[med-svn] [Git][med-team/jmodeltest][master] 6 commits: Point Vcs fields to salsa.debian.org

Sun Apr 29 06:45:53 BST 2018

Andreas Tille pushed to branch master at Debian Med / jmodeltest


Commits:
09bbbe63 by Andreas Tille at 2018-04-29T07:20:39+02:00
Point Vcs fields to salsa.debian.org

- - - - -
afe90034 by Andreas Tille at 2018-04-29T07:20:39+02:00
Standards-Version: 4.1.4

- - - - -
ba16650a by Andreas Tille at 2018-04-29T07:20:39+02:00
debhelper 11

- - - - -
42783922 by Andreas Tille at 2018-04-29T07:28:11+02:00
Fix FTBFS with TeX Live 2018

- - - - -
6dbbf5f2 by Andreas Tille at 2018-04-29T07:34:54+02:00
Remove unneeded get-orig-source-target

- - - - -
69753ad1 by Andreas Tille at 2018-04-29T07:45:32+02:00
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/compat
- debian/control
- + debian/patches/latex_encoding.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================

--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,17 @@
+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
+
+ -- Andreas Tille <tille at debian.org>  Sun, 29 Apr 2018 07:35:03 +0200
+
 jmodeltest (2.1.10+dfsg-5) unstable; urgency=medium
 
   * Remove BrowserLauncher also from Build-Depends


=====================================
debian/compat
=====================================
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-9
+11


=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9),
+Build-Depends: debhelper (>= 11~),
                javahelper,
                default-jdk,
                ant,
@@ -17,9 +17,9 @@ Build-Depends: debhelper (>= 9),
                texlive-latex-base,
                texlive-fonts-recommended,
                texlive-latex-recommended
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/jmodeltest.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/jmodeltest.git
+Standards-Version: 4.1.4
+Vcs-Browser: https://salsa.debian.org/med-team/jmodeltest
+Vcs-Git: https://salsa.debian.org/med-team/jmodeltest.git
 Homepage: https://github.com//ddarriba/jmodeltest2
 
 Package: jmodeltest


=====================================
debian/patches/latex_encoding.patch
=====================================
--- /dev/null
+++ b/debian/patches/latex_encoding.patch
@@ -0,0 +1,15 @@
+Description: Fix FTBFS with TeX Live 2018
+Author: Adrian Bunk <bunk at debian.org>
+Bug-Debian: https://bugs.debian.org/896484
+
+--- 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}


=====================================
debian/patches/series
=====================================
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ do_not_chmod_anything_in_usr_bin.patch
 adapt_config.patch
 replace_natbib_bst_by_plainnat.patch
 remove_BrowserLauncher_reference.patch
+latex_encoding.patch


=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -19,6 +19,3 @@ override_dh_installchangelogs:
 
 override_dh_compress:
 	dh_compress --exclude=.pdf
-
-get-orig-source:
-	uscan --verbose --force-download --repack --compression xz



View it on GitLab: https://salsa.debian.org/med-team/jmodeltest/compare/b5291b3dcbb11506fe17d1c2628197b8ecd7d1e8...69753ad1f236a58e8e903ceb5c39757fb0419b2c

---
View it on GitLab: https://salsa.debian.org/med-team/jmodeltest/compare/b5291b3dcbb11506fe17d1c2628197b8ecd7d1e8...69753ad1f236a58e8e903ceb5c39757fb0419b2c
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