Your message dated Fri, 03 Dec 2021 16:03:49 +0000 with message-id <e1mtb2l-00066e...@fasolo.debian.org> and subject line Bug#1000864: fixed in python-skbio 0.5.6-6 has caused the Debian Bug report #1000864, regarding python-skbio: FTBFS with Python 3.10 to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact ow...@bugs.debian.org immediately.) -- 1000864: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1000864 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: python-skbio Version: 0.5.6-5 Severity: serious Tags: ftbfs patch User: debian-pyt...@lists.debian.org Usertags: python3.10 Hi Maintainer Now that scikit-learn has at least built on amd64 [1], we can now see a new failure in python-skbio [2]. I have copied part of the log below. This is due to .c files in the upstream tarball being generated by an old version of cython. The solution is to add cython3 as a build-dependency and regenerate the .c files at build time. I've attached a patch that does this. Regards Graham [1] https://buildd.debian.org/status/package.php?p=scikit-learn [2] https://buildd.debian.org/status/package.php?p=python-skbio&suite=sid skbio/alignment/_ssw_wrapper.c: In function ‘__pyx_tp_dealloc_5skbio_9alignment_12_ssw_wrapper_AlignmentStructure’: skbio/alignment/_ssw_wrapper.c:10363:5: error: lvalue required as increment operand 10363 | ++Py_REFCNT(o); | ^~ skbio/alignment/_ssw_wrapper.c:10365:5: error: lvalue required as decrement operand 10365 | --Py_REFCNT(o); | ^~ skbio/alignment/_ssw_wrapper.c: In function ‘__pyx_tp_dealloc_5skbio_9alignment_12_ssw_wrapper_StripedSmithWaterman’: skbio/alignment/_ssw_wrapper.c:10570:5: error: lvalue required as increment operand 10570 | ++Py_REFCNT(o); | ^~ skbio/alignment/_ssw_wrapper.c:10572:5: error: lvalue required as decrement operand 10572 | --Py_REFCNT(o); | ^~ skbio/alignment/_ssw_wrapper.c: In function ‘__Pyx_ParseOptionalKeywords’: skbio/alignment/_ssw_wrapper.c:12453:21: warning: ‘_PyUnicode_get_wstr_length’ is deprecated [-Wdeprecated-declarations] 12453 | (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 : | ^
cythonize.debdiff
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--- Begin Message ---Source: python-skbio Source-Version: 0.5.6-6 Done: Graham Inggs <gin...@debian.org> We believe that the bug you reported is fixed in the latest version of python-skbio, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to 1000...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Graham Inggs <gin...@debian.org> (supplier of updated python-skbio package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing ftpmas...@ftp-master.debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 1.8 Date: Fri, 03 Dec 2021 15:24:18 +0000 Source: python-skbio Built-For-Profiles: noudeb Architecture: source Version: 0.5.6-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Graham Inggs <gin...@debian.org> Closes: 992676 999523 1000864 Changes: python-skbio (0.5.6-6) unstable; urgency=medium . * Team upload . [ Andreas Tille ] * Remove Tim Booth from Uploaders (Thanks to Tim for all his work) . [ Graham Inggs ] * Regenerate the .c files at build time by cython3 Closes: #1000864 * Cherry-pick upstream commit to fix dtypes and warnings Closes: #992676, #999523 * Drop skip_tests_failung_due_to_scipy.patch, no longer needed Checksums-Sha1: ea9e3878dc91008ed433d4dd08079299a8f01148 2791 python-skbio_0.5.6-6.dsc 3a9b8252acc525d4edd890745d4948e66b2c516a 17264 python-skbio_0.5.6-6.debian.tar.xz Checksums-Sha256: 5126f17930952bb22f1b670fee47ccbae72043f9015634d09804e2f4cf99734b 2791 python-skbio_0.5.6-6.dsc f929e306ae57b4c225e5ebf59e33560fd541945990d92384ce19794ca630bad3 17264 python-skbio_0.5.6-6.debian.tar.xz Files: 0d56ac95d6d992f02d8337160b535be1 2791 python optional python-skbio_0.5.6-6.dsc cb4873534abc61011837d27a50ce920a 17264 python optional python-skbio_0.5.6-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEJeP/LX9Gnb59DU5Qr8/sjmac4cIFAmGqOMIACgkQr8/sjmac 4cJoDxAAnD3jAgCgcwFEfxEB7Har0Wm24rwb+6xauZ3SvFw+4AL1XcdmhR9JcMt3 2EnEwL+ybAry/3QYDGLX0LSSfiInVHok6T92uipZqPhZrSwaROPBVZsphSlLk688 KRmFzzvuWrLlM9/A3R90iroHzE+k3w0SOFaAd05GFb3gqRk/LPcBnw0zDljP5Lol HnWbilZ+CbjE8oTUC45zJKIwVPf7uDI0FijQHnL7UEJMMpuPSl8XpaWIns0hwHwd q07ELHIdlqQTmZ7AdL3VpvIdKo6bhAhDH35lOC+q2VbAwI4ZCfai7VWaKq7AT5Rn RzLb34sof3X3PH5O889s1TYecBEl/SMOyew7OaFIhDyVgjUaw46ac0l7RueZrDaC 2vBNYNYeR+ptmNOaAcoeZmlSSu1HNhq82vrIlF3izsUz2gfEw6wyFQEmfFd7MPcd ntyttKc8cZllqT7ZuSN7zcuNtp7mwYXS/Huw8/a+fC+fl7iBlb2qASW3MZ6MMCEZ 1zPOk7mk5zQPOvX1RzmrQJm4guGzicFKs0e6b9N7otePtkNiuJaDfRvqPrPui0YW tm8e1YVz8kpoUBPlERNSBy/BpQ1J4IoCw1LdV57EOvD3TjWiIvxg9J81Eq46A8B6 SRL2EuJZhK7mlQhBrZ06uYdvvix/4yssJUtQ6S52wgkcfwnK+Xo= =JIjz -----END PGP SIGNATURE-----
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