef27eb2f5516ba9e9681ca399c5914b4fa01d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,315 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp34-cp34m-linux_armv6l.whl#sha256=e9936c67b8b3ee724e15ef197fef27eb2f5516ba9e9681ca399c5914b4fa01d9 (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,315 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp35-cp35m-linux_armv6l.whl#sha256=edb76e1344212be1373b20323904b92e0429f1b336a75b9b74a852152217fbab (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,315 Skipping link: No binaries permitted for rnacounter: https://archive1.piwheels.org/simple/rnacounter/rnacounter-1.1.2-cp35-cp35m-linux_armv7l.whl#sha256=edb76e1344212be1373b20323904b92e0429f1b336a75b9b74a852152217fbab (from https://www.piwheels.org/simple/rnacounter/) 2025-09-08T00:36:25,316 Skipping link: not a file: https://www.piwheels.org/simple/rnacounter/ 2025-09-08T00:36:25,316 Skipping link: not a file: https://pypi.org/simple/rnacounter/ 2025-09-08T00:36:25,340 Given no hashes to check 1 links for project 'rnacounter': discarding no candidates 2025-09-08T00:36:25,341 Collecting rnacounter==1.1.3.1 2025-09-08T00:36:25,342 Created temporary directory: /tmp/pip-unpack-4jehw4ep 2025-09-08T00:36:25,663 Downloading rnacounter-1.1.3.1.tar.gz (289 kB) 2025-09-08T00:36:25,751 Added rnacounter==1.1.3.1 from https://files.pythonhosted.org/packages/04/c4/e2924af98cbf63c98cc5a9d210c3c54d959cf961fba4df5da3972afc84ae/rnacounter-1.1.3.1.tar.gz to build tracker '/tmp/pip-build-tracker-rh8txr6k' 2025-09-08T00:36:25,752 Running setup.py (path:/tmp/pip-wheel-e5w_o3ta/rnacounter_59325443220944b791b8a2bffca5e5ed/setup.py) egg_info for package rnacounter 2025-09-08T00:36:25,753 Created temporary directory: /tmp/pip-pip-egg-info-mysw8gi3 2025-09-08T00:36:25,753 Preparing metadata (setup.py): started 2025-09-08T00:36:25,754 Running command python setup.py egg_info 2025-09-08T00:36:26,678 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T00:36:26,678 warnings.warn(msg) 2025-09-08T00:36:27,164 running egg_info 2025-09-08T00:36:27,241 creating /tmp/pip-pip-egg-info-mysw8gi3/rnacounter.egg-info 2025-09-08T00:36:27,241 writing /tmp/pip-pip-egg-info-mysw8gi3/rnacounter.egg-info/PKG-INFO 2025-09-08T00:36:27,243 writing dependency_links to /tmp/pip-pip-egg-info-mysw8gi3/rnacounter.egg-info/dependency_links.txt 2025-09-08T00:36:27,243 writing requirements to /tmp/pip-pip-egg-info-mysw8gi3/rnacounter.egg-info/requires.txt 2025-09-08T00:36:27,244 writing top-level names to /tmp/pip-pip-egg-info-mysw8gi3/rnacounter.egg-info/top_level.txt 2025-09-08T00:36:27,244 writing manifest file '/tmp/pip-pip-egg-info-mysw8gi3/rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:36:27,627 reading manifest file '/tmp/pip-pip-egg-info-mysw8gi3/rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:36:27,627 reading manifest template 'MANIFEST.in' 2025-09-08T00:36:27,632 writing manifest file '/tmp/pip-pip-egg-info-mysw8gi3/rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:36:27,768 Preparing metadata (setup.py): finished with status 'done' 2025-09-08T00:36:27,773 Source in /tmp/pip-wheel-e5w_o3ta/rnacounter_59325443220944b791b8a2bffca5e5ed has version 1.1.3.1, which satisfies requirement rnacounter==1.1.3.1 from https://files.pythonhosted.org/packages/04/c4/e2924af98cbf63c98cc5a9d210c3c54d959cf961fba4df5da3972afc84ae/rnacounter-1.1.3.1.tar.gz 2025-09-08T00:36:27,773 Removed rnacounter==1.1.3.1 from https://files.pythonhosted.org/packages/04/c4/e2924af98cbf63c98cc5a9d210c3c54d959cf961fba4df5da3972afc84ae/rnacounter-1.1.3.1.tar.gz from build tracker '/tmp/pip-build-tracker-rh8txr6k' 2025-09-08T00:36:27,777 Created temporary directory: /tmp/pip-unpack-4qhkxoqt 2025-09-08T00:36:27,778 Created temporary directory: /tmp/pip-unpack-ihjvye84 2025-09-08T00:36:27,778 Building wheels for collected packages: rnacounter 2025-09-08T00:36:27,779 Created temporary directory: /tmp/pip-wheel-w4livpev 2025-09-08T00:36:27,780 DEPRECATION: Building 'rnacounter' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'rnacounter'. Discussion can be found at https://github.com/pypa/pip/issues/6334 2025-09-08T00:36:27,781 Building wheel for rnacounter (setup.py): started 2025-09-08T00:36:27,781 Destination directory: /tmp/pip-wheel-w4livpev 2025-09-08T00:36:27,781 Running command python setup.py bdist_wheel 2025-09-08T00:36:28,689 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T00:36:28,690 warnings.warn(msg) 2025-09-08T00:36:29,081 running bdist_wheel 2025-09-08T00:36:29,445 running build 2025-09-08T00:36:29,446 running build_py 2025-09-08T00:36:29,523 creating build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:36:29,523 copying rnacounter/setup.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:36:29,524 copying rnacounter/main.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:36:29,524 copying rnacounter/__init__.py -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:36:29,525 running egg_info 2025-09-08T00:36:29,600 writing rnacounter.egg-info/PKG-INFO 2025-09-08T00:36:29,601 writing dependency_links to rnacounter.egg-info/dependency_links.txt 2025-09-08T00:36:29,602 writing requirements to rnacounter.egg-info/requires.txt 2025-09-08T00:36:29,602 writing top-level names to rnacounter.egg-info/top_level.txt 2025-09-08T00:36:29,678 reading manifest file 'rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:36:29,680 reading manifest template 'MANIFEST.in' 2025-09-08T00:36:29,684 writing manifest file 'rnacounter.egg-info/SOURCES.txt' 2025-09-08T00:36:29,686 /usr/local/lib/python3.13/dist-packages/setuptools/command/build_py.py:212: _Warning: Package 'rnacounter.testfiles' is absent from the `packages` configuration. 2025-09-08T00:36:29,686 !! 2025-09-08T00:36:29,686 ******************************************************************************** 2025-09-08T00:36:29,686 ############################ 2025-09-08T00:36:29,686 # Package would be ignored # 2025-09-08T00:36:29,686 ############################ 2025-09-08T00:36:29,687 Python recognizes 'rnacounter.testfiles' as an importable package[^1], 2025-09-08T00:36:29,687 but it is absent from setuptools' `packages` configuration. 2025-09-08T00:36:29,687 This leads to an ambiguous overall configuration. If you want to distribute this 2025-09-08T00:36:29,687 package, please make sure that 'rnacounter.testfiles' is explicitly added 2025-09-08T00:36:29,687 to the `packages` configuration field. 2025-09-08T00:36:29,687 Alternatively, you can also rely on setuptools' discovery methods 2025-09-08T00:36:29,687 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2025-09-08T00:36:29,687 instead of `find_packages(...)`/`find:`). 2025-09-08T00:36:29,688 You can read more about "package discovery" on setuptools documentation page: 2025-09-08T00:36:29,688 - https://setuptools.pypa.io/en/latest/userguide/package_discovery.html 2025-09-08T00:36:29,688 If you don't want 'rnacounter.testfiles' to be distributed and are 2025-09-08T00:36:29,688 already explicitly excluding 'rnacounter.testfiles' via 2025-09-08T00:36:29,688 `find_namespace_packages(...)/find_namespace` or `find_packages(...)/find`, 2025-09-08T00:36:29,688 you can try to use `exclude_package_data`, or `include-package-data=False` in 2025-09-08T00:36:29,688 combination with a more fine grained `package-data` configuration. 2025-09-08T00:36:29,688 You can read more about "package data files" on setuptools documentation page: 2025-09-08T00:36:29,689 - https://setuptools.pypa.io/en/latest/userguide/datafiles.html 2025-09-08T00:36:29,689 [^1]: For Python, any directory (with suitable naming) can be imported, 2025-09-08T00:36:29,689 even if it does not contain any `.py` files. 2025-09-08T00:36:29,689 On the other hand, currently there is no concept of package data 2025-09-08T00:36:29,689 directory, all directories are treated like packages. 2025-09-08T00:36:29,689 ******************************************************************************** 2025-09-08T00:36:29,689 !! 2025-09-08T00:36:29,690 check.warn(importable) 2025-09-08T00:36:29,690 copying rnacounter/rnacounter.c -> build/lib.