Your message dated Sun, 29 Apr 2018 06:05:07 +0000 with message-id <e1fcfsn-000fui...@fasolo.debian.org> and subject line Bug#896484: fixed in jmodeltest 2.1.10+dfsg-6 has caused the Debian Bug report #896484, regarding jmodeltest FTBFS with TeX Live 2018 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.) -- 896484: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=896484 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Source: jmodeltest Version: 2.1.10+dfsg-5 Severity: serious Tags: buster sid patch https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/jmodeltest.html ... ! Package inputenc Error: Unicode character χ (U+3C7) (inputenc) not set up for use with LaTeX. See the inputenc package documentation for explanation. Type H <return> for immediate help. ... l.75 ...stic is asymptotically distributed as a χ 2 with q degrees of freedo... ? ! Emergency stop. ... l.75 ...stic is asymptotically distributed as a χ 2 with q degrees of freedo... ! ==> Fatal error occurred, no output PDF file produced! Transcript written on manual.log. make[1]: *** [debian/rules:15: override_dh_auto_build] Error 1 Fix is attached.Description: Fix FTBFS with TeX Live 2018 Author: Adrian Bunk <b...@debian.org> --- jmodeltest-2.1.10+dfsg.orig/manual/sec-theory.tex +++ jmodeltest-2.1.10+dfsg/manual/sec-theory.tex @@ -72,7 +72,7 @@ In traditional statistical theory, a wid LRT=2(l_1-l_0) \] where $l_1$ is the maximum likelihood under the more parameter-rich, complex model (alternative hypothesis) and $l_0$ is the maximum likelihood under the less parameter-rich simple model (null hypothesis). - When the models compared are nested (the null hypothesis is a special case of the alternative hypothesis) and the null hypothesis is correct, the LRT statistic is asymptotically distributed as a χ2 with q degrees of freedom, where q is the difference in number of free parameters between the two models \citep{Kendall-1979, Goldman-1993b}. Note that, to preserve the nesting of the models, the likelihood scores need to be estimated upon the same tree. When some parameter is fixed at its boundary (p-inv, α), a mixed χ2 is used instead \citep{Ohta-1992, Goldman-2000}. The behavior of the χ2 approximation for the LRT has been investigated with quite a bit of detail \citep{Goldman-1993a, Goldman-1993b, Yang-1995, Whelan-1999, Goldman-2000}. + When the models compared are nested (the null hypothesis is a special case of the alternative hypothesis) and the null hypothesis is correct, the LRT statistic is asymptotically distributed as a $\chi^2$ with q degrees of freedom, where q is the difference in number of free parameters between the two models \citep{Kendall-1979, Goldman-1993b}. Note that, to preserve the nesting of the models, the likelihood scores need to be estimated upon the same tree. When some parameter is fixed at its boundary (p-inv, $\alpha$), a mixed $\chi^2$ is used instead \citep{Ohta-1992, Goldman-2000}. The behavior of the $\chi^2$ approximation for the LRT has been investigated with quite a bit of detail \citep{Goldman-1993a, Goldman-1993b, Yang-1995, Whelan-1999, Goldman-2000}. \subsection{Hierarchical Likelihood Ratio Tests (hLRT)} \label{sec:hlrt}
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--- Begin Message ---Source: jmodeltest Source-Version: 2.1.10+dfsg-6 We believe that the bug you reported is fixed in the latest version of jmodeltest, 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 896...@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 jmodeltest 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: SHA256 Format: 1.8 Date: Sun, 29 Apr 2018 07:35:03 +0200 Source: jmodeltest Binary: jmodeltest Architecture: source Version: 2.1.10+dfsg-6 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Changed-By: Andreas Tille <ti...@debian.org> Description: jmodeltest - HPC selection of models of nucleotide substitution Closes: 896484 Changes: jmodeltest (2.1.10+dfsg-6) unstable; urgency=medium . [ Andreas Tille ] * Point Vcs fields to salsa.debian.org * Standards-Version: 4.1.4 * debhelper 11 * Remove unneeded get-orig-source-target . [ Adrian Bunk ] * Fix FTBFS with TeX Live 2018 Closes: #896484 Checksums-Sha1: d70a2ca9a760102efd828fb22d0c1e9076ba94de 2227 jmodeltest_2.1.10+dfsg-6.dsc 819814579bce9302307d4a0f4c965daa756b4164 7980 jmodeltest_2.1.10+dfsg-6.debian.tar.xz Checksums-Sha256: 0bfff2e444a3c4eee1967e5250e10674daa83eccdc450e3cf8dfdf7204410077 2227 jmodeltest_2.1.10+dfsg-6.dsc 7ffe557b63c36dd6141d4a04a441a6c73fbef8a96d33e7d1d26cf8a665c2e10a 7980 jmodeltest_2.1.10+dfsg-6.debian.tar.xz Files: 6e4f2f4dceb97ffd5cf348c5fda9fa43 2227 science optional jmodeltest_2.1.10+dfsg-6.dsc c45f2c06d2d29e0f9f1e511985f9f5a2 7980 science optional jmodeltest_2.1.10+dfsg-6.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAlrlWyIRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtFhnRAAjWj6hOExIFCvNs2PUfrys+WTqVvU/VD0 bCdy/Kx9W826bNUrk89WAQFWNNrcgVU3MiiQgRmj3FxchDA6ejofqyjKuO1iygIL SBfe1h/QZLPo/jdFGjmJ5HLh+ERFmwj0CQ/3diWqL7uloYn1ryIa2KqlX5sFyDtq 5RO+xEUHZmihPGjFC0o/hRxjoTJ5GjfavyFtVG9oSk0jjjz1g9prXIpm1Ib4vT0T 62PVvOgBBMtZYGpnBjJ+2K6GV8PmO8hfKu1IEQhmihFcaZ874SOmFAEoIVfJIAbA 1K9Hrwya9omv7/HLMYvGfI+qJOZvR4ItLOK8UM3k9Jcb1NA8K4IeRWFZ0YmK+RzE LklOkDEGfvrgV3rbWPgbywX8olMJPKKj2Iu9UGeftQ4wNXRN2xuRXWEhS/jBLvQJ OejGWI5HmdFYyIbh3Tu+tNGosx5R/lfNdoQMFeEe08OFCxj5S/rQ1jrb8XZ9f9pQ WIDPMzyuLEUVufW+FlArwim9IwHu10WRIZCYghdiCnSuH/BA7R+ztFbmSv/iysGn dqom02ytDm9g7YQliF4R2+mZrTuKWnSCre8E07yM1rea2xGmigvLbe2ObJwfCZqi b1dkSr85lKTgkz9Molt6bMoSaUQGPv2AQz6YJDm7fn10SytBYr5DNZRmn4s1w2R2 guIMe8BMj/A= =+uuT -----END PGP SIGNATURE-----
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