2023-09-08T13:19:11,955 Created temporary directory: /tmp/pip-build-tracker-15994rjx 2023-09-08T13:19:11,956 Initialized build tracking at /tmp/pip-build-tracker-15994rjx 2023-09-08T13:19:11,956 Created build tracker: /tmp/pip-build-tracker-15994rjx 2023-09-08T13:19:11,957 Entered build tracker: /tmp/pip-build-tracker-15994rjx 2023-09-08T13:19:11,957 Created temporary directory: /tmp/pip-wheel-tlwep6cn 2023-09-08T13:19:11,960 Created temporary directory: /tmp/pip-ephem-wheel-cache-f8u7hgb9 2023-09-08T13:19:11,982 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-09-08T13:19:11,986 2 location(s) to search for versions of khmer: 2023-09-08T13:19:11,986 * https://pypi.org/simple/khmer/ 2023-09-08T13:19:11,986 * https://www.piwheels.org/simple/khmer/ 2023-09-08T13:19:11,987 Fetching project page and analyzing links: https://pypi.org/simple/khmer/ 2023-09-08T13:19:11,987 Getting page https://pypi.org/simple/khmer/ 2023-09-08T13:19:11,989 Found index url https://pypi.org/simple/ 2023-09-08T13:19:12,204 Fetched page https://pypi.org/simple/khmer/ as application/vnd.pypi.simple.v1+json 2023-09-08T13:19:12,211 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/a5/8e/d814af49f243e9628cc68cf9a89a290fa761a1acdfbf4044e69bb5f3185b/khmer-0.6-py2.7-linux-x86_64.egg (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,212 Skipping link: unsupported archive format: .egg: https://files.pythonhosted.org/packages/f1/61/71c0e5b337f3fb110d22314a90985f58d2a643c8fe701dd832f7a3b3cbe7/khmer-0.6-py2.7-macosx-10.8-intel.egg (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,212 Found link https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6 2023-09-08T13:19:12,213 Found link https://files.pythonhosted.org/packages/81/89/085bcb663ac1bd3a0b363b5a1de8f5a1c7d3b10e4a3ec197c976c2911ab9/khmer-0.6.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.6.1 2023-09-08T13:19:12,214 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/74/ff/a33663f83fd01cd5ffc9903d8116bd3dfc065f1f865db5c91b080991690b/khmer-0.7-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,215 Found link https://files.pythonhosted.org/packages/3a/bd/b1eb804f77e6ea99f9db02688c1474628d844e2f59a4f77d7bc00f8c990b/khmer-0.7.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7 2023-09-08T13:19:12,215 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d5/8b/ae021e29186d3f9ed8cfdd4f8a81db44f7d4105446dc9e119afd908eea21/khmer-0.7.1-cp27-none-macosx_10_8_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,216 Found link https://files.pythonhosted.org/packages/92/11/b17b809e155f35cfc17710ea67b7515b6025e141de6506a4af4e32e32b70/khmer-0.7.1.tar.gz (from https://pypi.org/simple/khmer/), version: 0.7.1 2023-09-08T13:19:12,217 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/84/a8/09ee794b0db1cc2b113a4f2f56beb325769389c35b48f802289d67297e24/khmer-0.8-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,217 Found link https://files.pythonhosted.org/packages/31/8f/7063987e7713dfbcd05bc53e4778c2284e3ea905112fc97d83d03afa60d9/khmer-0.8.tar.gz (from https://pypi.org/simple/khmer/), version: 0.8 2023-09-08T13:19:12,218 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/4e/6c/33badfa2550b73b7f037afa2e37aa09b7506b5dbd58175b0c24f40ed8179/khmer-1.0-cp27-none-macosx_10_9_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,218 Found link https://files.pythonhosted.org/packages/67/d0/334f8bba7befb5d671bf5663d1073c73cba841f13088d6426b93dbb884ce/khmer-1.0.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0 2023-09-08T13:19:12,219 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/fd/a6/5b64bad521c070581ecb1f22ecfcb33d2b297ec353094438d807028e4be0/khmer-1.0.1-cp27-none-macosx_10_9_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,220 Found link https://files.pythonhosted.org/packages/4e/73/cebb5f4952d79693ddd5c8a9efac21883f1b4cdff1d046adb2df1f2070bd/khmer-1.0.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.0.1 2023-09-08T13:19:12,221 Found link https://files.pythonhosted.org/packages/df/66/250be153108b73fa745d22b0e141d6d922cd011b6cda2233d46d34bcc596/khmer-1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.1 2023-09-08T13:19:12,221 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/6d/0b/97e3dd8339736c4f4ebf3906274bcf972b2d308bb76db1702c187bfbd9fd/khmer-1.2-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,222 Found link https://files.pythonhosted.org/packages/b8/b5/8143587dd5eba9204dea9eab50b990656b70e03538a44af56eec11a28f02/khmer-1.2.tar.gz (from https://pypi.org/simple/khmer/), version: 1.2 2023-09-08T13:19:12,223 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/41/7a/d94ad453d04782d82aebe7825ef4f1a38fc9e3374b0b3cfe9b1c5400482e/khmer-1.3-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,223 Found link https://files.pythonhosted.org/packages/6c/cf/37bd5901fe1322b59cd2cece9c53661944e18dddba3e8ebf2aa2d7834113/khmer-1.3.tar.gz (from https://pypi.org/simple/khmer/), version: 1.3 2023-09-08T13:19:12,224 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/89/b4/310a7e99bac77a488cc482f4184480aa803f65bad8ffacb961c94f819335/khmer-1.4-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,224 Found link https://files.pythonhosted.org/packages/5a/91/eb0c9a5fdab42699c56b8c60d0d02e806f4d4d42f809061eb9a1a9a59dfa/khmer-1.4.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4 2023-09-08T13:19:12,225 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5c/44/1d4273abe1bf162cd1a8c8d5424cec23e65971f90951659a0b590beaf364/khmer-1.4.1-cp27-none-macosx_10_10_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,225 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/96/b7/76a047a594778ad4d2646754e4454ac9d484b7e64548ebed24362c5aba4f/khmer-1.4.1-cp27-none-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,226 Found link https://files.pythonhosted.org/packages/5e/16/15243a0612c798595e8dd8bdf0477a7ce065929b9de5dbfebdf461006f05/khmer-1.4.1.tar.gz (from https://pypi.org/simple/khmer/), version: 1.4.1 2023-09-08T13:19:12,227 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5d/f6/791f79f68be58cb20c6426726063d742b3dd778b222873cb9f01ab65bc09/khmer-2.0-cp27-none-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,228 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/22/37/6c6fb54d9b8feb8a64e52e6e16cd409bc47d8240294caf8449fac6523f64/khmer-2.0-cp33-cp33m-macosx_10_6_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,228 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/69/21/de9ff69a24a90e6f4e788b57a6d911b046cbc768436060c18a0c18c2e187/khmer-2.0-cp34-cp34m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,229 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/36/cb/4a1638d5ca5a9b0d53c1b5484cefdcda9f3079bfb0b92e2ae2fac6d83bfd/khmer-2.0-cp35-cp35m-macosx_10_6_intel.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,230 Found link https://files.pythonhosted.org/packages/52/3b/2c52a13937197391775f274ed75b4a33b2d7767a904faaf4032e14e10a55/khmer-2.0.tar.gz (from https://pypi.org/simple/khmer/), version: 2.0 2023-09-08T13:19:12,230 Found link https://files.pythonhosted.org/packages/57/17/a1f05b13895e02cadeac06d61f7ea63e8c32eda38312d57e9ba218d0ca9b/khmer-2.1rc3.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1rc3 2023-09-08T13:19:12,231 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/c9/bb/8cccf9bf31082b3d78aa628ca62e8603f81de83b7a5056f0ce026cfb50fd/khmer-2.1-cp36-cp36m-macosx_10_12_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,232 Found link https://files.pythonhosted.org/packages/3e/e5/b3190cb9def69d665b42cd91ea27712f1d7de643f4b9c66ef2e5f1ab29c6/khmer-2.