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:36:29,694 creating build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:36:29,694 copying rnacounter/testfiles/gapdhKO.bam -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:36:29,695 copying rnacounter/testfiles/gapdhKO.bam.bai -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:36:29,696 copying rnacounter/testfiles/mm9_3genes_renamed.bed -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:36:29,696 copying rnacounter/testfiles/mm9_3genes_renamed.gtf -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:36:29,697 copying rnacounter/testfiles/mm9_Gapdh_renamed.gtf -> build/lib.linux-armv7l-cpython-313/rnacounter/testfiles 2025-09-08T00:36:29,698 running build_ext 2025-09-08T00:36:30,051 building 'rnacounter/rnacounter' extension 2025-09-08T00:36:30,051 creating build/temp.linux-armv7l-cpython-313/rnacounter 2025-09-08T00:36:30,052 arm-linux-gnueabihf-gcc -fno-strict-overflow -Wsign-compare -DNDEBUG -g -O2 -Wall -fPIC -I/usr/local/lib/python3.13/dist-packages/numpy/_core/include -I/usr/include/python3.13 -c rnacounter/rnacounter.c -o build/temp.linux-armv7l-cpython-313/rnacounter/rnacounter.o 2025-09-08T00:36:30,476 rnacounter/rnacounter.c: In function ‘__Pyx_ListComp_Append’: 2025-09-08T00:36:30,476 rnacounter/rnacounter.c:1355:23: error: lvalue required as left operand of assignment 2025-09-08T00:36:30,476 1355 | Py_SIZE(list) = len+1; 2025-09-08T00:36:30,476 | ^ 2025-09-08T00:36:30,477 rnacounter/rnacounter.c: In function ‘__Pyx_PyList_Append’: 2025-09-08T00:36:30,478 rnacounter/rnacounter.c:1422:23: error: lvalue required as left operand of assignment 2025-09-08T00:36:30,478 1422 | Py_SIZE(list) = len+1; 2025-09-08T00:36:30,478 | ^ 2025-09-08T00:36:30,487 rnacounter/rnacounter.c: In function ‘__Pyx_PyList_Extend’: 2025-09-08T00:36:30,487 rnacounter/rnacounter.c:1479:22: error: implicit declaration of function ‘_PyList_Extend’; did you mean ‘PyList_Extend’? [-Wimplicit-function-declaration] 2025-09-08T00:36:30,487 1479 | PyObject* none = _PyList_Extend((PyListObject*)L, v); 2025-09-08T00:36:30,488 | ^~~~~~~~~~~~~~ 2025-09-08T00:36:30,488 | PyList_Extend 2025-09-08T00:36:30,488 rnacounter/rnacounter.c:1479:22: error: initialization of ‘PyObject *’ {aka ‘struct _object *’} from ‘int’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:30,547 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_2parse_bed’: 2025-09-08T00:36:30,550 rnacounter/rnacounter.c:4156:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:30,550 4156 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:36:30,550 | ^~ 2025-09-08T00:36:30,551 In file included from /usr/include/python3.13/Python.h:76, 2025-09-08T00:36:30,551 from rnacounter/rnacounter.c:16: 2025-09-08T00:36:30,551 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:36:30,551 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:36:30,551 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:30,597 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_4join’: 2025-09-08T00:36:30,602 rnacounter/rnacounter.c:5391:9: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:30,602 5391 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:36:30,602 | ^~ 2025-09-08T00:36:30,602 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:36:30,602 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:36:30,603 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:30,638 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_13GenomicObject_2__and__’: 2025-09-08T00:36:30,644 rnacounter/rnacounter.c:6551:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:30,644 6551 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:36:30,644 | ^~ 2025-09-08T00:36:30,645 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:36:30,645 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:36:30,645 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:31,529 rnacounter/rnacounter.c: In function ‘__pyx_pf_10rnacounter_10rnacounter_14parse_args’: 2025-09-08T00:36:31,554 rnacounter/rnacounter.c:22043:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:31,554 22043 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:36:31,554 | ^~ 2025-09-08T00:36:31,554 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:36:31,554 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:36:31,555 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:31,581 rnacounter/rnacounter.c:22097:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:31,581 22097 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:36:31,581 | ^~ 2025-09-08T00:36:31,581 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:36:31,581 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:36:31,581 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:31,609 rnacounter/rnacounter.c:22192:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:31,609 22192 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:36:31,609 | ^~ 2025-09-08T00:36:31,610 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:36:31,610 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:36:31,610 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:31,636 rnacounter/rnacounter.c:22241:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:31,637 22241 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:36:31,637 | ^~ 2025-09-08T00:36:31,637 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:36:31,637 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:36:31,637 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:31,679 rnacounter/rnacounter.c:22377:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:31,679 22377 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:36:31,679 | ^~ 2025-09-08T00:36:31,679 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:36:31,679 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:36:31,679 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:31,734 rnacounter/rnacounter.c:22579:5: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:31,734 22579 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:36:31,734 | ^~ 2025-09-08T00:36:31,734 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:36:31,735 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:36:31,735 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:31,762 rnacounter/rnacounter.c:22644:3: warning: ‘Py_OptimizeFlag’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:31,762 22644 | if (unlikely(!Py_OptimizeFlag)) { 2025-09-08T00:36:31,762 | ^~ 2025-09-08T00:36:31,762 /usr/include/python3.13/cpython/pydebug.h:13:37: note: declared here 2025-09-08T00:36:31,762 13 | Py_DEPRECATED(3.12) PyAPI_DATA(int) Py_OptimizeFlag; 2025-09-08T00:36:31,762 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:31,806 rnacounter/rnacounter.c: In function ‘__pyx_pf_5numpy_7ndarray___getbuffer__’: 2025-09-08T00:36:31,844 rnacounter/rnacounter.c:23199:50: error: ‘NPY_C_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_C_CONTIGUOUS’? 2025-09-08T00:36:31,844 23199 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_C_CONTIGUOUS) != 0)) != 0); 2025-09-08T00:36:31,844 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:31,844 | PyBUF_C_CONTIGUOUS 2025-09-08T00:36:31,847 rnacounter/rnacounter.c:23199:50: note: each undeclared identifier is reported only once for each function it appears in 2025-09-08T00:36:31,906 rnacounter/rnacounter.c:23239:50: error: ‘NPY_F_CONTIGUOUS’ undeclared (first use in this function); did you mean ‘PyBUF_F_CONTIGUOUS’? 2025-09-08T00:36:31,906 23239 | __pyx_t_2 = ((!(PyArray_CHKFLAGS(__pyx_v_self, NPY_F_CONTIGUOUS) != 0)) != 0); 2025-09-08T00:36:31,906 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:31,906 | PyBUF_F_CONTIGUOUS 2025-09-08T00:36:31,913 rnacounter/rnacounter.c: In function ‘__pyx_f_5numpy__util_dtypestring’: 2025-09-08T00:36:31,940 rnacounter/rnacounter.c:24245:29: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T00:36:31,941 24245 | if (unlikely(__pyx_v_descr->names == Py_None)) { 2025-09-08T00:36:31,941 | ^~ 2025-09-08T00:36:31,941 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:36:31,941 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:36:31,941 | ^ 2025-09-08T00:36:31,971 rnacounter/rnacounter.c:24249:28: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘names’ 2025-09-08T00:36:31,971 24249 | __pyx_t_1 = __pyx_v_descr->names; __Pyx_INCREF(__pyx_t_1); __pyx_t_2 = 0; 2025-09-08T00:36:31,972 | ^~ 2025-09-08T00:36:32,005 rnacounter/rnacounter.c:24267:47: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘fields’ 2025-09-08T00:36:32,005 24267 | __pyx_t_3 = PyObject_GetItem(__pyx_v_descr->fields, __pyx_v_childname); if (unlikely(__pyx_t_3 == NULL)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 795; __pyx_clineno = __LINE__; goto __pyx_L1_error;}; 2025-09-08T00:36:32,005 | ^~ 2025-09-08T00:36:32,054 rnacounter/rnacounter.c:24448:79: error: ‘PyArray_Descr’ {aka ‘struct _PyArray_Descr’} has no member named ‘elsize’ 2025-09-08T00:36:32,054 24448 | (__pyx_v_offset[__pyx_t_8]) = ((__pyx_v_offset[__pyx_t_8]) + __pyx_v_child->elsize); 2025-09-08T00:36:32,054 | ^~ 2025-09-08T00:36:32,102 rnacounter/rnacounter.c: In function ‘__pyx_tp_dealloc_10rnacounter_10rnacounter_Counter’: 2025-09-08T00:36:32,130 rnacounter/rnacounter.c:25069:75: error: