[med-svn] r9470 - in trunk/packages/phy-spread/trunk/debian: . patches

[Andreas Tille]

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.