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1 2023-09-08T13:19:12,233 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/d3/55/d3f5da570677903679e0c40aa4b93323853ebe15e75944b4a0d7d25d11c8/khmer-2.1.1-cp27-cp27m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,233 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/40/5a/328d310361d98bb2f29361128eaa2493f44b51997d6837c72f1766c4ec7b/khmer-2.1.1-cp27-cp27mu-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,234 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/34/a5/f3815d5ec3ee20f884f140ae4a2f253ae6d59885684fa8adc5525a9ed4f4/khmer-2.1.1-cp35-cp35m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,234 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/5f/7a/dd356f3b267d2adf079deebdd94590e42edbc376a2058759ff78ee6a75c5/khmer-2.1.1-cp36-cp36m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,235 Skipping link: No binaries permitted for khmer: https://files.pythonhosted.org/packages/3f/1e/931281ac388cbb15d40319d0dcd54cfc3f1d972da5de2fa3063facedc966/khmer-2.1.1-cp37-cp37m-manylinux1_x86_64.whl (from https://pypi.org/simple/khmer/) 2023-09-08T13:19:12,235 Found link https://files.pythonhosted.org/packages/78/c9/caee0a310f249c86fd351706d2513e197e036231f4db6f3bda7a363ea1c4/khmer-2.1.1.tar.gz (from https://pypi.org/simple/khmer/), version: 2.1.1 2023-09-08T13:19:12,236 Fetching project page and analyzing links: https://www.piwheels.org/simple/khmer/ 2023-09-08T13:19:12,236 Getting page https://www.piwheels.org/simple/khmer/ 2023-09-08T13:19:12,238 Found index url https://www.piwheels.org/simple/ 2023-09-08T13:19:12,580 Fetched page https://www.piwheels.org/simple/khmer/ as text/html 2023-09-08T13:19:12,581 Skipping link: not a file: https://www.piwheels.org/simple/khmer/ 2023-09-08T13:19:12,582 Skipping link: not a file: https://pypi.org/simple/khmer/ 2023-09-08T13:19:12,611 Given no hashes to check 1 links for project 'khmer': discarding no candidates 2023-09-08T13:19:12,638 Collecting khmer==0.6 2023-09-08T13:19:12,641 Created temporary directory: /tmp/pip-unpack-75dp8n9e 2023-09-08T13:19:13,400 Downloading khmer-0.6.tar.gz (19.2 MB) 2023-09-08T13:19:22,379 Added khmer==0.6 from https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz to build tracker '/tmp/pip-build-tracker-15994rjx' 2023-09-08T13:19:22,382 Running setup.py (path:/tmp/pip-wheel-tlwep6cn/khmer_61a242e36190457b95a8b741949b2fd2/setup.py) egg_info for package khmer 2023-09-08T13:19:22,383 Created temporary directory: /tmp/pip-pip-egg-info-0zvaezxt 2023-09-08T13:19:22,383 Preparing metadata (setup.py): started 2023-09-08T13:19:22,385 Running command python setup.py egg_info 2023-09-08T13:19:23,576 warning: no previously-included files found matching 'data/1m-filtered.fa' 2023-09-08T13:19:23,692 Preparing metadata (setup.py): finished with status 'done' 2023-09-08T13:19:23,696 Source in /tmp/pip-wheel-tlwep6cn/khmer_61a242e36190457b95a8b741949b2fd2 has version 0.6, which satisfies requirement khmer==0.6 from https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz 2023-09-08T13:19:23,697 Removed khmer==0.6 from https://files.pythonhosted.org/packages/b9/d6/e343a534406110221eb690dc3ffa7548f03f2d51c4d9d407bf2e72278861/khmer-0.6.tar.gz from build tracker '/tmp/pip-build-tracker-15994rjx' 2023-09-08T13:19:23,702 Created temporary directory: /tmp/pip-unpack-ulfhqy1u 2023-09-08T13:19:23,703 Created temporary directory: /tmp/pip-unpack-_c_dw8o5 2023-09-08T13:19:23,708 Building wheels for collected packages: khmer 2023-09-08T13:19:23,712 Created temporary directory: /tmp/pip-wheel-yvb81eek 2023-09-08T13:19:23,712 Building wheel for khmer (setup.py): started 2023-09-08T13:19:23,714 Destination directory: /tmp/pip-wheel-yvb81eek 2023-09-08T13:19:23,714 Running command python setup.py bdist_wheel 2023-09-08T13:19:24,965 warning: no previously-included files found matching 'data/1m-filtered.fa' 2023-09-08T13:19:25,051 Checking for gcc... 2023-09-08T13:19:25,124 Checking for shared library support... 2023-09-08T13:19:25,287 Building shared library libz.so.1.2.3 with gcc. 2023-09-08T13:19:25,380 Checking for unistd.h... Yes. 2023-09-08T13:19:25,489 Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf() 2023-09-08T13:19:25,681 Checking for vsnprintf() in stdio.h... Yes. 2023-09-08T13:19:25,777 Checking for return value of vsnprintf()... Yes. 2023-09-08T13:19:25,852 Checking for errno.h... Yes. 2023-09-08T13:19:25,944 Checking for mmap support... Yes. 2023-09-08T13:19:25,971 gcc -O3 -fPIC -DUSE_MMAP -c -o adler32.o adler32.c 2023-09-08T13:19:26,304 gcc -O3 -fPIC -DUSE_MMAP -c -o compress.o compress.c 2023-09-08T13:19:26,423 gcc -O3 -fPIC -DUSE_MMAP -c -o crc32.o crc32.c 2023-09-08T13:19:26,843 gcc -O3 -fPIC -DUSE_MMAP -c -o gzio.o gzio.c 2023-09-08T13:19:27,903 gcc -O3 -fPIC -DUSE_MMAP -c -o uncompr.o uncompr.c 2023-09-08T13:19:28,015 gcc -O3 -fPIC -DUSE_MMAP -c -o deflate.o deflate.c 2023-09-08T13:19:29,579 gcc -O3 -fPIC -DUSE_MMAP -c -o trees.o trees.c 2023-09-08T13:19:30,988 gcc -O3 -fPIC -DUSE_MMAP -c -o zutil.o zutil.c 2023-09-08T13:19:31,124 gcc -O3 -fPIC -DUSE_MMAP -c -o inflate.o inflate.c 2023-09-08T13:19:32,815 gcc -O3 -fPIC -DUSE_MMAP -c -o infback.o infback.c 2023-09-08T13:19:33,630 gcc -O3 -fPIC -DUSE_MMAP -c -o inftrees.o inftrees.c 2023-09-08T13:19:34,110 gcc -O3 -fPIC -DUSE_MMAP -c -o inffast.o inffast.c 2023-09-08T13:19:34,545 ar rc libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o 2023-09-08T13:19:35,420 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c 2023-09-08T13:19:36,309 In function ‘mainSimpleSort’, 2023-09-08T13:19:36,310 inlined from ‘mainQSort3’ at blocksort.c:651:10, 2023-09-08T13:19:36,311 inlined from ‘mainSort’ at blocksort.c:897:19: 2023-09-08T13:19:36,311 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T13:19:36,312 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T13:19:36,313 | ^~~~~~~ 2023-09-08T13:19:36,313 blocksort.c:514:18: note: called from here 2023-09-08T13:19:36,314 514 | while ( mainGtU ( 2023-09-08T13:19:36,314 | ^~~~~~~~~ 2023-09-08T13:19:36,315 515 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T13:19:36,316 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:36,316 516 | ) ) { 2023-09-08T13:19:36,317 | ~ 2023-09-08T13:19:36,317 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T13:19:36,318 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T13:19:36,319 | ^~~~~~~ 2023-09-08T13:19:36,319 blocksort.c:528:18: note: called from here 2023-09-08T13:19:36,320 528 | while ( mainGtU ( 2023-09-08T13:19:36,321 | ^~~~~~~~~ 2023-09-08T13:19:36,321 529 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T13:19:36,322 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:36,323 530 | ) ) { 2023-09-08T13:19:36,324 | ~ 2023-09-08T13:19:36,324 blocksort.c:347:6: warning: inlining failed in call to ‘mainGtU’: --param max-inline-insns-single limit reached [-Winline] 2023-09-08T13:19:36,325 347 | Bool mainGtU ( UInt32 i1, 2023-09-08T13:19:36,325 | ^~~~~~~ 2023-09-08T13:19:36,326 blocksort.c:542:18: note: called from here 2023-09-08T13:19:36,326 542 | while ( mainGtU ( 2023-09-08T13:19:36,327 | ^~~~~~~~~ 2023-09-08T13:19:36,327 543 | ptr[j-h]+d, v+d, block, quadrant, nblock, budget 2023-09-08T13:19:36,328 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:36,328 544 | ) ) { 2023-09-08T13:19:36,328 | ~ 2023-09-08T13:19:37,122 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c 2023-09-08T13:19:37,612 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c 2023-09-08T13:19:37,723 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c 2023-09-08T13:19:37,835 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c 2023-09-08T13:19:42,325 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c 2023-09-08T13:19:44,871 gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c 2023-09-08T13:19:46,804 #gcc -shared -Wl,-soname -Wl,libbz2.so.1.0 -o libbz2.so.1.0.6 blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o 2023-09-08T13:19:46,806 #gcc -fpic -fPIC -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2-shared bzip2.c libbz2.so.1.0.6 2023-09-08T13:19:46,808 #rm -f libbz2.so.1.0 2023-09-08T13:19:46,811 #ln -s libbz2.so.1.0.6 libbz2.so.1.0 2023-09-08T13:19:49,573 khmer/_khmermodule.cc: In function ‘void khmer::python::_common_init_Type(PyTypeObject&, const char*, const char*)’: 2023-09-08T13:19:49,574 khmer/_khmermodule.cc:81:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_size’ 2023-09-08T13:19:49,574 81 | tobj.ob_size = 0; 2023-09-08T13:19:49,575 | ^~~~~~~ 2023-09-08T13:19:49,576 khmer/_khmermodule.cc:82:10: error: ‘PyTypeObject’ {aka ‘struct _typeobject’} has no member named ‘ob_type’ 2023-09-08T13:19:49,576 82 | tobj.ob_type = &PyType_Type; 2023-09-08T13:19:49,577 | ^~~~~~~ 2023-09-08T13:19:49,581 khmer/_khmermodule.cc: At global scope: 2023-09-08T13:19:49,582 khmer/_khmermodule.cc:198:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:19:49,582 198 | "Config", sizeof(khmer_ConfigObject), 2023-09-08T13:19:49,583 | ^~~~~~~~ 2023-09-08T13:19:49,584 | | 2023-09-08T13:19:49,584 | const char* 2023-09-08T13:19:49,585 khmer/_khmermodule.cc:200:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:19:49,586 200 | khmer_config_dealloc, /*tp_dealloc*/ 2023-09-08T13:19:49,587 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,587 | | 2023-09-08T13:19:49,588 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T13:19:49,589 