implicit declaration of function ‘_PyGC_FINALIZED’ [-Wimplicit-function-declaration] 2025-09-08T00:36:32,131 25069 | if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) { 2025-09-08T00:36:32,131 | ^~~~~~~~~~~~~~~ 2025-09-08T00:36:32,239 rnacounter/rnacounter.c: In function ‘__Pyx_InitCachedConstants’: 2025-09-08T00:36:32,271 rnacounter/rnacounter.c:28836:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:32,272 28836 | __pyx_codeobj__62 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__61, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 64, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,272 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,272 In file included from /usr/include/python3.13/Python.h:101: 2025-09-08T00:36:32,272 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,272 213 | PyCode_New( 2025-09-08T00:36:32,272 | ^~~~~~~~~~ 2025-09-08T00:36:32,308 rnacounter/rnacounter.c:28836:243: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:32,308 28836 | __pyx_codeobj__62 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__61, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 64, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,308 | ^~ 2025-09-08T00:36:32,308 | | 2025-09-08T00:36:32,308 | int 2025-09-08T00:36:32,308 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,309 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,309 | ^~~~~ 2025-09-08T00:36:32,309 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:36:32,309 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:32,309 | ~~~~~~~~~~^ 2025-09-08T00:36:32,344 rnacounter/rnacounter.c:28836:247: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:36:32,344 28836 | __pyx_codeobj__62 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__61, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 64, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,344 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,344 | | 2025-09-08T00:36:32,344 | PyObject * {aka struct _object *} 2025-09-08T00:36:32,345 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,345 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,345 | ^~~~ 2025-09-08T00:36:32,345 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:36:32,345 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:32,345 | ~~~~^ 2025-09-08T00:36:32,380 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:36:32,380 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,380 | ^~~~~~~~~~ 2025-09-08T00:36:32,380 rnacounter/rnacounter.c:28836:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,380 28836 | __pyx_codeobj__62 = (PyObject*)__Pyx_PyCode_New(2, 0, 9, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__61, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_gtf, 64, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__62)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 64; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,381 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,381 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,381 213 | PyCode_New( 2025-09-08T00:36:32,381 | ^~~~~~~~~~ 2025-09-08T00:36:32,413 rnacounter/rnacounter.c:28848:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:32,413 28848 | __pyx_codeobj__64 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 84, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,413 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,413 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,413 213 | PyCode_New( 2025-09-08T00:36:32,413 | ^~~~~~~~~~ 2025-09-08T00:36:32,449 rnacounter/rnacounter.c:28848:244: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:32,449 28848 | __pyx_codeobj__64 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 84, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,449 | ^~ 2025-09-08T00:36:32,449 | | 2025-09-08T00:36:32,449 | int 2025-09-08T00:36:32,449 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,449 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,449 | ^~~~~ 2025-09-08T00:36:32,449 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:36:32,450 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:32,450 | ~~~~~~~~~~^ 2025-09-08T00:36:32,485 rnacounter/rnacounter.c:28848:248: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:36:32,485 28848 | __pyx_codeobj__64 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 84, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,485 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,485 | | 2025-09-08T00:36:32,485 | PyObject * {aka struct _object *} 2025-09-08T00:36:32,485 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,485 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,485 | ^~~~ 2025-09-08T00:36:32,486 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:36:32,486 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:32,486 | ~~~~^ 2025-09-08T00:36:32,521 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:36:32,521 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,521 | ^~~~~~~~~~ 2025-09-08T00:36:32,521 rnacounter/rnacounter.c:28848:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,521 28848 | __pyx_codeobj__64 = (PyObject*)__Pyx_PyCode_New(2, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__63, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_bed, 84, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__64)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 84; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,521 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,521 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,522 213 | PyCode_New( 2025-09-08T00:36:32,522 | ^~~~~~~~~~ 2025-09-08T00:36:32,553 rnacounter/rnacounter.c:28860:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:32,554 28860 | __pyx_codeobj__66 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 110, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,554 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,554 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,554 213 | PyCode_New( 2025-09-08T00:36:32,554 | ^~~~~~~~~~ 2025-09-08T00:36:32,589 rnacounter/rnacounter.c:28860:239: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:32,590 28860 | __pyx_codeobj__66 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 110, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,590 | ^~~ 2025-09-08T00:36:32,590 | | 2025-09-08T00:36:32,590 | int 2025-09-08T00:36:32,590 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,590 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,590 | ^~~~~ 2025-09-08T00:36:32,590 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:36:32,590 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:32,590 | ~~~~~~~~~~^ 2025-09-08T00:36:32,626 rnacounter/rnacounter.c:28860:244: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:36:32,626 28860 | __pyx_codeobj__66 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 110, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,626 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,626 | | 2025-09-08T00:36:32,626 | PyObject * {aka struct _object *} 2025-09-08T00:36:32,626 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,626 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,626 | ^~~~ 2025-09-08T00:36:32,626 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:36:32,627 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:32,627 | ~~~~^ 2025-09-08T00:36:32,662 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:36:32,662 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,662 | ^~~~~~~~~~ 2025-09-08T00:36:32,662 rnacounter/rnacounter.c:28860:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,662 28860 | __pyx_codeobj__66 = (PyObject*)__Pyx_PyCode_New(1, 0, 18, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__65, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_join, 110, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__66)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 110; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,662 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,662 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,662 213 | PyCode_New( 2025-09-08T00:36:32,663 | ^~~~~~~~~~ 2025-09-08T00:36:32,695 rnacounter/rnacounter.c:28872:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:32,695 28872 | __pyx_codeobj__68 = (PyObject*)__Pyx_PyCode_New(4, 0, 54, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 589, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,695 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,695 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,695 213 | PyCode_New( 2025-09-08T00:36:32,695 | ^~~~~~~~~~ 