[med-svn] [Git][med-team/phylip][master] 12 commits: New upstream version 3.697+dfsg
Andreas Tille
gitlab at salsa.debian.org
Mon Oct 29 10:51:49 GMT 2018
Andreas Tille pushed to branch master at Debian Med / phylip
Commits:
cbcb3b1d by Andreas Tille at 2018-10-29T10:43:02Z
New upstream version 3.697+dfsg
- - - - -
464a6f99 by Andreas Tille at 2018-10-29T10:43:08Z
Update upstream source from tag 'upstream/3.697+dfsg'
Update to upstream version '3.697+dfsg'
with Debian dir 7fc57c779b4657ec93aaa7f2e9fd14c2e43a62b6
- - - - -
038ed1e3 by Andreas Tille at 2018-10-29T10:43:08Z
New upstream version
- - - - -
5e04256e by Andreas Tille at 2018-10-29T10:43:08Z
debhelper 11
- - - - -
c486a93a by Andreas Tille at 2018-10-29T10:43:11Z
Point Vcs fields to salsa.debian.org
- - - - -
a1e26858 by Andreas Tille at 2018-10-29T10:43:11Z
Standards-Version: 4.2.1
- - - - -
c5614e65 by Andreas Tille at 2018-10-29T10:43:12Z
Secure URI in copyright format
- - - - -
7eaa6904 by Andreas Tille at 2018-10-29T10:43:12Z
Drop useless get-orig-source target
- - - - -
ad6a2d73 by Andreas Tille at 2018-10-29T10:43:12Z
Remove trailing whitespace in debian/changelog
- - - - -
a6514a88 by Andreas Tille at 2018-10-29T10:43:12Z
Remove trailing whitespace in debian/control
- - - - -
f27f6887 by Andreas Tille at 2018-10-29T10:44:40Z
Do not parse d/changelog
- - - - -
6cd8445c by Andreas Tille at 2018-10-29T10:49:47Z
Upload to unstable
- - - - -
8 changed files:
- debian/changelog
- debian/compat
- debian/control
- debian/copyright
- debian/rules
- doc/main.html
- src/cons.c
- src/phylip.h
Changes:
=====================================
debian/changelog
=====================================
@@ -1,11 +1,22 @@
-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 at 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 at 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 at 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 at 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 at pasteur.fr> fo fix #67657 is
+ * A patch by Patrice Godard <pgodard at 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 at 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/compat
=====================================
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Andreas Tille <tille at debian.org>,
Manuel Prinz <manuel at 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
=====================================
@@ -1,4 +1,4 @@
-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 at gs.washington.edu>
Source: http://evolution.gs.washington.edu/phylip/download/
=====================================
debian/rules
=====================================
@@ -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
=====================================
@@ -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
=====================================
@@ -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
=====================================
@@ -1,11 +1,11 @@
#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 */
View it on GitLab: https://salsa.debian.org/med-team/phylip/compare/3c6cc3c6957e35f815adec7e8f268efebe3451a9...6cd8445c66b70947018ee81fe1c810f5d2daab00
--
View it on GitLab: https://salsa.debian.org/med-team/phylip/compare/3c6cc3c6957e35f815adec7e8f268efebe3451a9...6cd8445c66b70947018ee81fe1c810f5d2daab00
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