khmer/_khmermodule.cc:202:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T13:19:49,590 202 | khmer_config_getattr, /*tp_getattr*/ 2023-09-08T13:19:49,590 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,591 | | 2023-09-08T13:19:49,591 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T13:19:49,592 In file included from /usr/include/python3.11/Python.h:44, 2023-09-08T13:19:49,593 from khmer/_khmermodule.cc:13: 2023-09-08T13:19:49,593 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T13:19:49,594 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T13:19:49,595 | ~~~ 2023-09-08T13:19:49,595 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T13:19:49,596 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T13:19:49,596 | | 2023-09-08T13:19:49,597 | int 2023-09-08T13:19:49,597 424 | 0) 2023-09-08T13:19:49,597 | ~~ 2023-09-08T13:19:49,598 khmer/_khmermodule.cc:215:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T13:19:49,598 215 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T13:19:49,599 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,599 khmer/_khmermodule.cc:216:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T13:19:49,599 216 | "config object", /* tp_doc */ 2023-09-08T13:19:49,600 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:49,601 | | 2023-09-08T13:19:49,601 | const char* 2023-09-08T13:19:49,611 khmer/_khmermodule.cc: In function ‘PyObject* config_get_number_of_threads(PyObject*, PyObject*)’: 2023-09-08T13:19:49,612 khmer/_khmermodule.cc:300:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T13:19:49,613 300 | return PyInt_FromSize_t( (size_t)config->get_number_of_threads( ) ); 2023-09-08T13:19:49,613 | ^~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,614 | PyLong_FromSize_t 2023-09-08T13:19:49,636 khmer/_khmermodule.cc: In function ‘PyObject* config_get_input_buffer_trace_level(PyObject*, PyObject*)’: 2023-09-08T13:19:49,637 khmer/_khmermodule.cc:358:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T13:19:49,638 358 | return PyInt_FromSize_t( (size_t)config->get_input_buffer_trace_level( ) ); 2023-09-08T13:19:49,638 | ^~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,639 | PyLong_FromSize_t 2023-09-08T13:19:49,660 khmer/_khmermodule.cc: In function ‘PyObject* config_get_reads_parser_trace_level(PyObject*, PyObject*)’: 2023-09-08T13:19:49,661 khmer/_khmermodule.cc:386:10: error: ‘PyInt_FromSize_t’ was not declared in this scope; did you mean ‘PyLong_FromSize_t’? 2023-09-08T13:19:49,661 386 | return PyInt_FromSize_t( (size_t)config->get_reads_parser_trace_level( ) ); 2023-09-08T13:19:49,662 | ^~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,663 | PyLong_FromSize_t 2023-09-08T13:19:49,684 khmer/_khmermodule.cc: In function ‘PyObject* khmer_config_getattr(PyObject*, char*)’: 2023-09-08T13:19:49,685 khmer/_khmermodule.cc:434:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T13:19:49,686 434 | return Py_FindMethod(khmer_config_methods, obj, name); 2023-09-08T13:19:49,686 | ^~~~~~~~~~~~~ 2023-09-08T13:19:49,687 | PyCMethod 2023-09-08T13:19:49,711 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_name(PyObject*, void*)’: 2023-09-08T13:19:49,712 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:19:49,712 472 | PyString_FromString( \ 2023-09-08T13:19:49,713 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,714 khmer/_khmermodule.cc:480:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T13:19:49,715 480 | { return KHMER_READ_STRING_GETTER( self, name ); } 2023-09-08T13:19:49,716 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,738 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_sequence(PyObject*, void*)’: 2023-09-08T13:19:49,738 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:19:49,739 472 | PyString_FromString( \ 2023-09-08T13:19:49,739 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,740 khmer/_khmermodule.cc:486:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T13:19:49,741 486 | { return KHMER_READ_STRING_GETTER( self, sequence ); } 2023-09-08T13:19:49,741 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,764 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_accuracy(PyObject*, void*)’: 2023-09-08T13:19:49,765 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:19:49,765 472 | PyString_FromString( \ 2023-09-08T13:19:49,766 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,767 khmer/_khmermodule.cc:492:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T13:19:49,767 492 | { return KHMER_READ_STRING_GETTER( self, accuracy ); } 2023-09-08T13:19:49,768 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,791 khmer/_khmermodule.cc: In function ‘PyObject* khmer::python::Read_get_annotations(PyObject*, void*)’: 2023-09-08T13:19:49,791 khmer/_khmermodule.cc:472:5: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:19:49,792 472 | PyString_FromString( \ 2023-09-08T13:19:49,792 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,793 khmer/_khmermodule.cc:498:10: note: in expansion of macro ‘KHMER_READ_STRING_GETTER’ 2023-09-08T13:19:49,794 498 | { return KHMER_READ_STRING_GETTER( self, annotations ); } 2023-09-08T13:19:49,794 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,837 khmer/_khmermodule.cc: In function ‘void khmer::python::_init_ReadParser_Type()’: 2023-09-08T13:19:49,838 khmer/_khmermodule.cc:816:9: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:49,838 816 | PyInt_FromLong( IParser:: PAIR_MODE_ALLOW_UNPAIRED ) 2023-09-08T13:19:49,839 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:49,840 | PyLong_FromLong 2023-09-08T13:19:49,866 khmer/_khmermodule.cc: In function ‘PyObject* ktable_reverse_hash(PyObject*, PyObject*)’: 2023-09-08T13:19:49,867 khmer/_khmermodule.cc:959:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:19:49,868 959 | return PyString_FromString(khmer::_revhash(val, ktable->ksize()).c_str()); 2023-09-08T13:19:49,868 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:49,869 | PyLong_FromString 2023-09-08T13:19:49,889 khmer/_khmermodule.cc: In function ‘PyObject* ktable_count(PyObject*, PyObject*)’: 2023-09-08T13:19:49,889 khmer/_khmermodule.cc:985:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:49,890 985 | return PyInt_FromLong(1); 2023-09-08T13:19:49,891 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:49,891 | PyLong_FromLong 2023-09-08T13:19:49,911 khmer/_khmermodule.cc: In function ‘PyObject* ktable_consume(PyObject*, PyObject*)’: 2023-09-08T13:19:49,912 khmer/_khmermodule.cc:1013:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:49,913 1013 | return PyInt_FromLong(n_consumed); 2023-09-08T13:19:49,914 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:49,915 | PyLong_FromLong 2023-09-08T13:19:49,930 khmer/_khmermodule.cc: In function ‘PyObject* ktable_get(PyObject*, PyObject*)’: 2023-09-08T13:19:49,931 khmer/_khmermodule.cc:1032:14: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T13:19:49,931 1032 | } else if (PyInt_Check(arg)) { 2023-09-08T13:19:49,932 | ^~~~~~~~~~~ 2023-09-08T13:19:49,933 | PySet_Check 2023-09-08T13:19:49,949 khmer/_khmermodule.cc:1033:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T13:19:49,950 1033 | long pos = PyInt_AsLong(arg); 2023-09-08T13:19:49,950 | ^~~~~~~~~~~~ 2023-09-08T13:19:49,951 | PyLong_AsLong 2023-09-08T13:19:49,972 khmer/_khmermodule.cc:1035:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T13:19:49,972 1035 | } else if (PyString_Check(arg)) { 2023-09-08T13:19:49,973 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:49,974 | PyMapping_Check 2023-09-08T13:19:49,998 khmer/_khmermodule.cc:1036:21: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T13:19:49,999 1036 | std::string s = PyString_AsString(arg); 2023-09-08T13:19:50,000 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,020 khmer/_khmermodule.cc:1040:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,020 1040 | return PyInt_FromLong(count); 2023-09-08T13:19:50,021 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,022 | PyLong_FromLong 2023-09-08T13:19:50,042 khmer/_khmermodule.cc: In function ‘PyObject* ktable__getitem__(PyObject*, Py_ssize_t)’: 2023-09-08T13:19:50,042 khmer/_khmermodule.cc:1050:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,043 1050 | return PyInt_FromLong(count); 2023-09-08T13:19:50,044 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,045 | PyLong_FromLong 2023-09-08T13:19:50,069 khmer/_khmermodule.cc: In function ‘int ktable__contains__(PyObject*, PyObject*)’: 2023-09-08T13:19:50,069 