2025-09-08T00:36:32,731 rnacounter/rnacounter.c:28872:248: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:32,731 28872 | __pyx_codeobj__68 = (PyObject*)__Pyx_PyCode_New(4, 0, 54, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 589, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,731 | ^~~ 2025-09-08T00:36:32,731 | | 2025-09-08T00:36:32,731 | int 2025-09-08T00:36:32,731 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,731 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,731 | ^~~~~ 2025-09-08T00:36:32,731 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:36:32,732 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:32,732 | ~~~~~~~~~~^ 2025-09-08T00:36:32,767 rnacounter/rnacounter.c:28872:253: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:36:32,767 28872 | __pyx_codeobj__68 = (PyObject*)__Pyx_PyCode_New(4, 0, 54, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 589, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,767 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,767 | | 2025-09-08T00:36:32,767 | PyObject * {aka struct _object *} 2025-09-08T00:36:32,767 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,767 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,768 | ^~~~ 2025-09-08T00:36:32,768 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:36:32,768 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:32,768 | ~~~~^ 2025-09-08T00:36:32,803 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:36:32,804 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,804 | ^~~~~~~~~~ 2025-09-08T00:36:32,804 rnacounter/rnacounter.c:28872:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,804 28872 | __pyx_codeobj__68 = (PyObject*)__Pyx_PyCode_New(4, 0, 54, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__67, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_process_chunk, 589, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__68)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 589; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,804 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,804 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,804 213 | PyCode_New( 2025-09-08T00:36:32,804 | ^~~~~~~~~~ 2025-09-08T00:36:32,837 rnacounter/rnacounter.c:28884:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:32,837 28884 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 717, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,837 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,838 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,838 213 | PyCode_New( 2025-09-08T00:36:32,838 | ^~~~~~~~~~ 2025-09-08T00:36:32,873 rnacounter/rnacounter.c:28884:247: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:32,874 28884 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 717, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,874 | ^~~ 2025-09-08T00:36:32,874 | | 2025-09-08T00:36:32,874 | int 2025-09-08T00:36:32,874 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,874 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,874 | ^~~~~ 2025-09-08T00:36:32,875 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:36:32,875 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:32,875 | ~~~~~~~~~~^ 2025-09-08T00:36:32,911 rnacounter/rnacounter.c:28884:252: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:36:32,911 28884 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 717, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,911 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,911 | | 2025-09-08T00:36:32,911 | PyObject * {aka struct _object *} 2025-09-08T00:36:32,911 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,911 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,911 | ^~~~ 2025-09-08T00:36:32,911 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:36:32,912 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:32,912 | ~~~~^ 2025-09-08T00:36:32,947 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:36:32,947 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:32,947 | ^~~~~~~~~~ 2025-09-08T00:36:32,947 rnacounter/rnacounter.c:28884:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:32,947 28884 | __pyx_codeobj__70 = (PyObject*)__Pyx_PyCode_New(7, 0, 14, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__69, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_print_output, 717, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__70)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 717; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,947 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,947 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,948 213 | PyCode_New( 2025-09-08T00:36:32,948 | ^~~~~~~~~~ 2025-09-08T00:36:32,980 rnacounter/rnacounter.c:28896:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:32,980 28896 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(3, 0, 20, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 737, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:32,980 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:32,980 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:32,980 213 | PyCode_New( 2025-09-08T00:36:32,980 | ^~~~~~~~~~ 2025-09-08T00:36:33,016 rnacounter/rnacounter.c:28896:250: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:33,016 28896 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(3, 0, 20, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 737, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,016 | ^~~ 2025-09-08T00:36:33,016 | | 2025-09-08T00:36:33,016 | int 2025-09-08T00:36:33,016 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:33,016 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:33,016 | ^~~~~ 2025-09-08T00:36:33,017 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:36:33,017 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:33,017 | ~~~~~~~~~~^ 2025-09-08T00:36:33,052 rnacounter/rnacounter.c:28896:255: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:36:33,052 28896 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(3, 0, 20, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 737, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,052 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:33,052 | | 2025-09-08T00:36:33,052 | PyObject * {aka struct _object *} 2025-09-08T00:36:33,052 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:33,053 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:33,053 | ^~~~ 2025-09-08T00:36:33,053 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:36:33,053 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:33,053 | ~~~~^ 2025-09-08T00:36:33,088 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:36:33,088 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:33,088 | ^~~~~~~~~~ 2025-09-08T00:36:33,088 rnacounter/rnacounter.c:28896:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:33,088 28896 | __pyx_codeobj__73 = (PyObject*)__Pyx_PyCode_New(3, 0, 20, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__72, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_rnacounter_main, 737, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__73)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 737; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,089 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:33,089 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:33,089 213 | PyCode_New( 2025-09-08T00:36:33,089 | ^~~~~~~~~~ 2025-09-08T00:36:33,121 rnacounter/rnacounter.c:28905:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:33,121 28905 | __pyx_codeobj__74 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_usage_string, 823, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,121 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:33,121 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:33,121 213 | PyCode_New( 2025-09-08T00:36:33,121 | ^~~~~~~~~~ 2025-09-08T00:36:33,157 rnacounter/rnacounter.c:28905:248: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:33,157 28905 | __pyx_codeobj__74 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_usage_string, 823, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,157 | ^~~ 2025-09-08T00:36:33,157 | | 2025-09-08T00:36:33,157 | int 2025-09-08T00:36:33,157 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:33,157 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:33,157 | ^~~~~ 2025-09-08T00:36:33,158 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:36:33,158 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:33,158 | ~~~~~~~~~~^ 2025-09-08T00:36:33,193 rnacounter/rnacounter.c:28905:253: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:36:33,193 28905 | __pyx_codeobj__74 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_usage_string, 823, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,193 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:33,193 | | 2025-09-08T00:36:33,193 | PyObject * {aka struct _object *} 2025-09-08T00:36:33,194 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:33,194 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:33,194 | ^~~~ 2025-09-08T00:36:33,194 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:36:33,194 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:33,194 | ~~~~^ 2025-09-08T00:36:33,229 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:36:33,229 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:33,229 | ^~~~~~~~~~ 2025-09-08T00:36:33,229 rnacounter/rnacounter.c:28905:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:33,230 28905 | __pyx_codeobj__74 = (PyObject*)__Pyx_PyCode_New(0, 0, 0, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_usage_string, 823, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__74)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 823; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,230 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:33,230 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:33,230 213 | PyCode_New( 2025-09-08T00:36:33,230 | ^~~~~~~~~~ 2025-09-08T00:36:33,262 rnacounter/rnacounter.c:28917:3: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:33,262 28917 | __pyx_codeobj__76 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 826, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,262 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:33,262 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:33,262 213 | PyCode_New( 2025-09-08T00:36:33,262 | ^~~~~~~~~~ 2025-09-08T00:36:33,298 rnacounter/rnacounter.c:28917:245: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:33,298 28917 | __pyx_codeobj__76 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 826, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,298 | ^~~ 2025-09-08T00:36:33,298 | | 2025-09-08T00:36:33,299 | int 2025-09-08T00:36:33,299 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:33,299 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:33,299 | ^~~~~ 2025-09-08T00:36:33,299 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:36:33,299 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:33,299 | ~~~~~~~~~~^ 2025-09-08T00:36:33,334 rnacounter/rnacounter.c:28917:250: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:36:33,335 28917 | __pyx_codeobj__76 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 826, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,335 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:33,335 | | 2025-09-08T00:36:33,335 | PyObject * {aka struct _object *} 2025-09-08T00:36:33,335 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:33,335 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:33,335 | ^~~~ 2025-09-08T00:36:33,335 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:36:33,335 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:33,335 | ~~~~^ 2025-09-08T00:36:33,370 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:36:33,371 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:33,371 | ^~~~~~~~~~ 2025-09-08T00:36:33,371 rnacounter/rnacounter.c:28917:34: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:33,371 28917 | __pyx_codeobj__76 = (PyObject*)__Pyx_PyCode_New(1, 0, 11, 0, 0, __pyx_empty_bytes, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_tuple__75, __pyx_empty_tuple, __pyx_empty_tuple, __pyx_kp_s_Users_delafont_repos_rnacounter, __pyx_n_s_parse_args, 826, __pyx_empty_bytes); if (unlikely(!__pyx_codeobj__76)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 826; __pyx_clineno = __LINE__; goto __pyx_L1_error;} 2025-09-08T00:36:33,371 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:33,371 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:33,371 213 | PyCode_New( 2025-09-08T00:36:33,371 | ^~~~~~~~~~ 2025-09-08T00:36:33,374 rnacounter/rnacounter.c: In function ‘PyInit_rnacounter’: 2025-09-08T00:36:33,406 rnacounter/rnacounter.c:29020:47: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,407 29020 | __pyx_type_10rnacounter_10rnacounter_Counter.tp_print = 0; 2025-09-08T00:36:33,407 | ^ 2025-09-08T00:36:33,439 rnacounter/rnacounter.c:29024:53: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,439 29024 | __pyx_type_10rnacounter_10rnacounter_GenomicObject.tp_print = 0; 2025-09-08T00:36:33,440 | ^ 2025-09-08T00:36:33,473 rnacounter/rnacounter.c:29041:44: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,473 29041 | __pyx_type_10rnacounter_10rnacounter_Exon.tp_print = 0; 2025-09-08T00:36:33,473 | ^ 2025-09-08T00:36:33,506 rnacounter/rnacounter.c:29047:50: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,506 29047 | __pyx_type_10rnacounter_10rnacounter_Transcript.tp_print = 0; 2025-09-08T00:36:33,506 | ^ 2025-09-08T00:36:33,538 rnacounter/rnacounter.c:29052:44: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,539 29052 | __pyx_type_10rnacounter_10rnacounter_Gene.tp_print = 0; 2025-09-08T00:36:33,539 | ^ 2025-09-08T00:36:33,571 rnacounter/rnacounter.c:29056:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,572 29056 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct__parse_gtf.tp_print = 0; 2025-09-08T00:36:33,572 | ^ 2025-09-08T00:36:33,604 rnacounter/rnacounter.c:29059:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,604 29059 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_1_genexpr.tp_print = 0; 2025-09-08T00:36:33,604 | ^ 2025-09-08T00:36:33,637 rnacounter/rnacounter.c:29062:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,637 29062 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_2_genexpr.tp_print = 0; 2025-09-08T00:36:33,637 | ^ 2025-09-08T00:36:33,670 rnacounter/rnacounter.c:29065:65: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,670 29065 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_3_join.tp_print = 0; 2025-09-08T00:36:33,670 | ^ 2025-09-08T00:36:33,703 rnacounter/rnacounter.c:29068:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,703 29068 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_4_genexpr.tp_print = 0; 2025-09-08T00:36:33,703 | ^ 2025-09-08T00:36:33,735 rnacounter/rnacounter.c:29071:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,736 29071 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_5_genexpr.tp_print = 0; 2025-09-08T00:36:33,736 | ^ 2025-09-08T00:36:33,768 rnacounter/rnacounter.c:29074:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,768 29074 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_6_genexpr.tp_print = 0; 2025-09-08T00:36:33,769 | ^ 2025-09-08T00:36:33,801 rnacounter/rnacounter.c:29077:74: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,801 29077 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_7_process_chunk.tp_print = 0; 2025-09-08T00:36:33,801 | ^ 2025-09-08T00:36:33,834 rnacounter/rnacounter.c:29080:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,834 29080 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_8_genexpr.tp_print = 0; 2025-09-08T00:36:33,834 | ^ 2025-09-08T00:36:33,867 rnacounter/rnacounter.c:29083:68: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,867 29083 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_9_genexpr.tp_print = 0; 2025-09-08T00:36:33,867 | ^ 2025-09-08T00:36:33,900 rnacounter/rnacounter.c:29086:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,900 29086 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_10_genexpr.tp_print = 0; 2025-09-08T00:36:33,900 | ^ 2025-09-08T00:36:33,933 rnacounter/rnacounter.c:29089:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,933 29089 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_11_genexpr.tp_print = 0; 2025-09-08T00:36:33,933 | ^ 2025-09-08T00:36:33,965 rnacounter/rnacounter.c:29092:74: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,966 29092 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_12_print_output.tp_print = 0; 2025-09-08T00:36:33,966 | ^ 2025-09-08T00:36:33,999 rnacounter/rnacounter.c:29095:72: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:33,999 29095 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_13_parse_args.tp_print = 0; 2025-09-08T00:36:33,999 | ^ 2025-09-08T00:36:34,033 rnacounter/rnacounter.c:29098:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:34,033 29098 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_14_genexpr.tp_print = 0; 2025-09-08T00:36:34,033 | ^ 2025-09-08T00:36:34,066 rnacounter/rnacounter.c:29101:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:34,066 29101 