Your message dated Wed, 15 Jul 2020 22:03:39 +0000 with message-id <e1jvpv5-000bsn...@fasolo.debian.org> and subject line Bug#965073: fixed in macs 2.2.7.1-3 has caused the Debian Bug report #965073, regarding macs: shared library is not properly linked with libm 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.) -- 965073: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=965073 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: macs Version: 2.2.7.1-2 Severity: serious Tags: patch macs use the log() math function, but doesn't link link with libm.so. This causes the non-versioned __log_finite symbol to be used, which in turn causes issues when glibc version is upgraded: https://ci.debian.net/data/autopkgtest/testing/amd64/m/macs/6261687/log.gz The attached patch fixes that.--- macs-2.2.7.1.orig/setup.py +++ macs-2.2.7.1/setup.py @@ -59,8 +59,8 @@ def main(): Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=extra_c_args), - Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ), - Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), + Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ), + Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), #Extension("MACS2.Statistics", ["MACS2/Statistics.pyx"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args), ]
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--- Begin Message ---Source: macs Source-Version: 2.2.7.1-3 Done: Andreas Tille <ti...@debian.org> We believe that the bug you reported is fixed in the latest version of macs, 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 965...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Andreas Tille <ti...@debian.org> (supplier of updated macs 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: Wed, 15 Jul 2020 23:27:39 +0200 Source: macs Architecture: source Version: 2.2.7.1-3 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Closes: 965073 Changes: macs (2.2.7.1-3) unstable; urgency=medium . * Link properly with libm Closes: #965073 * debhelper-compat 13 (routine-update) Checksums-Sha1: c8901732b20445ba74b95e2567c182c35a9fc2a6 2102 macs_2.2.7.1-3.dsc 68332c8e20356ed0356364a6d105054abe97f324 1267660 macs_2.2.7.1-3.debian.tar.xz 815a5862d34da3ddec8e8df674330d658c80a7c2 7252 macs_2.2.7.1-3_amd64.buildinfo Checksums-Sha256: 1ad42909d66d5530a6db80a5f28897b2e8acb3b2436760bf1f1bd6e73ff8ce1b 2102 macs_2.2.7.1-3.dsc ec8667e7d3c85f3de72a87238266236470dd8c04a5631ad0f75f31545f5ee6f5 1267660 macs_2.2.7.1-3.debian.tar.xz 07014944a3f38cc4b580eb0e32dc63ceb309c8c10969aa1430f34982f31b69d3 7252 macs_2.2.7.1-3_amd64.buildinfo Files: 31b785b4272776fb74179acdc148afb6 2102 science optional macs_2.2.7.1-3.dsc c1b0b0f58baae3f2d4cf1221dc19e46f 1267660 science optional macs_2.2.7.1-3.debian.tar.xz e45af06503361f208cfc0e584f9bba82 7252 science optional macs_2.2.7.1-3_amd64.buildinfo -----BEGIN PGP SIGNATURE----- iQJFBAEBCgAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAl8PecARHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFvvQ//VCNVqsBVewQj2nh7kf99O2dg0/Cwx9BV PJy0U2pGxxdbh3UGG6+T5lulUSlp2B/qVfY2013h4Q8OjkHnQYQ3wiiqsU62+mTa hnHhtPDHyA1sMxQzK1Dpg+4LYWffccofN3BHdNoIhRkpcJypuPkgPWE3ZtTBSWCr 3F6KwdlTo4G9r64IF2uDeSSZlV+D3764ooI/MmLkVHvwoPP/4luZ8B/D9eqLeqe4 3Q1ye0byj4m/UFcObGkGMxX6h+qNsBJWFqIIjUGidAcHkKGEL6+epjM+TpCbtEmk /URrcE7jQJfOGGJZRH6MW7zVwZLJpExft6Sp9cDbquotw4/VmGuQ5+HECa8nxVfu x5otAO1rJxpRLaAtGRuUl85BNE9BxfnWK4dnodUJw4dcVEykrOdnhr/gLa3gUG6E 9F4ImtSMv4nk4sZddfp///s7tKOXtDtk62k1sPt0qBljHqDeNgspiqbn3KniYAhz wTTK0A4XYRn9iaaag1PHNVTbJRzuP9mjBW5UlOS+ODVgjqWzsIBJ5PShKzGnvfeM BiiDpBFpfLgZI3GA3HGkS25dA8ZW9onywLP0e4R2sxjAZ8fbUF8oyc0lzGQRmxOn m02STZJLk4w/jtQilASv3b2rLrXbdz2kWc7Nhm6VyTVrCMfE4+t+WUqo7jSua6UC aj4k5MufQco= =+Zgq -----END PGP SIGNATURE-----
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