khmer/_khmermodule.cc:1058:21: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T13:19:50,070 1058 | char * kmer_str = PyString_AsString( val ); 2023-09-08T13:19:50,071 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,086 khmer/_khmermodule.cc: In function ‘PyObject* ktable_set(PyObject*, PyObject*)’: 2023-09-08T13:19:50,087 khmer/_khmermodule.cc:1076:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T13:19:50,088 1076 | if (PyInt_Check(arg)) { 2023-09-08T13:19:50,089 | ^~~~~~~~~~~ 2023-09-08T13:19:50,089 | PySet_Check 2023-09-08T13:19:50,106 khmer/_khmermodule.cc:1077:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T13:19:50,107 1077 | long pos = PyInt_AsLong(arg); 2023-09-08T13:19:50,107 | ^~~~~~~~~~~~ 2023-09-08T13:19:50,108 | PyLong_AsLong 2023-09-08T13:19:50,128 khmer/_khmermodule.cc:1079:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T13:19:50,129 1079 | } else if (PyString_Check(arg)) { 2023-09-08T13:19:50,130 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,131 | PyMapping_Check 2023-09-08T13:19:50,155 khmer/_khmermodule.cc:1080:21: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T13:19:50,156 1080 | std::string s = PyString_AsString(arg); 2023-09-08T13:19:50,157 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,177 khmer/_khmermodule.cc: In function ‘PyObject* ktable_max_hash(PyObject*, PyObject*)’: 2023-09-08T13:19:50,178 khmer/_khmermodule.cc:1097:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,179 1097 | return PyInt_FromLong(ktable->max_hash()); 2023-09-08T13:19:50,179 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,180 | PyLong_FromLong 2023-09-08T13:19:50,199 khmer/_khmermodule.cc: In function ‘PyObject* ktable_n_entries(PyObject*, PyObject*)’: 2023-09-08T13:19:50,200 khmer/_khmermodule.cc:1109:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,201 1109 | return PyInt_FromLong(ktable->n_entries()); 2023-09-08T13:19:50,201 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,202 | PyLong_FromLong 2023-09-08T13:19:50,222 khmer/_khmermodule.cc: In function ‘PyObject* ktable_ksize(PyObject*, PyObject*)’: 2023-09-08T13:19:50,222 khmer/_khmermodule.cc:1129:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,223 1129 | return PyInt_FromLong(ktable->ksize()); 2023-09-08T13:19:50,223 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,224 | PyLong_FromLong 2023-09-08T13:19:50,246 khmer/_khmermodule.cc: In function ‘PyObject* khmer_ktable_getattr(PyObject*, char*)’: 2023-09-08T13:19:50,247 khmer/_khmermodule.cc:1175:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T13:19:50,248 1175 | return Py_FindMethod(khmer_ktable_methods, obj, name); 2023-09-08T13:19:50,248 | ^~~~~~~~~~~~~ 2023-09-08T13:19:50,249 | PyCMethod 2023-09-08T13:19:50,249 khmer/_khmermodule.cc: At global scope: 2023-09-08T13:19:50,250 khmer/_khmermodule.cc:1196:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:19:50,251 1196 | "KTable", sizeof(khmer_KTableObject), 2023-09-08T13:19:50,251 | ^~~~~~~~ 2023-09-08T13:19:50,252 | | 2023-09-08T13:19:50,253 | const char* 2023-09-08T13:19:50,253 khmer/_khmermodule.cc:1198:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:19:50,254 1198 | khmer_ktable_dealloc, /*tp_dealloc*/ 2023-09-08T13:19:50,255 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,256 | | 2023-09-08T13:19:50,256 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T13:19:50,257 khmer/_khmermodule.cc:1200:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T13:19:50,258 1200 | khmer_ktable_getattr, /*tp_getattr*/ 2023-09-08T13:19:50,258 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,259 | | 2023-09-08T13:19:50,260 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T13:19:50,260 khmer/_khmermodule.cc:1205:5: error: cannot convert ‘PySequenceMethods*’ to ‘PyMappingMethods*’ in initialization 2023-09-08T13:19:50,261 1205 | &khmer_KTable_SequenceMethods, /*tp_as_sequence*/ 2023-09-08T13:19:50,262 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,262 | | 2023-09-08T13:19:50,263 | PySequenceMethods* 2023-09-08T13:19:50,264 khmer/_khmermodule.cc:1314:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:19:50,265 1314 | "KHashbits", sizeof(khmer_KHashbitsObject), 2023-09-08T13:19:50,265 | ^~~~~~~~~~~ 2023-09-08T13:19:50,266 | | 2023-09-08T13:19:50,266 | const char* 2023-09-08T13:19:50,267 khmer/_khmermodule.cc:1316:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:19:50,267 1316 | khmer_hashbits_dealloc, /*tp_dealloc*/ 2023-09-08T13:19:50,268 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,269 | | 2023-09-08T13:19:50,269 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T13:19:50,269 khmer/_khmermodule.cc:1318:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T13:19:50,270 1318 | khmer_hashbits_getattr, /*tp_getattr*/ 2023-09-08T13:19:50,270 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,271 | | 2023-09-08T13:19:50,271 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T13:19:50,271 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T13:19:50,272 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T13:19:50,272 | ~~~ 2023-09-08T13:19:50,273 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T13:19:50,273 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T13:19:50,273 | | 2023-09-08T13:19:50,274 | int 2023-09-08T13:19:50,274 424 | 0) 2023-09-08T13:19:50,274 | ~~ 2023-09-08T13:19:50,275 khmer/_khmermodule.cc:1331:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T13:19:50,275 1331 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T13:19:50,276 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,276 khmer/_khmermodule.cc:1332:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T13:19:50,277 1332 | "hashbits object", /* tp_doc */ 2023-09-08T13:19:50,277 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,278 | | 2023-09-08T13:19:50,278 | const char* 2023-09-08T13:19:50,282 khmer/_khmermodule.cc: In function ‘PyObject* hash_n_occupied(PyObject*, PyObject*)’: 2023-09-08T13:19:50,283 khmer/_khmermodule.cc:1389:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,284 1389 | return PyInt_FromLong(n); 2023-09-08T13:19:50,284 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,285 | PyLong_FromLong 2023-09-08T13:19:50,304 khmer/_khmermodule.cc: In function ‘PyObject* hash_n_entries(PyObject*, PyObject*)’: 2023-09-08T13:19:50,305 khmer/_khmermodule.cc:1401:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,306 1401 | return PyInt_FromLong(counting->n_entries()); 2023-09-08T13:19:50,306 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,307 | PyLong_FromLong 2023-09-08T13:19:50,327 khmer/_khmermodule.cc: In function ‘PyObject* hash_count(PyObject*, PyObject*)’: 2023-09-08T13:19:50,328 khmer/_khmermodule.cc:1423:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,329 1423 | return PyInt_FromLong(1); 2023-09-08T13:19:50,329 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,330 | PyLong_FromLong 2023-09-08T13:19:50,350 khmer/_khmermodule.cc: In function ‘PyObject* hash_output_fasta_kmer_pos_freq(PyObject*, PyObject*)’: 2023-09-08T13:19:50,351 khmer/_khmermodule.cc:1440:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,351 1440 | return PyInt_FromLong(0); 2023-09-08T13:19:50,352 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,353 | PyLong_FromLong 2023-09-08T13:19:50,375 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume(PyObject*, PyObject*)’: 2023-09-08T13:19:50,376 khmer/_khmermodule.cc:1526:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,377 1526 | return PyInt_FromLong(n_consumed); 2023-09-08T13:19:50,378 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,378 | PyLong_FromLong 2023-09-08T13:19:50,399 khmer/_khmermodule.cc: In function ‘PyObject* hash_consume_high_abund_kmers(PyObject*, PyObject*)’: 2023-09-08T13:19:50,399 khmer/_khmermodule.cc:1558:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,400 1558 | return PyInt_FromLong(n_consumed); 2023-09-08T13:19:50,401 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,401 | PyLong_FromLong 2023-09-08T13:19:50,421 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_min_count(PyObject*, PyObject*)’: 2023-09-08T13:19:50,422 khmer/_khmermodule.cc:1581:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,423 1581 | return PyInt_FromLong(N); 2023-09-08T13:19:50,423 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,424 | PyLong_FromLong 2023-09-08T13:19:50,444 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_max_count(PyObject*, PyObject*)’: 2023-09-08T13:19:50,445 