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_15_genexpr.tp_print = 0; 2025-09-08T00:36:34,066 | ^ 2025-09-08T00:36:34,100 rnacounter/rnacounter.c:29104:69: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘tp_print’ 2025-09-08T00:36:34,100 29104 | __pyx_type_10rnacounter_10rnacounter___pyx_scope_struct_16_genexpr.tp_print = 0; 2025-09-08T00:36:34,100 | ^ 2025-09-08T00:36:34,154 rnacounter/rnacounter.c: In function ‘__Pyx_PyUnicode_Equals’: 2025-09-08T00:36:34,192 rnacounter/rnacounter.c:84:51: error: implicit declaration of function ‘_PyUnicode_Ready’; did you mean ‘PyUnicode_READY’? [-Wimplicit-function-declaration] 2025-09-08T00:36:34,192 84 | 0 : _PyUnicode_Ready((PyObject *)(op))) 2025-09-08T00:36:34,192 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:34,192 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:36:34,192 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:36:34,192 | ^ 2025-09-08T00:36:34,192 rnacounter/rnacounter.c:29616:22: note: in expansion of macro ‘__Pyx_PyUnicode_READY’ 2025-09-08T00:36:34,192 29616 | if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0)) 2025-09-08T00:36:34,192 | ^~~~~~~~~~~~~~~~~~~~~ 2025-09-08T00:36:34,240 rnacounter/rnacounter.c: In function ‘__Pyx_ErrRestore’: 2025-09-08T00:36:34,274 rnacounter/rnacounter.c:29708:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:36:34,274 29708 | tmp_type = tstate->curexc_type; 2025-09-08T00:36:34,274 | ^~ 2025-09-08T00:36:34,308 rnacounter/rnacounter.c:29709:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:36:34,308 29709 | tmp_value = tstate->curexc_value; 2025-09-08T00:36:34,308 | ^~ 2025-09-08T00:36:34,342 rnacounter/rnacounter.c:29710:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:36:34,342 29710 | tmp_tb = tstate->curexc_traceback; 2025-09-08T00:36:34,342 | ^~ 2025-09-08T00:36:34,376 rnacounter/rnacounter.c:29711:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:36:34,376 29711 | tstate->curexc_type = type; 2025-09-08T00:36:34,376 | ^~ 2025-09-08T00:36:34,410 rnacounter/rnacounter.c:29712:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:36:34,410 29712 | tstate->curexc_value = value; 2025-09-08T00:36:34,410 | ^~ 2025-09-08T00:36:34,444 rnacounter/rnacounter.c:29713:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:36:34,444 29713 | tstate->curexc_traceback = tb; 2025-09-08T00:36:34,444 | ^~ 2025-09-08T00:36:34,444 rnacounter/rnacounter.c: In function ‘__Pyx_ErrFetch’: 2025-09-08T00:36:34,478 rnacounter/rnacounter.c:29724:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:36:34,478 29724 | *type = tstate->curexc_type; 2025-09-08T00:36:34,478 | ^~ 2025-09-08T00:36:34,512 rnacounter/rnacounter.c:29725:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:36:34,512 29725 | *value = tstate->curexc_value; 2025-09-08T00:36:34,512 | ^~ 2025-09-08T00:36:34,546 rnacounter/rnacounter.c:29726:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:36:34,546 29726 | *tb = tstate->curexc_traceback; 2025-09-08T00:36:34,546 | ^~ 2025-09-08T00:36:34,580 rnacounter/rnacounter.c:29727:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:36:34,580 29727 | tstate->curexc_type = 0; 2025-09-08T00:36:34,580 | ^~ 2025-09-08T00:36:34,614 rnacounter/rnacounter.c:29728:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:36:34,614 29728 | tstate->curexc_value = 0; 2025-09-08T00:36:34,615 | ^~ 2025-09-08T00:36:34,648 rnacounter/rnacounter.c:29729:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:36:34,648 29729 | tstate->curexc_traceback = 0; 2025-09-08T00:36:34,649 | ^~ 2025-09-08T00:36:34,715 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionSave’: 2025-09-08T00:36:34,764 rnacounter/rnacounter.c:29926:21: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:36:34,764 29926 | *type = tstate->exc_type; 2025-09-08T00:36:34,764 | ^~~~~~~~ 2025-09-08T00:36:34,764 | exc_state 2025-09-08T00:36:34,798 rnacounter/rnacounter.c:29927:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:36:34,798 29927 | *value = tstate->exc_value; 2025-09-08T00:36:34,798 | ^~ 2025-09-08T00:36:34,831 rnacounter/rnacounter.c:29928:17: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:36:34,831 29928 | *tb = tstate->exc_traceback; 2025-09-08T00:36:34,832 | ^~ 2025-09-08T00:36:34,832 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionReset’: 2025-09-08T00:36:34,880 rnacounter/rnacounter.c:29940:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:36:34,880 29940 | tmp_type = tstate->exc_type; 2025-09-08T00:36:34,880 | ^~~~~~~~ 2025-09-08T00:36:34,880 | exc_state 2025-09-08T00:36:34,914 rnacounter/rnacounter.c:29941:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:36:34,914 29941 | tmp_value = tstate->exc_value; 2025-09-08T00:36:34,914 | ^~ 2025-09-08T00:36:34,948 rnacounter/rnacounter.c:29942:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:36:34,948 29942 | tmp_tb = tstate->exc_traceback; 2025-09-08T00:36:34,948 | ^~ 2025-09-08T00:36:34,996 rnacounter/rnacounter.c:29943:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:36:34,996 29943 | tstate->exc_type = type; 2025-09-08T00:36:34,996 | ^~~~~~~~ 2025-09-08T00:36:34,997 | exc_state 2025-09-08T00:36:35,030 rnacounter/rnacounter.c:29944:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:36:35,030 29944 | tstate->exc_value = value; 2025-09-08T00:36:35,030 | ^~ 2025-09-08T00:36:35,064 rnacounter/rnacounter.c:29945:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:36:35,064 29945 | tstate->exc_traceback = tb; 2025-09-08T00:36:35,064 | ^~ 2025-09-08T00:36:35,064 rnacounter/rnacounter.c: In function ‘__Pyx_GetException’: 2025-09-08T00:36:35,098 rnacounter/rnacounter.c:29959:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:36:35,098 29959 | local_type = tstate->curexc_type; 2025-09-08T00:36:35,098 | ^~ 2025-09-08T00:36:35,131 rnacounter/rnacounter.c:29960:25: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:36:35,131 29960 | local_value = tstate->curexc_value; 2025-09-08T00:36:35,132 | ^~ 2025-09-08T00:36:35,165 rnacounter/rnacounter.c:29961:22: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:36:35,165 29961 | local_tb = tstate->curexc_traceback; 2025-09-08T00:36:35,165 | ^~ 2025-09-08T00:36:35,199 rnacounter/rnacounter.c:29962:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:36:35,200 29962 | tstate->curexc_type = 0; 2025-09-08T00:36:35,200 | ^~ 2025-09-08T00:36:35,234 rnacounter/rnacounter.c:29963:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:36:35,234 29963 | tstate->curexc_value = 0; 2025-09-08T00:36:35,234 | ^~ 2025-09-08T00:36:35,268 rnacounter/rnacounter.c:29964:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:36:35,268 29964 | tstate->curexc_traceback = 0; 2025-09-08T00:36:35,268 | ^~ 2025-09-08T00:36:35,303 rnacounter/rnacounter.c:29970:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:36:35,303 29970 | if (unlikely(tstate->curexc_type)) 2025-09-08T00:36:35,303 | ^~ 2025-09-08T00:36:35,303 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:36:35,303 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:36:35,303 | ^ 2025-09-08T00:36:35,364 rnacounter/rnacounter.c:29988:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:36:35,364 29988 | tmp_type = tstate->exc_type; 2025-09-08T00:36:35,364 | ^~~~~~~~ 2025-09-08T00:36:35,364 | exc_state 2025-09-08T00:36:35,397 rnacounter/rnacounter.c:29989:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:36:35,397 29989 | tmp_value = tstate->exc_value; 2025-09-08T00:36:35,398 | ^~ 2025-09-08T00:36:35,431 rnacounter/rnacounter.c:29990:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:36:35,431 29990 | tmp_tb = tstate->exc_traceback; 2025-09-08T00:36:35,431 | ^~ 2025-09-08T00:36:35,480 rnacounter/rnacounter.c:29991:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:36:35,480 29991 | tstate->exc_type = local_type; 2025-09-08T00:36:35,480 | ^~~~~~~~ 2025-09-08T00:36:35,480 | exc_state 2025-09-08T00:36:35,513 rnacounter/rnacounter.c:29992:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:36:35,514 29992 | tstate->exc_value = local_value; 2025-09-08T00:36:35,514 | ^~ 2025-09-08T00:36:35,547 rnacounter/rnacounter.c:29993:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:36:35,547 29993 | tstate->exc_traceback = local_tb; 2025-09-08T00:36:35,547 | ^~ 2025-09-08T00:36:35,574 rnacounter/rnacounter.c: In function ‘__Pyx_ParseOptionalKeywords’: 2025-09-08T00:36:35,632 rnacounter/rnacounter.c:30097:22: error: implicit declaration of function ‘PyUnicode_GET_SIZE’; did you mean ‘PyDict_GET_SIZE’? [-Wimplicit-function-declaration] 2025-09-08T00:36:35,632 30097 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : 2025-09-08T00:36:35,632 | ^~~~~~~~~~~~~~~~~~ 2025-09-08T00:36:35,632 | PyDict_GET_SIZE 2025-09-08T00:36:35,742 rnacounter/rnacounter.c: In function ‘__Pyx_Raise’: 2025-09-08T00:36:35,769 rnacounter/rnacounter.c:30323:34: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:36:35,769 30323 | PyObject* tmp_tb = tstate->curexc_traceback; 2025-09-08T00:36:35,769 | ^~ 2025-09-08T00:36:35,804 rnacounter/rnacounter.c:30326:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:36:35,804 30326 | tstate->curexc_traceback = tb; 2025-09-08T00:36:35,804 | ^~ 2025-09-08T00:36:35,862 rnacounter/rnacounter.c: In function ‘__Pyx_PyIter_Next2’: 2025-09-08T00:36:35,896 rnacounter/rnacounter.c:30371:31: error: ‘_PyObject_NextNotImplemented’ undeclared (first use in this function); did you mean ‘PyObject_HashNotImplemented’? 