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debian/changelog
View file @ 6cd8445c
phylip (1:3.696+dfsg-6) UNRELEASED; urgency=medium
phylip (1:3.697+dfsg-1) unstable; urgency=medium
* Fix watch file
[ Steffen Moeller ]
* d/upstream/metadata: Added references to registries.
-- Andreas Tille <tille@debian.org> Mon, 19 Jun 2017 15:38:11 +0200
[ Andreas Tille ]
* New upstream version
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.2.1
* Secure URI in copyright format
* Drop useless get-orig-source target
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/control
* Do not parse d/changelog
-- Andreas Tille <tille@debian.org> Mon, 29 Oct 2018 11:44:41 +0100
phylip (1:3.696+dfsg-5) unstable; urgency=medium
......@@ -36,7 +47,7 @@ phylip (1:3.696+dfsg-3) unstable; urgency=medium
* fix java wrappers
[ Canberk Koç ]
* autopkgtest added
* autopkgtest added
-- Canberk Koç <canberkkoc@gmail.com> Sat, 23 Jul 2016 17:21:18 +0300
......@@ -100,7 +111,7 @@ phylip (1:3.68-2) unstable; urgency=low
phylip (1:3.68-1) unstable; urgency=low
* New upstream version
* New upstream version
-- Andreas Tille <tille@debian.org> Sun, 17 Aug 2008 11:40:34 -0300
......@@ -200,7 +211,7 @@ phylip (3.573c-6) unstable; urgency=low
phylip (3.573c-5) unstable; urgency=low
* New Maintainer
* A patch by Patrice Godard <pgodard@pasteur.fr> fo fix #67657 is
* A patch by Patrice Godard <pgodard@pasteur.fr> fo fix #67657 is
applied because it compiles well for me in contrast to 3.573c-2
where it was enclosed as patch.diff.
closes: #67657
......@@ -216,7 +227,7 @@ phylip (3.573c-4) unstable; urgency=low
phylip (3.573c-3) unstable; urgency=low
* Phylip manpage completely revised.
* Phylip manpage completely revised.
-- Dr. Guenter Bechly <gbechly@debian.org> Mon, 16 Apr 2001 19:21:10 +0200
......@@ -244,7 +255,7 @@ phylip (3.573c-1) unstable; urgency=low
phylip (3.5c-3) unstable; urgency=low
* Bug in dnapars fixed (incompatible with glibc).
* Bug in dnapars fixed (incompatible with glibc).
* New "tests" directory with samples.
* Fonts now included (they were forgotten)
......
debian/control
View file @ 6cd8445c
......@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille@debian.org>,
Manuel Prinz <manuel@debian.org>
Section: science
Priority: optional
Build-Depends: debhelper (>= 10),
Build-Depends: debhelper (>= 11~),
dh-exec,
libx11-dev,
libxt-dev,
......@@ -13,9 +13,9 @@ Build-Depends: debhelper (>= 10),
default-jdk,
libjna-java,
javahelper
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/phylip.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/phylip.git
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/phylip
Vcs-Git: https://salsa.debian.org/med-team/phylip.git
Homepage: http://evolution.genetics.washington.edu/phylip.html
Package: phylip
......@@ -24,13 +24,13 @@ Depends: ${shlibs:Depends},
${misc:Depends}
Suggests: phylip-doc
Description: package of programs for inferring phylogenies
The PHYLogeny Inference Package is a package of programs for inferring
The PHYLogeny Inference Package is a package of programs for inferring
phylogenies (evolutionary trees) from sequences.
Methods that are available in the package include parsimony, distance
matrix, and likelihood methods, including bootstrapping and consensus
trees. Data types that can be handled include molecular sequences, gene
frequencies, restriction sites, distance matrices, and 0/1 discrete
characters.
Methods that are available in the package include parsimony, distance
matrix, and likelihood methods, including bootstrapping and consensus
trees. Data types that can be handled include molecular sequences, gene
frequencies, restriction sites, distance matrices, and 0/1 discrete
characters.
Package: phylip-doc
Architecture: all
......@@ -38,12 +38,12 @@ Section: doc
Depends: ${misc:Depends}
Suggests: phylip
Description: package of programs for inferring phylogenies (documentation)
The PHYLogeny Inference Package is a package of programs for inferring
The PHYLogeny Inference Package is a package of programs for inferring
phylogenies (evolutionary trees) from sequences.
Methods that are available in the package include parsimony, distance
matrix, and likelihood methods, including bootstrapping and consensus
trees. Data types that can be handled include molecular sequences, gene
frequencies, restriction sites, distance matrices, and 0/1 discrete
characters.
Methods that are available in the package include parsimony, distance
matrix, and likelihood methods, including bootstrapping and consensus
trees. Data types that can be handled include molecular sequences, gene
frequencies, restriction sites, distance matrices, and 0/1 discrete
characters.
.
This package contains the HTML documentation
debian/copyright
View file @ 6cd8445c
Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: PHYLIP
Upstream-Contact: Joe Felsenstein <joe@gs.washington.edu>
Source: http://evolution.gs.washington.edu/phylip/download/
......
debian/rules
View file @ 6cd8445c
......@@ -4,9 +4,10 @@
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
include /usr/share/dpkg/default.mk
DEB_HOST_MULTIARCH ?= $(shell dpkg-architecture -qDEB_HOST_MULTIARCH)
LIBDIR := $(CURDIR)/debian/$(DEBPKGNAME)/usr/lib/ # $(DEB_HOST_MULTIARCH)
LIBDIR := $(CURDIR)/debian/$(DEB_SOURCE)/usr/lib/ # $(DEB_HOST_MULTIARCH)
export JAVA_HOME=/usr/lib/jvm/default-java
......@@ -35,5 +36,3 @@ override_dh_auto_clean:
rm -rf dist build.xml ; \
fi
get-orig-source:
uscan --verbose --force-download --repack --compress xz
doc/main.html
View file @ 6cd8445c
......@@ -16,9 +16,9 @@
<P>
<IMG SRC="phylip.gif" ALT="PHYLIP Logo">
<P>
<H3>Version 3.696</H3>
<H3>Version 3.697</H3>
<P>
<H3>September, 2014</H3>
<H3>December, 2017</H3>
<P>
<H2>by Joseph Felsenstein</H2>
<P>
......
src/cons.c
View file @ 6cd8445c
......@@ -941,8 +941,8 @@ void rehash()
memcpy(s, grouping[old_index], setsz * sizeof(group_type));
ss = 0.0;
for (j = 0; j < setsz; j++)
ss += s[j] /* pow(2, SETBITS*j)*/;
temp = ss * smult;
ss += s[j] * smult; /* pow(2, SETBITS*j)*/;
temp = ss;
new_index = (long)(new_maxgrp * (temp - floor(temp)));
done = false;
while (!done) {
......
src/phylip.h
View file @ 6cd8445c
#ifndef _PHYLIP_H_
#define _PHYLIP_H_
/* version 3.696.
/* version 3.697.
Written by Joseph Felsenstein, Akiko Fuseki, Sean Lamont, Andrew Keeffe,
Mike Palczewski, Doug Buxton and Dan Fineman.
Copyright (c) 1980-2014, Joseph Felsenstein
Copyright (c) 1980-2017, Joseph Felsenstein
All rights reserved.
Redistribution and use in source and binary forms, with or without
......@@ -31,7 +31,7 @@
POSSIBILITY OF SUCH DAMAGE.
*/
#define VERSION "3.696"
#define VERSION "3.697"
/* Debugging options */
/* Define this to disable assertions */
......