khmer/_khmermodule.cc:1604:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,446 1604 | return PyInt_FromLong(N); 2023-09-08T13:19:50,446 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,447 | PyLong_FromLong 2023-09-08T13:19:50,467 khmer/_khmermodule.cc: In function ‘PyObject* hash_get(PyObject*, PyObject*)’: 2023-09-08T13:19:50,467 khmer/_khmermodule.cc:1707:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T13:19:50,468 1707 | if (PyInt_Check(arg)) { 2023-09-08T13:19:50,469 | ^~~~~~~~~~~ 2023-09-08T13:19:50,469 | PySet_Check 2023-09-08T13:19:50,486 khmer/_khmermodule.cc:1708:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T13:19:50,487 1708 | long pos = PyInt_AsLong(arg); 2023-09-08T13:19:50,488 | ^~~~~~~~~~~~ 2023-09-08T13:19:50,488 | PyLong_AsLong 2023-09-08T13:19:50,509 khmer/_khmermodule.cc:1710:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T13:19:50,510 1710 | } else if (PyString_Check(arg)) { 2023-09-08T13:19:50,510 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,511 | PyMapping_Check 2023-09-08T13:19:50,536 khmer/_khmermodule.cc:1711:21: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T13:19:50,537 1711 | std::string s = PyString_AsString(arg); 2023-09-08T13:19:50,537 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,557 khmer/_khmermodule.cc:1715:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,558 1715 | return PyInt_FromLong(count); 2023-09-08T13:19:50,559 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,560 | PyLong_FromLong 2023-09-08T13:19:50,580 khmer/_khmermodule.cc: In function ‘PyObject* hash_max_hamming1_count(PyObject*, PyObject*)’: 2023-09-08T13:19:50,580 khmer/_khmermodule.cc:1731:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,582 1731 | return PyInt_FromLong(count); 2023-09-08T13:19:50,583 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,584 | PyLong_FromLong 2023-09-08T13:19:50,608 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_on_abundance(PyObject*, PyObject*)’: 2023-09-08T13:19:50,609 khmer/_khmermodule.cc:1755:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:19:50,610 1755 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:19:50,611 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,611 | PyBytes_FromStringAndSize 2023-09-08T13:19:50,637 khmer/_khmermodule.cc: In function ‘PyObject* count_trim_below_abundance(PyObject*, PyObject*)’: 2023-09-08T13:19:50,637 khmer/_khmermodule.cc:1782:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:19:50,638 1782 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:19:50,639 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,639 | PyBytes_FromStringAndSize 2023-09-08T13:19:50,661 In file included from /usr/include/python3.11/Python.h:38: 2023-09-08T13:19:50,661 khmer/_khmermodule.cc: In function ‘PyObject* hash_abundance_distribution(PyObject*, PyObject*)’: 2023-09-08T13:19:50,662 khmer/_khmermodule.cc:1814:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,663 1814 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2023-09-08T13:19:50,663 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,664 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:19:50,665 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:19:50,666 | ^~~~ 2023-09-08T13:19:50,666 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:19:50,667 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:19:50,668 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,669 khmer/_khmermodule.cc:1814:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:19:50,670 1814 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2023-09-08T13:19:50,670 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:50,686 khmer/_khmermodule.cc: In function ‘PyObject* hash_abundance_distribution_with_reads_parser(PyObject*, PyObject*)’: 2023-09-08T13:19:50,687 khmer/_khmermodule.cc:1850:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,687 1850 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2023-09-08T13:19:50,688 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,689 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:19:50,690 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:19:50,690 | ^~~~ 2023-09-08T13:19:50,691 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:19:50,692 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:19:50,692 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,693 khmer/_khmermodule.cc:1850:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:19:50,694 1850 | PyList_SET_ITEM(x, i, PyInt_FromLong(dist[i])); 2023-09-08T13:19:50,694 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:50,710 khmer/_khmermodule.cc: In function ‘PyObject* hash_fasta_count_kmers_by_position(PyObject*, PyObject*)’: 2023-09-08T13:19:50,711 khmer/_khmermodule.cc:1880:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,712 1880 | PyList_SET_ITEM(x, i, PyInt_FromLong(counts[i])); 2023-09-08T13:19:50,713 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,714 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:19:50,715 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:19:50,715 | ^~~~ 2023-09-08T13:19:50,716 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:19:50,717 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:19:50,717 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,718 khmer/_khmermodule.cc:1880:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:19:50,718 1880 | PyList_SET_ITEM(x, i, PyInt_FromLong(counts[i])); 2023-09-08T13:19:50,719 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:50,739 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_ksize(PyObject*, PyObject*)’: 2023-09-08T13:19:50,739 khmer/_khmermodule.cc:1987:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,740 1987 | return PyInt_FromLong(k); 2023-09-08T13:19:50,741 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,741 | PyLong_FromLong 2023-09-08T13:19:50,761 khmer/_khmermodule.cc: In function ‘PyObject* hash_get_hashsizes(PyObject*, PyObject*)’: 2023-09-08T13:19:50,762 khmer/_khmermodule.cc:2004:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,762 2004 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2023-09-08T13:19:50,763 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,763 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:19:50,764 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:19:50,765 | ^~~~ 2023-09-08T13:19:50,766 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:19:50,766 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:19:50,767 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,768 khmer/_khmermodule.cc:2004:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:19:50,769 2004 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2023-09-08T13:19:50,770 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:50,787 khmer/_khmermodule.cc: In function ‘PyObject* khmer_counting_getattr(PyObject*, char*)’: 2023-09-08T13:19:50,788 khmer/_khmermodule.cc:2052:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T13:19:50,789 2052 | return Py_FindMethod(khmer_counting_methods, obj, name); 2023-09-08T13:19:50,790 | ^~~~~~~~~~~~~ 2023-09-08T13:19:50,790 | PyCMethod 2023-09-08T13:19:50,791 khmer/_khmermodule.cc: At global scope: 2023-09-08T13:19:50,792 khmer/_khmermodule.cc:2060:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:19:50,792 2060 | "KCountingHash", sizeof(khmer_KCountingHashObject), 2023-09-08T13:19:50,793 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:50,794 | | 2023-09-08T13:19:50,795 | const char* 2023-09-08T13:19:50,795 khmer/_khmermodule.cc:2062:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:19:50,796 2062 | khmer_counting_dealloc, /*tp_dealloc*/ 2023-09-08T13:19:50,797 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,798 | | 2023-09-08T13:19:50,798 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T13:19:50,799 khmer/_khmermodule.cc:2064:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T13:19:50,800 2064 | khmer_counting_getattr, /*tp_getattr*/ 2023-09-08T13:19:50,801 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,801 | | 2023-09-08T13:19:50,802 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T13:19:50,802 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T13:19:50,803 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T13:19:50,803 | ~~~ 2023-09-08T13:19:50,803 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T13:19:50,804 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T13:19:50,804 | | 2023-09-08T13:19:50,805 | int 