2025-09-08T00:36:35,896 30371 | if (unlikely(iternext == &_PyObject_NextNotImplemented)) 2025-09-08T00:36:35,896 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T00:36:35,896 rnacounter/rnacounter.c:405:43: note: in definition of macro ‘unlikely’ 2025-09-08T00:36:35,896 405 | #define unlikely(x) __builtin_expect(!!(x), 0) 2025-09-08T00:36:35,896 | ^ 2025-09-08T00:36:35,942 rnacounter/rnacounter.c: In function ‘__Pyx_IterFinish’: 2025-09-08T00:36:35,976 rnacounter/rnacounter.c:30574:32: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:36:35,976 30574 | PyObject* exc_type = tstate->curexc_type; 2025-09-08T00:36:35,977 | ^~ 2025-09-08T00:36:36,012 rnacounter/rnacounter.c:30578:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:36:36,012 30578 | exc_value = tstate->curexc_value; 2025-09-08T00:36:36,012 | ^~ 2025-09-08T00:36:36,047 rnacounter/rnacounter.c:30579:28: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:36:36,047 30579 | exc_tb = tstate->curexc_traceback; 2025-09-08T00:36:36,048 | ^~ 2025-09-08T00:36:36,083 rnacounter/rnacounter.c:30580:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_type’ 2025-09-08T00:36:36,083 30580 | tstate->curexc_type = 0; 2025-09-08T00:36:36,083 | ^~ 2025-09-08T00:36:36,117 rnacounter/rnacounter.c:30581:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_value’ 2025-09-08T00:36:36,118 30581 | tstate->curexc_value = 0; 2025-09-08T00:36:36,118 | ^~ 2025-09-08T00:36:36,152 rnacounter/rnacounter.c:30582:19: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘curexc_traceback’ 2025-09-08T00:36:36,152 30582 | tstate->curexc_traceback = 0; 2025-09-08T00:36:36,153 | ^~ 2025-09-08T00:36:36,641 rnacounter/rnacounter.c: In function ‘__Pyx_CyFunction_Call’: 2025-09-08T00:36:36,692 rnacounter/rnacounter.c:31926:16: error: implicit declaration of function ‘PyCFunction_Call’; did you mean ‘PyCFunction_New’? [-Wimplicit-function-declaration] 2025-09-08T00:36:36,692 31926 | return PyCFunction_Call(func, arg, kw); 2025-09-08T00:36:36,693 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:36,693 | PyCFunction_New 2025-09-08T00:36:36,732 rnacounter/rnacounter.c:31926:16: error: returning ‘int’ from a function with return type ‘PyObject *’ {aka ‘struct _object *’} makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:36,732 31926 | return PyCFunction_Call(func, arg, kw); 2025-09-08T00:36:36,732 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2025-09-08T00:36:36,752 rnacounter/rnacounter.c: In function ‘__Pyx_CyFunction_init’: 2025-09-08T00:36:36,804 rnacounter/rnacounter.c:31991:41: error: ‘PyCFunction_Call’ undeclared (first use in this function); did you mean ‘PyCFunction_New’? 2025-09-08T00:36:36,804 31991 | __pyx_CyFunctionType_type.tp_call = PyCFunction_Call; 2025-09-08T00:36:36,804 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:36,804 | PyCFunction_New 2025-09-08T00:36:36,848 rnacounter/rnacounter.c: In function ‘__Pyx_CreateCodeObjectForTraceback’: 2025-09-08T00:36:36,885 rnacounter/rnacounter.c:32167:5: warning: ‘PyCode_New’ is deprecated [-Wdeprecated-declarations] 2025-09-08T00:36:36,885 32167 | py_code = __Pyx_PyCode_New( 2025-09-08T00:36:36,885 | ^~~~~~~ 2025-09-08T00:36:36,885 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:36,885 213 | PyCode_New( 2025-09-08T00:36:36,885 | ^~~~~~~~~~ 2025-09-08T00:36:36,922 rnacounter/rnacounter.c:32181:9: error: passing argument 14 of ‘PyCode_New’ makes pointer from integer without a cast [-Wint-conversion] 2025-09-08T00:36:36,922 32181 | py_line, 2025-09-08T00:36:36,922 | ^~~~~~~ 2025-09-08T00:36:36,922 | | 2025-09-08T00:36:36,922 | int 2025-09-08T00:36:36,922 rnacounter/rnacounter.c:70:72: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:36,923 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:36,923 | ^~~~~ 2025-09-08T00:36:36,923 /usr/include/python3.13/cpython/code.h:216:45: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘int’ 2025-09-08T00:36:36,923 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:36,923 | ~~~~~~~~~~^ 2025-09-08T00:36:36,964 rnacounter/rnacounter.c:32182:9: error: passing argument 15 of ‘PyCode_New’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:36:36,964 32182 | __pyx_empty_bytes /*PyObject *lnotab*/ 2025-09-08T00:36:36,964 | ^~~~~~~~~~~~~~~~~ 2025-09-08T00:36:36,964 | | 2025-09-08T00:36:36,964 | PyObject * {aka struct _object *} 2025-09-08T00:36:36,964 rnacounter/rnacounter.c:70:79: note: in definition of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:36,964 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:36,964 | ^~~~ 2025-09-08T00:36:36,965 /usr/include/python3.13/cpython/code.h:216:52: note: expected ‘int’ but argument is of type ‘PyObject *’ {aka ‘struct _object *’} 2025-09-08T00:36:36,965 216 | PyObject *l, PyObject *m, PyObject *n, int o, PyObject *p, 2025-09-08T00:36:36,965 | ~~~~^ 2025-09-08T00:36:37,005 rnacounter/rnacounter.c:70:11: error: too few arguments to function ‘PyCode_New’ 2025-09-08T00:36:37,006 70 | PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) 2025-09-08T00:36:37,006 | ^~~~~~~~~~ 2025-09-08T00:36:37,006 rnacounter/rnacounter.c:32167:15: note: in expansion of macro ‘__Pyx_PyCode_New’ 2025-09-08T00:36:37,006 32167 | py_code = __Pyx_PyCode_New( 2025-09-08T00:36:37,006 | ^~~~~~~~~~~~~~~~ 2025-09-08T00:36:37,006 /usr/include/python3.13/cpython/code.h:213:1: note: declared here 2025-09-08T00:36:37,006 213 | PyCode_New( 2025-09-08T00:36:37,006 | ^~~~~~~~~~ 2025-09-08T00:36:37,023 rnacounter/rnacounter.c: In function ‘__Pyx_AddTraceback’: 2025-09-08T00:36:37,060 rnacounter/rnacounter.c:32210:13: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:36:37,060 32210 | py_frame->f_lineno = py_line; 2025-09-08T00:36:37,060 | ^~ 2025-09-08T00:36:37,062 rnacounter/rnacounter.c: In function ‘__Pyx_PyInt_As_int’: 2025-09-08T00:36:37,099 rnacounter/rnacounter.c:32331:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T00:36:37,099 32331 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T00:36:37,099 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:36:37,099 In file included from /usr/include/python3.13/longobject.h:107, 2025-09-08T00:36:37,100 from /usr/include/python3.13/Python.h:81: 2025-09-08T00:36:37,100 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T00:36:37,100 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T00:36:37,100 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:36:37,145 rnacounter/rnacounter.c: In function ‘__Pyx_PyInt_As_long’: 2025-09-08T00:36:37,182 rnacounter/rnacounter.c:32786:27: error: too few arguments to function ‘_PyLong_AsByteArray’ 2025-09-08T00:36:37,183 32786 | int ret = _PyLong_AsByteArray((PyLongObject *)v, 2025-09-08T00:36:37,183 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:36:37,183 /usr/include/python3.13/cpython/longobject.h:111:17: note: declared here 2025-09-08T00:36:37,183 111 | PyAPI_FUNC(int) _PyLong_AsByteArray(PyLongObject* v, 2025-09-08T00:36:37,183 | ^~~~~~~~~~~~~~~~~~~ 2025-09-08T00:36:37,192 rnacounter/rnacounter.c: In function ‘__Pyx_ExceptionSwap’: 2025-09-08T00:36:37,246 rnacounter/rnacounter.c:32818:24: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:36:37,247 32818 | tmp_type = tstate->exc_type; 2025-09-08T00:36:37,247 | ^~~~~~~~ 2025-09-08T00:36:37,247 | exc_state 2025-09-08T00:36:37,284 rnacounter/rnacounter.c:32819:23: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:36:37,285 32819 | tmp_value = tstate->exc_value; 2025-09-08T00:36:37,285 | ^~ 2025-09-08T00:36:37,322 rnacounter/rnacounter.c:32820:20: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:36:37,323 32820 | tmp_tb = tstate->exc_traceback; 2025-09-08T00:36:37,323 | ^~ 2025-09-08T00:36:37,377 rnacounter/rnacounter.c:32821:13: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_type’; did you mean ‘exc_state’? 