Your message dated Fri, 03 Jan 2020 20:44:01 +0000 with message-id <e1intnd-000gmj...@fasolo.debian.org> and subject line Bug#947426: fixed in python-pysam 0.15.3+ds-1 has caused the Debian Bug report #947426, regarding python-pysam ftbfs with htslib 1.10.2 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.) -- 947426: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=947426 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: python-pysam Version: 0.15.2+ds-2 Severity: serious Justification: ftbfs Tags: ftbfs sid bullseye Dear maintainer, Your package is part of the htslib 1.10.2 transition. I tried to binNMU your package but it fails to build from source. Please have a look. Paul https://buildd.debian.org/status/package.php?p=python-pysam Tail of log for python-pysam on amd64: 24840 | __pyx_t_12 = PyFloat_FromDouble(__pyx_v_qual); if (unlikely(!__pyx_t_12)) __PYX_ERR(0, 873, __pyx_L1_error) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-z,relro -Wl,-z,now -Wl,--as-needed -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 build/temp.linux-amd64-3.7/pysam/libcvcf.o -L/<<PKGBUILDDIR>>/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -L/<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam -lz -lhts -lchtslib.cpython-37m-x86_64-linux-gnu -lcutils.cpython-37m-x86_64-linux-gnu -o /<<PKGBUILDDIR>>/.pybuild/cpython3_3.7_pysam/build/pysam/libcvcf.cpython-37m-x86_64-linux-gnu.so -Wl,-rpath,$ORIGIN debian/rules override_dh_auto_test make[1]: Entering directory '/<<PKGBUILDDIR>>' cd tests/pysam_data && /usr/bin/make all make[2]: Entering directory '/<<PKGBUILDDIR>>/tests/pysam_data' samtools faidx ex1.fa samtools import ex1.fa.fai ex1.sam.gz ex1.bam make[2]: *** [Makefile:56: ex1.bam] Segmentation fault make[2]: *** Deleting file 'ex1.bam' make[2]: Leaving directory '/<<PKGBUILDDIR>>/tests/pysam_data' make[1]: *** [debian/rules:51: pysam_data.all] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>' make: *** [debian/rules:24: build-arch] Error 2
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--- Begin Message ---Source: python-pysam Source-Version: 0.15.3+ds-1 We believe that the bug you reported is fixed in the latest version of python-pysam, 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 947...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Michael R. Crusoe <michael.cru...@gmail.com> (supplier of updated python-pysam 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 Jan 2020 21:25:33 +0100 Source: python-pysam Architecture: source Version: 0.15.3+ds-1 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Michael R. Crusoe <michael.cru...@gmail.com> Closes: 947426 Changes: python-pysam (0.15.3+ds-1) unstable; urgency=medium . * Team upload. * New upstream release. Not yet dropping py2 due to paleomix and pbsuite * debhelper-compat 12 * Standards-Version: 4.4.0 * Trim trailing whitespace. * Use secure URI in Homepage field. * Set upstream metadata fields: Repository. * New patch to remove symbols that were dropped in htslib 1.10: hts_utell, hts_useek (Closes: #947426) Checksums-Sha1: 7f0d61748bf7042b469254fdfae9ca21b2c78061 2533 python-pysam_0.15.3+ds-1.dsc f94f259969052b8954c86b0eca709cb5947ca36d 1364456 python-pysam_0.15.3+ds.orig.tar.xz 3f41a5f304c887cde179f9b55305bfaee4a68958 11088 python-pysam_0.15.3+ds-1.debian.tar.xz d1a644da5e05eb0459f1e52a7a5017b297060eaa 10795 python-pysam_0.15.3+ds-1_source.buildinfo Checksums-Sha256: 4b7c895293e7795e09e7149c8e8a6513d5acb94b544d616d8c26b28ac7469f79 2533 python-pysam_0.15.3+ds-1.dsc 0968a90e5b1d5418d21f94cdb6f43cd9f496f04fdfeefc8bf5b50aae8e2b950d 1364456 python-pysam_0.15.3+ds.orig.tar.xz 1c2e9c7cf3f34a956074a8d67b192d2cce36f7a66590d8af7767460099106f7f 11088 python-pysam_0.15.3+ds-1.debian.tar.xz 33b9c96f5599c9122fbc942df9425f4c45092193c220466c5c91101dda0d87b1 10795 python-pysam_0.15.3+ds-1_source.buildinfo Files: af6a6f18d00ea8115601f525050a7ce1 2533 python optional python-pysam_0.15.3+ds-1.dsc 7c118934f275b79a61c36a05333cfd08 1364456 python optional python-pysam_0.15.3+ds.orig.tar.xz eb92c743f3a92eae401fd22fc3118943 11088 python optional python-pysam_0.15.3+ds-1.debian.tar.xz ba3dced2703f5ad73131d3b27a9c3746 10795 python optional python-pysam_0.15.3+ds-1_source.buildinfo -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl4Po7cACgkQPCZ2P2xn 5uJwjg/+OkwUR9JVQ6NQuo3XdWu9PmWsh7pfmZVV2HrEjWhuwxX8PZsoV6FVru8Q YgRg2Csa9DPmI5JXZqH2JEFf989v4A37bosUHi32QiSpHsb2g0MQXPJfTfcPRoxW 0ukswHtxUhFqQBfILVgoX5qttGz33I6O0zBc80PZwbV2E6ZOwVWuPP4EpQ7Zfhcm 7jRAIlUH6mpEAL/kPS84Pe5w3NOd7ozeZzga+70y8UQpCVloLnFy0bFksJND+A7w ZltKoml9QDolRKNj2b4YU74o6jxi3Qwq2gqW547xcUAjTGvT9325boi+Mfj0rp5+ y47xyajcwm8ZvZyOr3h3EfBdtraH4jS6FO/VaD4wcIA2UHjWQMES4uGC9SMn6WO3 VehM0/8iN9o2yp4+40kzmPjTbKmU1Qkbc2j0Y0AyH20jWoMf2fwR1zAUJ2ksfKy6 2N4dZdEZLMxePnm/ovAy4HjXa5kLTfbApcPlgBnLOJZ9ut/I3jZq7EO4JflzAvwd AOh/ELNAJDpkoqLswsYoImRXXUJbtwtUstZGkCiTvtiJUTzS4Mk0g1MOzC7QkcmQ ombuJXZN2jbZRUJYoPfO9cKwjJpoHNY47rnUDI2gfit0lR7NH6nruUvIzr5XJaV8 a51FvPEtLvhWURjVKuoMY8K6pGMRpOzmQEJbqHAPHWu91QAYbI4= =grtW -----END PGP SIGNATURE-----
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