2023-09-08T13:19:50,805 424 | 0) 2023-09-08T13:19:50,806 | ~~ 2023-09-08T13:19:50,806 khmer/_khmermodule.cc:2077:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T13:19:50,807 2077 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T13:19:50,807 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,808 khmer/_khmermodule.cc:2078:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T13:19:50,808 2078 | "counting hash object", /* tp_doc */ 2023-09-08T13:19:50,809 | ^~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,809 | | 2023-09-08T13:19:50,809 | const char* 2023-09-08T13:19:50,816 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_unique_kmers(PyObject*, PyObject*)’: 2023-09-08T13:19:50,816 khmer/_khmermodule.cc:2147:12: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,817 2147 | return PyInt_FromLong(n); 2023-09-08T13:19:50,818 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,818 | PyLong_FromLong 2023-09-08T13:19:50,841 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_occupied(PyObject*, PyObject*)’: 2023-09-08T13:19:50,841 khmer/_khmermodule.cc:2209:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,842 2209 | return PyInt_FromLong(n); 2023-09-08T13:19:50,843 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,844 | PyLong_FromLong 2023-09-08T13:19:50,863 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_n_tags(PyObject*, PyObject*)’: 2023-09-08T13:19:50,864 khmer/_khmermodule.cc:2221:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,864 2221 | return PyInt_FromLong(hashbits->n_tags()); 2023-09-08T13:19:50,865 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,866 | PyLong_FromLong 2023-09-08T13:19:50,886 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_count(PyObject*, PyObject*)’: 2023-09-08T13:19:50,886 khmer/_khmermodule.cc:2243:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,887 2243 | return PyInt_FromLong(1); 2023-09-08T13:19:50,888 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,889 | PyLong_FromLong 2023-09-08T13:19:50,908 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_consume(PyObject*, PyObject*)’: 2023-09-08T13:19:50,909 khmer/_khmermodule.cc:2266:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,910 2266 | return PyInt_FromLong(n_consumed); 2023-09-08T13:19:50,911 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,911 | PyLong_FromLong 2023-09-08T13:19:50,942 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_repartition_largest_partition(PyObject*, PyObject*)’: 2023-09-08T13:19:50,943 khmer/_khmermodule.cc:2377:43: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:19:50,944 2377 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_o); 2023-09-08T13:19:50,945 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:50,945 | PyLong_AsVoidPtr 2023-09-08T13:19:50,964 khmer/_khmermodule.cc:2386:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:50,965 2386 | return PyInt_FromLong(next_largest); 2023-09-08T13:19:50,966 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:50,966 | PyLong_FromLong 2023-09-08T13:19:50,983 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get(PyObject*, PyObject*)’: 2023-09-08T13:19:50,984 khmer/_khmermodule.cc:2423:7: error: ‘PyInt_Check’ was not declared in this scope; did you mean ‘PySet_Check’? 2023-09-08T13:19:50,985 2423 | if (PyInt_Check(arg)) { 2023-09-08T13:19:50,985 | ^~~~~~~~~~~ 2023-09-08T13:19:50,986 | PySet_Check 2023-09-08T13:19:51,003 khmer/_khmermodule.cc:2424:16: error: ‘PyInt_AsLong’ was not declared in this scope; did you mean ‘PyLong_AsLong’? 2023-09-08T13:19:51,004 2424 | long pos = PyInt_AsLong(arg); 2023-09-08T13:19:51,004 | ^~~~~~~~~~~~ 2023-09-08T13:19:51,005 | PyLong_AsLong 2023-09-08T13:19:51,026 khmer/_khmermodule.cc:2426:14: error: ‘PyString_Check’ was not declared in this scope; did you mean ‘PyMapping_Check’? 2023-09-08T13:19:51,026 2426 | } else if (PyString_Check(arg)) { 2023-09-08T13:19:51,027 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,028 | PyMapping_Check 2023-09-08T13:19:51,053 khmer/_khmermodule.cc:2427:21: error: ‘PyString_AsString’ was not declared in this scope 2023-09-08T13:19:51,054 2427 | std::string s = PyString_AsString(arg); 2023-09-08T13:19:51,054 | ^~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,074 khmer/_khmermodule.cc:2431:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,075 2431 | return PyInt_FromLong(count); 2023-09-08T13:19:51,076 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,077 | PyLong_FromLong 2023-09-08T13:19:51,098 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_calc_connected_graph_size(PyObject*, PyObject*)’: 2023-09-08T13:19:51,098 khmer/_khmermodule.cc:2459:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,099 2459 | return PyInt_FromLong(size); 2023-09-08T13:19:51,100 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,101 | PyLong_FromLong 2023-09-08T13:19:51,120 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_kmer_degree(PyObject*, PyObject*)’: 2023-09-08T13:19:51,121 khmer/_khmermodule.cc:2474:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,122 2474 | return PyInt_FromLong(hashbits->kmer_degree(kmer_s)); 2023-09-08T13:19:51,122 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,123 | PyLong_FromLong 2023-09-08T13:19:51,149 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_degree(PyObject*, PyObject*)’: 2023-09-08T13:19:51,149 khmer/_khmermodule.cc:2496:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:19:51,150 2496 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:19:51,151 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,152 | PyBytes_FromStringAndSize 2023-09-08T13:19:51,177 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_sodd(PyObject*, PyObject*)’: 2023-09-08T13:19:51,178 khmer/_khmermodule.cc:2522:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:19:51,178 2522 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:19:51,179 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,180 | PyBytes_FromStringAndSize 2023-09-08T13:19:51,206 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_stoptags(PyObject*, PyObject*)’: 2023-09-08T13:19:51,207 khmer/_khmermodule.cc:2547:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:19:51,207 2547 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:19:51,208 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,208 | PyBytes_FromStringAndSize 2023-09-08T13:19:51,249 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_do_subset_partition(PyObject*, PyObject*)’: 2023-09-08T13:19:51,250 khmer/_khmermodule.cc:2625:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T13:19:51,251 2625 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2023-09-08T13:19:51,251 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,252 | PyLong_FromVoidPtr 2023-09-08T13:19:51,275 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge_subset(PyObject*, PyObject*)’: 2023-09-08T13:19:51,276 khmer/_khmermodule.cc:2654:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2023-09-08T13:19:51,277 2654 | if (!PyCObject_Check(subset_obj)) { 2023-09-08T13:19:51,278 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:51,278 | PyODict_Check 2023-09-08T13:19:51,305 khmer/_khmermodule.cc:2659:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:19:51,305 2659 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T13:19:51,306 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,307 | PyLong_AsVoidPtr 2023-09-08T13:19:51,348 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_all_tags(PyObject*, PyObject*)’: 2023-09-08T13:19:51,349 khmer/_khmermodule.cc:2951:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T13:19:51,349 2951 | return PyCObject_FromVoidPtr(ppi, free_pre_partition_info); 2023-09-08T13:19:51,350 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,351 | PyLong_FromVoidPtr 2023-09-08T13:19:51,373 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_assign_partition_id(PyObject*, PyObject*)’: 2023-09-08T13:19:51,374 khmer/_khmermodule.cc:2964:8: error: ‘PyCObject_Check’ was not declared in this scope; did you mean ‘PyODict_Check’? 