2025-09-08T00:36:37,377 32821 | tstate->exc_type = *type; 2025-09-08T00:36:37,377 | ^~~~~~~~ 2025-09-08T00:36:37,377 | exc_state 2025-09-08T00:36:37,415 rnacounter/rnacounter.c:32822:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_value’ 2025-09-08T00:36:37,415 32822 | tstate->exc_value = *value; 2025-09-08T00:36:37,415 | ^~ 2025-09-08T00:36:37,453 rnacounter/rnacounter.c:32823:11: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘exc_traceback’ 2025-09-08T00:36:37,453 32823 | tstate->exc_traceback = *tb; 2025-09-08T00:36:37,453 | ^~ 2025-09-08T00:36:37,456 In file included from /usr/include/python3.13/Python.h:63: 2025-09-08T00:36:37,456 rnacounter/rnacounter.c: In function ‘__Pyx_Generator_SendEx’: 2025-09-08T00:36:37,534 rnacounter/rnacounter.c:32943:30: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T00:36:37,534 32943 | Py_XINCREF(tstate->frame); 2025-09-08T00:36:37,534 | ^~ 2025-09-08T00:36:37,534 /usr/include/python3.13/pyport.h:19:38: note: in definition of macro ‘_Py_CAST’ 2025-09-08T00:36:37,534 19 | #define _Py_CAST(type, expr) ((type)(expr)) 2025-09-08T00:36:37,534 | ^~~~ 2025-09-08T00:36:37,534 /usr/include/python3.13/object.h:1041:37: note: in expansion of macro ‘_PyObject_CAST’ 2025-09-08T00:36:37,534 1041 | # define Py_XINCREF(op) Py_XINCREF(_PyObject_CAST(op)) 2025-09-08T00:36:37,535 | ^~~~~~~~~~~~~~ 2025-09-08T00:36:37,535 rnacounter/rnacounter.c:32943:13: note: in expansion of macro ‘Py_XINCREF’ 2025-09-08T00:36:37,535 32943 | Py_XINCREF(tstate->frame); 2025-09-08T00:36:37,535 | ^~~~~~~~~~ 2025-09-08T00:36:37,571 rnacounter/rnacounter.c:32945:14: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:36:37,572 32945 | f->f_back = tstate->frame; 2025-09-08T00:36:37,572 | ^~ 2025-09-08T00:36:37,615 rnacounter/rnacounter.c:32945:31: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘frame’ 2025-09-08T00:36:37,615 32945 | f->f_back = tstate->frame; 2025-09-08T00:36:37,615 | ^~ 2025-09-08T00:36:37,692 rnacounter/rnacounter.c:32964:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:36:37,692 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:36:37,692 | ^~ 2025-09-08T00:36:37,693 /usr/include/python3.13/pyport.h:558:39: note: in definition of macro ‘_Py_TYPEOF’ 2025-09-08T00:36:37,693 558 | # define _Py_TYPEOF(expr) __typeof__(expr) 2025-09-08T00:36:37,693 | ^~~~ 2025-09-08T00:36:37,693 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:36:37,693 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:36:37,693 | ^~~~~~~~ 2025-09-08T00:36:37,733 In file included from /usr/include/python3.13/Python.h:72: 2025-09-08T00:36:37,733 rnacounter/rnacounter.c:32964:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:36:37,733 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:36:37,733 | ^~ 2025-09-08T00:36:37,733 /usr/include/python3.13/object.h:1012:41: note: in definition of macro ‘Py_CLEAR’ 2025-09-08T00:36:37,733 1012 | _Py_TYPEOF(op)* _tmp_op_ptr = &(op); \ 2025-09-08T00:36:37,733 | ^~ 2025-09-08T00:36:37,813 rnacounter/rnacounter.c:32964:23: error: invalid use of incomplete typedef ‘PyFrameObject’ {aka ‘struct _frame’} 2025-09-08T00:36:37,814 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:36:37,814 | ^~ 2025-09-08T00:36:37,814 /usr/include/python3.13/pyport.h:558:39: note: in definition of macro ‘_Py_TYPEOF’ 2025-09-08T00:36:37,814 558 | # define _Py_TYPEOF(expr) __typeof__(expr) 2025-09-08T00:36:37,814 | ^~~~ 2025-09-08T00:36:37,814 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:36:37,814 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:36:37,814 | ^~~~~~~~ 2025-09-08T00:36:37,854 /usr/include/python3.13/object.h:1014:25: warning: comparison between pointer and integer 2025-09-08T00:36:37,854 1014 | if (_tmp_old_op != NULL) { \ 2025-09-08T00:36:37,854 | ^~ 2025-09-08T00:36:37,854 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:36:37,854 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:36:37,854 | ^~~~~~~~ 2025-09-08T00:36:37,894 /usr/include/python3.13/object.h:1015:26: error: assignment to ‘int’ from ‘void *’ makes integer from pointer without a cast [-Wint-conversion] 2025-09-08T00:36:37,895 1015 | *_tmp_op_ptr = _Py_NULL; \ 2025-09-08T00:36:37,895 | ^ 2025-09-08T00:36:37,895 rnacounter/rnacounter.c:32964:13: note: in expansion of macro ‘Py_CLEAR’ 2025-09-08T00:36:37,895 32964 | Py_CLEAR(f->f_back); 2025-09-08T00:36:37,895 | ^~~~~~~~ 2025-09-08T00:36:38,486 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2025-09-08T00:36:38,657 ERROR: python setup.py bdist_wheel exited with 1 2025-09-08T00:36:38,669 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2025-09-08T00:36:38,669 exec(compile('"'"''"'"''"'"' 2025-09-08T00:36:38,669 # This is -- a caller that pip uses to run setup.py 2025-09-08T00:36:38,669 # 2025-09-08T00:36:38,669 # - It imports setuptools before invoking setup.py, to enable projects that directly 2025-09-08T00:36:38,669 # import from `distutils.core` to work with newer packaging standards. 2025-09-08T00:36:38,669 # - It provides a clear error message when setuptools is not installed. 2025-09-08T00:36:38,669 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2025-09-08T00:36:38,669 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2025-09-08T00:36:38,669 # manifest_maker: standard file '"'"'-c'"'"' not found". 2025-09-08T00:36:38,669 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2025-09-08T00:36:38,669 import os, sys, tokenize, traceback 2025-09-08T00:36:38,669 2025-09-08T00:36:38,669 try: 2025-09-08T00:36:38,669 import setuptools 2025-09-08T00:36:38,669 except ImportError: 2025-09-08T00:36:38,669 print( 2025-09-08T00:36:38,669 "ERROR: Can not execute `setup.py` since setuptools failed to import in " 2025-09-08T00:36:38,669 "the build environment with exception:", 2025-09-08T00:36:38,669 file=sys.stderr, 2025-09-08T00:36:38,669 ) 2025-09-08T00:36:38,669 traceback.print_exc() 2025-09-08T00:36:38,669 sys.exit(1) 2025-09-08T00:36:38,669 2025-09-08T00:36:38,669 __file__ = %r 2025-09-08T00:36:38,669 sys.argv[0] = __file__ 2025-09-08T00:36:38,669 2025-09-08T00:36:38,669 if os.path.exists(__file__): 2025-09-08T00:36:38,669 filename = __file__ 2025-09-08T00:36:38,669 with tokenize.open(__file__) as f: 2025-09-08T00:36:38,669 setup_py_code = f.read() 2025-09-08T00:36:38,669 else: 2025-09-08T00:36:38,669 filename = "" 2025-09-08T00:36:38,669 setup_py_code = "from setuptools import setup; setup()" 2025-09-08T00:36:38,669 2025-09-08T00:36:38,669 exec(compile(setup_py_code, filename, "exec")) 2025-09-08T00:36:38,669 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-e5w_o3ta/rnacounter_59325443220944b791b8a2bffca5e5ed/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-w4livpev[/] 2025-09-08T00:36:38,669 [bold magenta]cwd[/]: /tmp/pip-wheel-e5w_o3ta/rnacounter_59325443220944b791b8a2bffca5e5ed/ 2025-09-08T00:36:38,669 Building wheel for rnacounter (setup.py): finished with status 'error' 2025-09-08T00:36:38,670 ERROR: Failed building wheel for rnacounter 2025-09-08T00:36:38,670 Running setup.py clean for rnacounter 2025-09-08T00:36:38,671 Running command python setup.py clean 2025-09-08T00:36:39,580 /usr/local/lib/python3.13/dist-packages/setuptools/_distutils/dist.py:289: UserWarning: Unknown distribution option: 'test_suite' 2025-09-08T00:36:39,581 warnings.warn(msg) 2025-09-08T00:36:40,053 running clean 2025-09-08T00:36:40,200 removing 'build/temp.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T00:36:40,200 removing 'build/lib.linux-armv7l-cpython-313' (and everything under it) 2025-09-08T00:36:40,202 'build/bdist.linux-armv7l' does not exist -- can't clean it 2025-09-08T00:36:40,202 'build/scripts-3.13' does not exist -- can't clean it 2025-09-08T00:36:40,202 removing 'build' 2025-09-08T00:36:40,337 Failed to build rnacounter 2025-09-08T00:36:40,338 ERROR: Failed to build one or more wheels 2025-09-08T00:36:40,339 Exception information: 2025-09-08T00:36:40,339 Traceback (most recent call last): 2025-09-08T00:36:40,339 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 105, in _run_wrapper 2025-09-08T00:36:40,339 status = _inner_run() 2025-09-08T00:36:40,339 File "/usr/lib/python3/dist-packages/pip/_internal/cli/base_command.py", line 96, in _inner_run 2025-09-08T00:36:40,339 return self.run(options, args) 2025-09-08T00:36:40,339 ~~~~~~~~^^^^^^^^^^^^^^^ 2025-09-08T00:36:40,339 File "/usr/lib/python3/dist-packages/pip/_internal/cli/req_command.py", line 68, in wrapper 2025-09-08T00:36:40,339 return func(self, options, args) 2025-09-08T00:36:40,339 File "/usr/lib/python3/dist-packages/pip/_internal/commands/wheel.py", line 180, in run 2025-09-08T00:36:40,339 raise CommandError("Failed to build one or more wheels") 2025-09-08T00:36:40,339 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2025-09-08T00:36:40,343 Removed build tracker: '/tmp/pip-build-tracker-rh8txr6k'