[med-svn] r9470 - in trunk/packages/phy-spread/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Sat Jan 28 08:12:42 UTC 2012
Author: tille
Date: 2012-01-28 08:12:41 +0000 (Sat, 28 Jan 2012)
New Revision: 9470
Added:
trunk/packages/phy-spread/trunk/debian/manpages
trunk/packages/phy-spread/trunk/debian/patches/encoding.patch
trunk/packages/phy-spread/trunk/debian/phy-spread.1
Modified:
trunk/packages/phy-spread/trunk/debian/changelog
trunk/packages/phy-spread/trunk/debian/control
trunk/packages/phy-spread/trunk/debian/patches/series
Log:
Added manpage
Modified: trunk/packages/phy-spread/trunk/debian/changelog
===================================================================
--- trunk/packages/phy-spread/trunk/debian/changelog 2012-01-28 07:19:45 UTC (rev 9469)
+++ trunk/packages/phy-spread/trunk/debian/changelog 2012-01-28 08:12:41 UTC (rev 9470)
@@ -2,4 +2,4 @@
* Initial release. (Closes: #657585)
- -- Andreas Tille <tille at debian.org> Thu, 26 Jan 2012 18:51:29 +0100
+ -- Andreas Tille <tille at debian.org> Sat, 28 Jan 2012 08:59:13 +0100
Modified: trunk/packages/phy-spread/trunk/debian/control
===================================================================
--- trunk/packages/phy-spread/trunk/debian/control 2012-01-28 07:19:45 UTC (rev 9469)
+++ trunk/packages/phy-spread/trunk/debian/control 2012-01-28 08:12:41 UTC (rev 9470)
@@ -7,7 +7,7 @@
Build-Depends: debhelper (>= 8), javahelper (>=0.25),
ant, ant-optional, openjdk-6-jdk | default-jdk,
libcolorpicker-java, libjebl2-java, libcolt-java,
- libprocessing-core-java
+ libprocessing-core-java, libkmlframework-java
Standards-Version: 3.9.2
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/phy-spread/trunk/
Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/phy-spread/trunk/
Added: trunk/packages/phy-spread/trunk/debian/manpages
===================================================================
--- trunk/packages/phy-spread/trunk/debian/manpages (rev 0)
+++ trunk/packages/phy-spread/trunk/debian/manpages 2012-01-28 08:12:41 UTC (rev 9470)
@@ -0,0 +1 @@
+debian/*.1
Added: trunk/packages/phy-spread/trunk/debian/patches/encoding.patch
===================================================================
--- trunk/packages/phy-spread/trunk/debian/patches/encoding.patch (rev 0)
+++ trunk/packages/phy-spread/trunk/debian/patches/encoding.patch 2012-01-28 08:12:41 UTC (rev 9470)
@@ -0,0 +1,16 @@
+Author: Andreas Tille <tille at debian.org>
+Date: Sat, 28 Jan 2012 08:59:13 +0100
+Description: Java called in a pbuilder environment just fails if
+ finding the '°' character in the comment - so it was replaced
+
+--- spread-1.0.2.orig/src/utils/Utils.java
++++ spread-1.0.2/src/utils/Utils.java
+@@ -414,7 +414,7 @@
+ // line
+ // gives
+ // dPhi=0
+- // if dLon over 180° take shorter rhumb across 180° meridian:
++ // if dLon over 180 degree take shorter rhumb across 180 degree meridian:
+ if (dLon > Math.PI)
+ dLon = 2 * Math.PI - dLon;
+ double distance = Math.sqrt(dLat * dLat + q * q * dLon * dLon)
Modified: trunk/packages/phy-spread/trunk/debian/patches/series
===================================================================
--- trunk/packages/phy-spread/trunk/debian/patches/series 2012-01-28 07:19:45 UTC (rev 9469)
+++ trunk/packages/phy-spread/trunk/debian/patches/series 2012-01-28 08:12:41 UTC (rev 9470)
@@ -1,2 +1,3 @@
follow_hint_from_README.patch
build_xml.patch
+encoding.patch
Added: trunk/packages/phy-spread/trunk/debian/phy-spread.1
===================================================================
--- trunk/packages/phy-spread/trunk/debian/phy-spread.1 (rev 0)
+++ trunk/packages/phy-spread/trunk/debian/phy-spread.1 2012-01-28 08:12:41 UTC (rev 9470)
@@ -0,0 +1,28 @@
+.TH "SPREAD" "1" "01/28/2012" "SPREAD 1.0.2" "SPREAD Manual"
+.SH "NAME"
+spread \- analyze and visualize phylogeographic reconstructions
+.SH "SYNOPSIS"
+\fBphy-spread\fR
+.SH "DESCRIPTION"
+.PP
+SPREAD is a user-friendly application to analyze and visualize
+phylogeographic reconstructions resulting from Bayesian inference of
+spatio-temporal diffusion.
+.PP
+There is a tutorial for SPREAD online at
+http://www.kuleuven.be/aidslab/phylogeography/tutorial/spread_tutorial.html
+.PP
+Originally this program is named \fBspread\fR. However, there is just such a
+package inside Debian and thus a '\fBphy-\fR' for phylogeny was prepended.
+.SH "SEE ALSO"
+.PP
+\fBbeast-mcmc\fR(1)\&.
+.SH "REFERENCES"
+.PP
+Bielejec F., Rambaut A., Suchard M.A & Lemey P. SPREAD: Spatial Phylogenetic Reconstruction of Evolutionary Dynamics. Bioinformatics, 2011. doi:10.1093
+.SH "AUTHORS"
+.PP
+The authors of the software \fBSPREAD\fR are Filip Bielejec, Andrew Rambaut, Marc A. Suchard, Philippe Lemey.
+.PP
+This manual page was written for the Debian distribution by
+Andreas Tille <tille at debian.org>. It can be used freely by others.
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