2023-09-08T13:19:51,375 2964 | if (!PyCObject_Check(ppi_obj)) { 2023-09-08T13:19:51,375 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:51,376 | PyODict_Check 2023-09-08T13:19:51,402 khmer/_khmermodule.cc:2969:33: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:19:51,403 2969 | ppi = (_pre_partition_info *) PyCObject_AsVoidPtr(ppi_obj); 2023-09-08T13:19:51,404 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,405 | PyLong_AsVoidPtr 2023-09-08T13:19:51,424 khmer/_khmermodule.cc:2975:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,425 2975 | return PyInt_FromLong(p); 2023-09-08T13:19:51,426 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,427 | PyLong_FromLong 2023-09-08T13:19:51,453 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_output_partitions(PyObject*, PyObject*)’: 2023-09-08T13:19:51,454 khmer/_khmermodule.cc:3093:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,454 3093 | return PyInt_FromLong(n_partitions); 2023-09-08T13:19:51,455 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,456 | PyLong_FromLong 2023-09-08T13:19:51,476 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_find_unpart(PyObject*, PyObject*)’: 2023-09-08T13:19:51,477 khmer/_khmermodule.cc:3124:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,478 3124 | return PyInt_FromLong(n_singletons); 2023-09-08T13:19:51,478 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,479 | PyLong_FromLong 2023-09-08T13:19:51,510 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_count_partitions(PyObject*, PyObject*)’: 2023-09-08T13:19:51,511 khmer/_khmermodule.cc:3227:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:19:51,512 3227 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T13:19:51,512 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,513 | PyLong_AsVoidPtr 2023-09-08T13:19:51,540 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_subset_partition_size_distribution(PyObject*, PyObject*)’: 2023-09-08T13:19:51,541 khmer/_khmermodule.cc:3245:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:19:51,541 3245 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T13:19:51,542 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,543 | PyLong_AsVoidPtr 2023-09-08T13:19:51,604 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_save_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T13:19:51,605 khmer/_khmermodule.cc:3347:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:19:51,606 3347 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T13:19:51,607 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,607 | PyLong_AsVoidPtr 2023-09-08T13:19:51,636 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_load_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T13:19:51,636 khmer/_khmermodule.cc:3379:10: error: ‘PyCObject_FromVoidPtr’ was not declared in this scope; did you mean ‘PyLong_FromVoidPtr’? 2023-09-08T13:19:51,637 3379 | return PyCObject_FromVoidPtr(subset_p, free_subset_partition_info); 2023-09-08T13:19:51,638 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,638 | PyLong_FromVoidPtr 2023-09-08T13:19:51,659 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__get_tag_density(PyObject*, PyObject*)’: 2023-09-08T13:19:51,660 khmer/_khmermodule.cc:3409:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,660 3409 | return PyInt_FromLong(d); 2023-09-08T13:19:51,661 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,662 | PyLong_FromLong 2023-09-08T13:19:51,689 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_subset(PyObject*, PyObject*)’: 2023-09-08T13:19:51,689 khmer/_khmermodule.cc:3425:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:19:51,690 3425 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2023-09-08T13:19:51,691 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,692 | PyLong_AsVoidPtr 2023-09-08T13:19:51,719 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_merge2_from_disk(PyObject*, PyObject*)’: 2023-09-08T13:19:51,719 khmer/_khmermodule.cc:3451:42: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:19:51,720 3451 | subset1_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset1_obj); 2023-09-08T13:19:51,720 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,721 | PyLong_AsVoidPtr 2023-09-08T13:19:51,749 khmer/_khmermodule.cc: In function ‘PyObject* hashbits__validate_subset_partitionmap(PyObject*, PyObject*)’: 2023-09-08T13:19:51,749 khmer/_khmermodule.cc:3472:41: error: ‘PyCObject_AsVoidPtr’ was not declared in this scope; did you mean ‘PyLong_AsVoidPtr’? 2023-09-08T13:19:51,750 3472 | subset_p = (khmer::SubsetPartition *) PyCObject_AsVoidPtr(subset_obj); 2023-09-08T13:19:51,751 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,752 | PyLong_AsVoidPtr 2023-09-08T13:19:51,773 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_join_partitions(PyObject*, PyObject*)’: 2023-09-08T13:19:51,773 khmer/_khmermodule.cc:3510:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,774 3510 | return PyInt_FromLong(p1); 2023-09-08T13:19:51,775 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,776 | PyLong_FromLong 2023-09-08T13:19:51,796 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_partition_id(PyObject*, PyObject*)’: 2023-09-08T13:19:51,796 khmer/_khmermodule.cc:3527:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,797 3527 | return PyInt_FromLong(partition_id); 2023-09-08T13:19:51,798 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,798 | PyLong_FromLong 2023-09-08T13:19:51,829 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_trim_on_density_explosion(PyObject*, PyObject*)’: 2023-09-08T13:19:51,830 khmer/_khmermodule.cc:3651:25: error: ‘PyString_FromStringAndSize’ was not declared in this scope; did you mean ‘PyBytes_FromStringAndSize’? 2023-09-08T13:19:51,831 3651 | PyObject * trim_seq = PyString_FromStringAndSize(seq, trim_at); 2023-09-08T13:19:51,832 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,833 | PyBytes_FromStringAndSize 2023-09-08T13:19:51,854 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_ksize(PyObject*, PyObject*)’: 2023-09-08T13:19:51,854 khmer/_khmermodule.cc:3696:10: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,855 3696 | return PyInt_FromLong(k); 2023-09-08T13:19:51,856 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,857 | PyLong_FromLong 2023-09-08T13:19:51,877 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_get_hashsizes(PyObject*, PyObject*)’: 2023-09-08T13:19:51,878 khmer/_khmermodule.cc:3713:27: error: ‘PyInt_FromLong’ was not declared in this scope; did you mean ‘PyLong_FromLong’? 2023-09-08T13:19:51,879 3713 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2023-09-08T13:19:51,879 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,880 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:19:51,881 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:19:51,882 | ^~~~ 2023-09-08T13:19:51,882 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:19:51,883 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:19:51,883 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,884 khmer/_khmermodule.cc:3713:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:19:51,884 3713 | PyList_SET_ITEM(x, i, PyInt_FromLong(ts[i])); 2023-09-08T13:19:51,885 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:51,916 khmer/_khmermodule.cc: In function ‘PyObject* hashbits_extract_unique_paths(PyObject*, PyObject*)’: 2023-09-08T13:19:51,917 khmer/_khmermodule.cc:3736:27: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:19:51,918 3736 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2023-09-08T13:19:51,918 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,919 /usr/include/python3.11/pyport.h:24:38: note: in definition of macro ‘_Py_CAST’ 2023-09-08T13:19:51,919 24 | #define _Py_CAST(type, expr) ((type)(expr)) 2023-09-08T13:19:51,920 | ^~~~ 2023-09-08T13:19:51,920 /usr/include/python3.11/cpython/listobject.h:50:48: note: in expansion of macro ‘_PyObject_CAST’ 2023-09-08T13:19:51,920 50 | PyList_SET_ITEM(_PyObject_CAST(op), index, _PyObject_CAST(value)) 2023-09-08T13:19:51,921 | ^~~~~~~~~~~~~~ 2023-09-08T13:19:51,922 khmer/_khmermodule.cc:3736:5: note: in expansion of macro ‘PyList_SET_ITEM’ 2023-09-08T13:19:51,922 3736 | PyList_SET_ITEM(x, i, PyString_FromString(results[i].c_str())); 2023-09-08T13:19:51,922 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:51,946 khmer/_khmermodule.cc: In function ‘PyObject* khmer_hashbits_getattr(PyObject*, char*)’: 2023-09-08T13:19:51,946 khmer/_khmermodule.cc:3847:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T13:19:51,947 3847 | return Py_FindMethod(khmer_hashbits_methods, obj, name); 2023-09-08T13:19:51,948 | ^~~~~~~~~~~~~ 2023-09-08T13:19:51,948 | PyCMethod 2023-09-08T13:19:51,975 khmer/_khmermodule.cc: In function ‘PyObject* khmer_readaligner_getattr(PyObject*, char*)’: 2023-09-08T13:19:51,976 khmer/_khmermodule.cc:3922:10: error: ‘Py_FindMethod’ was not declared in this scope; did you mean ‘PyCMethod’? 2023-09-08T13:19:51,977 3922 | return Py_FindMethod(khmer_ReadAligner_methods, obj, name); 2023-09-08T13:19:51,978 | ^~~~~~~~~~~~~ 2023-09-08T13:19:51,978 | PyCMethod 2023-09-08T13:19:51,979 khmer/_khmermodule.cc: At global scope: 2023-09-08T13:19:51,980 khmer/_khmermodule.cc:3940:5: error: invalid conversion from ‘const char*’ to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:19:51,980 3940 | "ReadAligner", sizeof(khmer_ReadAlignerObject), 2023-09-08T13:19:51,981 | ^~~~~~~~~~~~~ 2023-09-08T13:19:51,982 | | 2023-09-08T13:19:51,982 | const char* 2023-09-08T13:19:51,983 khmer/_khmermodule.cc:3942:5: error: invalid conversion from ‘void (*)(PyObject*)’ {aka ‘void (*)(_object*)’} to ‘Py_ssize_t’ {aka ‘int’} [-fpermissive] 2023-09-08T13:19:51,983 3942 | khmer_readaligner_dealloc, /*tp_dealloc*/ 2023-09-08T13:19:51,984 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,985 | | 2023-09-08T13:19:51,985 | void (*)(PyObject*) {aka void (*)(_object*)} 2023-09-08T13:19:51,986 khmer/_khmermodule.cc:3944:5: error: invalid conversion from ‘PyObject* (*)(PyObject*, char*)’ {aka ‘_object* (*)(_object*, char*)’} to ‘setattrfunc’ {aka ‘int (*)(_object*, char*, _object*)’} [-fpermissive] 2023-09-08T13:19:51,987 3944 | khmer_readaligner_getattr, /*tp_getattr*/ 2023-09-08T13:19:51,988 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,988 | | 2023-09-08T13:19:51,989 | PyObject* (*)(PyObject*, char*) {aka _object* (*)(_object*, char*)} 2023-09-08T13:19:51,989 /usr/include/python3.11/object.h:423:54: error: invalid conversion from ‘int’ to ‘const char*’ [-fpermissive] 2023-09-08T13:19:51,990 422 | #define Py_TPFLAGS_DEFAULT ( \ 2023-09-08T13:19:51,991 | ~~~ 2023-09-08T13:19:51,991 423 | Py_TPFLAGS_HAVE_STACKLESS_EXTENSION | \ 2023-09-08T13:19:51,992 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ 2023-09-08T13:19:51,992 | | 2023-09-08T13:19:51,993 | int 2023-09-08T13:19:51,994 424 | 0) 2023-09-08T13:19:51,994 | ~~ 2023-09-08T13:19:51,995 khmer/_khmermodule.cc:3957:5: note: in expansion of macro ‘Py_TPFLAGS_DEFAULT’ 2023-09-08T13:19:51,995 3957 | Py_TPFLAGS_DEFAULT, /*tp_flags*/ 2023-09-08T13:19:51,996 | ^~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,997 khmer/_khmermodule.cc:3958:5: error: cannot convert ‘const char*’ to ‘traverseproc’ {aka ‘int (*)(_object*, int (*)(_object*, void*), void*)’} in initialization 2023-09-08T13:19:51,997 3958 | "ReadAligner object", /* tp_doc */ 2023-09-08T13:19:51,998 | ^~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:51,998 | | 2023-09-08T13:19:51,999 | const char* 2023-09-08T13:19:52,019 khmer/_khmermodule.cc: In function ‘PyObject* reverse_hash(PyObject*, PyObject*)’: 2023-09-08T13:19:52,020 khmer/_khmermodule.cc:4139:10: error: ‘PyString_FromString’ was not declared in this scope; did you mean ‘PyLong_FromString’? 2023-09-08T13:19:52,020 4139 | return PyString_FromString(khmer::_revhash(val, ksize).c_str()); 2023-09-08T13:19:52,021 | ^~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:52,021 | PyLong_FromString 2023-09-08T13:19:52,022 khmer/_khmermodule.cc: At global scope: 2023-09-08T13:19:52,023 khmer/_khmermodule.cc:4195:17: error: expected constructor, destructor, or type conversion before ‘init_khmer’ 2023-09-08T13:19:52,023 4195 | DL_EXPORT(void) init_khmer(void) 2023-09-08T13:19:52,024 | ^~~~~~~~~~ 2023-09-08T13:19:52,863 khmer/_khmermodule.cc:4162:20: warning: ‘KhmerMethods’ defined but not used [-Wunused-variable] 2023-09-08T13:19:52,864 4162 | static PyMethodDef KhmerMethods[] = { 2023-09-08T13:19:52,865 | ^~~~~~~~~~~~ 2023-09-08T13:19:52,866 khmer/_khmermodule.cc:845:1: warning: ‘void khmer::python::_init_ReadPairIterator_Type()’ defined but not used [-Wunused-function] 2023-09-08T13:19:52,867 845 | _init_ReadPairIterator_Type( ) 2023-09-08T13:19:52,867 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:52,868 khmer/_khmermodule.cc:789:1: warning: ‘void khmer::python::_init_ReadParser_Type()’ defined but not used [-Wunused-function] 2023-09-08T13:19:52,868 789 | _init_ReadParser_Type( ) 2023-09-08T13:19:52,869 | ^~~~~~~~~~~~~~~~~~~~~ 2023-09-08T13:19:52,870 khmer/_khmermodule.cc:525:1: warning: ‘void khmer::python::_init_Read_Type()’ defined but not used [-Wunused-function] 2023-09-08T13:19:52,871 525 | _init_Read_Type( ) 2023-09-08T13:19:52,871 | ^~~~~~~~~~~~~~~ 2023-09-08T13:19:52,872 khmer/_khmermodule.cc:134:18: warning: ‘KhmerError’ defined but not used [-Wunused-variable] 2023-09-08T13:19:52,873 134 | static PyObject *KhmerError; 2023-09-08T13:19:52,873 | ^~~~~~~~~~ 2023-09-08T13:19:52,879 error: command '/usr/bin/arm-linux-gnueabihf-gcc' failed with exit code 1 2023-09-08T13:19:52,994 ERROR: [present-rich] python setup.py bdist_wheel exited with 1 2023-09-08T13:19:53,008 [bold magenta]full command[/]: [blue]/usr/bin/python3 -u -c ' 2023-09-08T13:19:53,008 exec(compile('"'"''"'"''"'"' 2023-09-08T13:19:53,008 # This is -- a caller that pip uses to run setup.py 2023-09-08T13:19:53,008 # 2023-09-08T13:19:53,008 # - It imports setuptools before invoking setup.py, to enable projects that directly 2023-09-08T13:19:53,008 # import from `distutils.core` to work with newer packaging standards. 2023-09-08T13:19:53,008 # - It provides a clear error message when setuptools is not installed. 2023-09-08T13:19:53,008 # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so 2023-09-08T13:19:53,008 # setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning: 2023-09-08T13:19:53,008 # manifest_maker: standard file '"'"'-c'"'"' not found". 2023-09-08T13:19:53,008 # - It generates a shim setup.py, for handling setup.cfg-only projects. 2023-09-08T13:19:53,008 import os, sys, tokenize 2023-09-08T13:19:53,008 2023-09-08T13:19:53,008 try: 2023-09-08T13:19:53,008 import setuptools 2023-09-08T13:19:53,008 except ImportError as error: 2023-09-08T13:19:53,008 print( 2023-09-08T13:19:53,008 "ERROR: Can not execute `setup.py` since setuptools is not available in " 2023-09-08T13:19:53,008 "the build environment.", 2023-09-08T13:19:53,008 file=sys.stderr, 2023-09-08T13:19:53,008 ) 2023-09-08T13:19:53,008 sys.exit(1) 2023-09-08T13:19:53,008 2023-09-08T13:19:53,008 __file__ = %r 2023-09-08T13:19:53,008 sys.argv[0] = __file__ 2023-09-08T13:19:53,008 2023-09-08T13:19:53,008 if os.path.exists(__file__): 2023-09-08T13:19:53,008 filename = __file__ 2023-09-08T13:19:53,008 with tokenize.open(__file__) as f: 2023-09-08T13:19:53,008 setup_py_code = f.read() 2023-09-08T13:19:53,008 else: 2023-09-08T13:19:53,008 filename = "" 2023-09-08T13:19:53,008 setup_py_code = "from setuptools import setup; setup()" 2023-09-08T13:19:53,008 2023-09-08T13:19:53,008 exec(compile(setup_py_code, filename, "exec")) 2023-09-08T13:19:53,008 '"'"''"'"''"'"' % ('"'"'/tmp/pip-wheel-tlwep6cn/khmer_61a242e36190457b95a8b741949b2fd2/setup.py'"'"',), "", "exec"))' bdist_wheel -d /tmp/pip-wheel-yvb81eek[/] 2023-09-08T13:19:53,009 [bold magenta]cwd[/]: /tmp/pip-wheel-tlwep6cn/khmer_61a242e36190457b95a8b741949b2fd2/ 2023-09-08T13:19:53,009 Building wheel for khmer (setup.py): finished with status 'error' 2023-09-08T13:19:53,011 ERROR: Failed building wheel for khmer 2023-09-08T13:19:53,012 Running setup.py clean for khmer 2023-09-08T13:19:53,014 Running command python setup.py clean 2023-09-08T13:19:54,094 'build/bdist.linux-armv7l' does not exist -- can't clean it 2023-09-08T13:19:54,095 'build/scripts-3.11' does not exist -- can't clean it 2023-09-08T13:19:54,209 Failed to build khmer 2023-09-08T13:19:54,210 ERROR: Failed to build one or more wheels 2023-09-08T13:19:54,211 Exception information: 2023-09-08T13:19:54,211 Traceback (most recent call last): 2023-09-08T13:19:54,211 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/base_command.py", line 180, in exc_logging_wrapper 2023-09-08T13:19:54,211 status = run_func(*args) 2023-09-08T13:19:54,211 ^^^^^^^^^^^^^^^ 2023-09-08T13:19:54,211 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/cli/req_command.py", line 248, in wrapper 2023-09-08T13:19:54,211 return func(self, options, args) 2023-09-08T13:19:54,211 ^^^^^^^^^^^^^^^^^^^^^^^^^ 2023-09-08T13:19:54,211 File "/usr/local/lib/python3.11/dist-packages/pip/_internal/commands/wheel.py", line 181, in run 2023-09-08T13:19:54,211 raise CommandError("Failed to build one or more wheels") 2023-09-08T13:19:54,211 pip._internal.exceptions.CommandError: Failed to build one or more wheels 2023-09-08T13:19:54,215 Removed build tracker: '/tmp/pip-build-tracker-15994rjx'