Author: tille
Date: 2011-02-16 16:53:59 +0000 (Wed, 16 Feb 2011)
New Revision: 6003
Added:
trunk/packages/beast-mcmc/trunk/debian/patches/_fix_paths.patch
trunk/packages/beast-mcmc/trunk/debian/patches/_native_flags.patch
Removed:
trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch
trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch
Modified:
trunk/packages/beast-mcmc/trunk/debian/get-orig-source
trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
trunk/packages/beast-mcmc/trunk/debian/rules
Log:
Remove further docs from orig.tar.gz, rebuild them in build target and care for
proper cleaning in clean target
Modified: trunk/packages/beast-mcmc/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2011-02-16
14:57:27 UTC (rev 6002)
+++ trunk/packages/beast-mcmc/trunk/debian/get-orig-source 2011-02-16
16:53:59 UTC (rev 6003)
@@ -28,15 +28,15 @@
rm -rf ${TARDIR}/release/Mac ${TARDIR}/release/Windows
${TARDIR}/release/Linux/lib/*
-set -x
-# remove duplicated docs
+# Remove all preprocessed (duplicated!) docs
+rm -rf ${TARDIR}/release/common/doc/*
+# remove preprocessed docs which can be recreated using LaTeX to make sure
that we
+# really have the source and to save some disk space in source archive
for pdf in \
- release/common/doc/PackageStructure.pdf \
- release/common/doc/Practical_BEAST.pdf \
- "doc/Virus*Tex/Practical_BEAST.pdf" \
+ 'doc/Virus*Tex/Practical_BEAST.pdf' \
'doc/Virus*Tex/Practical_BEAST.aux' \
- release/common/doc/Yule.pdf \
doc/Yule.pdf \
+ doc/SerialSampleCoalescent.pdf \
doc/StarBEAST/STARBEAST.pdf \
; do
rm -rf ${TARDIR}/$pdf
Added: trunk/packages/beast-mcmc/trunk/debian/patches/_fix_paths.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/_fix_paths.patch
(rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/_fix_paths.patch
2011-02-16 16:53:59 UTC (rev 6003)
@@ -0,0 +1,50 @@
+--- beast-mcmc-1.5.3+svnr2672.orig/scripts/beast
++++ beast-mcmc-1.5.3+svnr2672/scripts/beast
+@@ -22,6 +22,6 @@
+ cd "$saveddir"
+ fi
+
+-BEAST_LIB=$BEAST/lib
++BEAST_LIB="/usr/share/beast-mcmc/lib/"
+ java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/lib" -cp
"$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
+
+--- trunk.orig/scripts/beauti
++++ trunk/scripts/beauti
+@@ -22,6 +22,6 @@
+ cd "$saveddir"
+ fi
+
+-BEAST_LIB=$BEAST/lib
++BEAST_LIB="/usr/share/beast-mcmc/lib/"
+ java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -jar
$BEAST_LIB/beauti.jar $*
+
+--- trunk.orig/scripts/loganalyser
++++ trunk/scripts/loganalyser
+@@ -22,6 +22,6 @@
+ cd "$saveddir"
+ fi
+
+-BEAST_LIB=$BEAST/lib
++BEAST_LIB="/usr/share/beast-mcmc/lib/"
+ java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar
dr.app.tools.LogAnalyser $*
+
+--- trunk.orig/scripts/logcombiner
++++ trunk/scripts/logcombiner
+@@ -22,6 +22,6 @@
+ cd "$saveddir"
+ fi
+
+-BEAST_LIB=$BEAST/lib
++BEAST_LIB="/usr/share/beast-mcmc/lib/"
+ java -Xms64m -Xmx128m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar
dr.app.tools.LogCombiner $*
+
+--- trunk.orig/scripts/treeannotator
++++ trunk/scripts/treeannotator
+@@ -22,6 +22,6 @@
+ cd "$saveddir"
+ fi
+
+-BEAST_LIB=$BEAST/lib
++BEAST_LIB="/usr/share/beast-mcmc/lib/"
+ java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar
dr.app.tools.TreeAnnotator $*
+
Added: trunk/packages/beast-mcmc/trunk/debian/patches/_native_flags.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/_native_flags.patch
(rev 0)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/_native_flags.patch
2011-02-16 16:53:59 UTC (rev 6003)
@@ -0,0 +1,10 @@
+--- beast-mcmc-1.5.3+svnr2672.orig/native/Makefile
++++ beast-mcmc-1.5.3+svnr2672/native/Makefile
+@@ -36,6 +36,6 @@
+ -output lib$(OUTNAME).jnilib
+
+ linux :
+- gcc -c -O4 $(OPTIONS) $(LINUX_INCLUDES) -c $(INNAME) -std=c99
-DSTATE_COUNT=$(STATE_COUNT) -o lib$(OUTNAME).o
++ gcc -fPIC -c -O4 $(OPTIONS) $(LINUX_INCLUDES) -c $(INNAME) -std=c99
-DSTATE_COUNT=$(STATE_COUNT) -o lib$(OUTNAME).o
+ ld -$(LINUX_LINK) -o lib$(OUTNAME).so lib$(OUTNAME).o
+
Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch
2011-02-16 14:57:27 UTC (rev 6002)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/fix_paths.patch
2011-02-16 16:53:59 UTC (rev 6003)
@@ -1,50 +0,0 @@
---- beast-mcmc-1.5.3+svnr2672.orig/scripts/beast
-+++ beast-mcmc-1.5.3+svnr2672/scripts/beast
-@@ -22,6 +22,6 @@
- cd "$saveddir"
- fi
-
--BEAST_LIB=$BEAST/lib
-+BEAST_LIB="/usr/share/beast-mcmc/lib/"
- java -Xms64m -Xmx1024m -Djava.library.path="$BEAST_LIB:/usr/lib" -cp
"$BEAST_LIB/beast.jar:$BEAST_LIB/beast-beagle.jar" dr.app.beast.BeastMain $*
-
---- trunk.orig/scripts/beauti
-+++ trunk/scripts/beauti
-@@ -22,6 +22,6 @@
- cd "$saveddir"
- fi
-
--BEAST_LIB=$BEAST/lib
-+BEAST_LIB="/usr/share/beast-mcmc/lib/"
- java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -jar
$BEAST_LIB/beauti.jar $*
-
---- trunk.orig/scripts/loganalyser
-+++ trunk/scripts/loganalyser
-@@ -22,6 +22,6 @@
- cd "$saveddir"
- fi
-
--BEAST_LIB=$BEAST/lib
-+BEAST_LIB="/usr/share/beast-mcmc/lib/"
- java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar
dr.app.tools.LogAnalyser $*
-
---- trunk.orig/scripts/logcombiner
-+++ trunk/scripts/logcombiner
-@@ -22,6 +22,6 @@
- cd "$saveddir"
- fi
-
--BEAST_LIB=$BEAST/lib
-+BEAST_LIB="/usr/share/beast-mcmc/lib/"
- java -Xms64m -Xmx128m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar
dr.app.tools.LogCombiner $*
-
---- trunk.orig/scripts/treeannotator
-+++ trunk/scripts/treeannotator
-@@ -22,6 +22,6 @@
- cd "$saveddir"
- fi
-
--BEAST_LIB=$BEAST/lib
-+BEAST_LIB="/usr/share/beast-mcmc/lib/"
- java -Xms64m -Xmx256m -Djava.library.path=$BEAST_LIB -cp $BEAST_LIB/beast.jar
dr.app.tools.TreeAnnotator $*
-
Deleted: trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch
2011-02-16 14:57:27 UTC (rev 6002)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/native_flags.patch
2011-02-16 16:53:59 UTC (rev 6003)
@@ -1,10 +0,0 @@
---- beast-mcmc-1.5.3+svnr2672.orig/native/Makefile
-+++ beast-mcmc-1.5.3+svnr2672/native/Makefile
-@@ -36,6 +36,6 @@
- -output lib$(OUTNAME).jnilib
-
- linux :
-- gcc -c -O4 $(OPTIONS) $(LINUX_INCLUDES) -c $(INNAME) -std=c99
-DSTATE_COUNT=$(STATE_COUNT) -o lib$(OUTNAME).o
-+ gcc -fPIC -c -O4 $(OPTIONS) $(LINUX_INCLUDES) -c $(INNAME) -std=c99
-DSTATE_COUNT=$(STATE_COUNT) -o lib$(OUTNAME).o
- ld -$(LINUX_LINK) -o lib$(OUTNAME).so lib$(OUTNAME).o
-
Modified: trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
2011-02-16 14:57:27 UTC (rev 6002)
+++ trunk/packages/beast-mcmc/trunk/debian/patches/patch_tex_docs.patch
2011-02-16 16:53:59 UTC (rev 6003)
@@ -38,3 +38,25 @@
\makeatother
\begin{document}
+--- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/SerialSampleCoalescent.tex
++++ beast-mcmc-1.6.1+svnr3660.orig/doc/SerialSampleCoalescent.tex
+@@ -33,7 +33,7 @@
+ \begin{document}
+
+ \title{\textbf{The serially-sampled coalescent}}
+-
++\date{July 12, 2007}
+ \author{\textsc{Alexei J. Drummond}}
+
+ \maketitle
+--- beast-mcmc-1.6.1+svnr3660.orig.orig/doc/BEAST14_Manual.tex
++++ beast-mcmc-1.6.1+svnr3660.orig/doc/BEAST14_Manual.tex
+@@ -35,7 +35,7 @@
+ \begin{document}
+
+ \title{\textbf{A Rough Guide to BEAST 1.4}}
+-
++\date{July 6, 2007}
+
+ \author{\textsc{Alexei J. Drummond}$^{1}$, \textsc{Simon Y.W. Ho},\\
+ \textsc{Nic Rawlence} and \textsc{Andrew Rambaut}$^{2}$\\
Modified: trunk/packages/beast-mcmc/trunk/debian/rules
===================================================================
--- trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-16 14:57:27 UTC
(rev 6002)
+++ trunk/packages/beast-mcmc/trunk/debian/rules 2011-02-16 16:53:59 UTC
(rev 6003)
@@ -18,13 +18,23 @@
ANT_BIN := $(ANT_HOME)/bin/ant
ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true
-
%:
dh $@ --with javahelper
override_dh_auto_clean:
rm -f build-stamp configure-stamp
rm -f native/*\.o native/*\.so
+ for cleantex in \
+ Practical_BEAST \
+ BookSection \
+ STARBEAST \
+ Practical_BEAST \
+ Yule \
+ SerialSampleCoalescent \
+ BEAST14_Manual \
+ ; do \
+ find doc -not -name "*.tex" -a -not -name "*.bib" -and -name
"$${cleantex}.*" -exec rm -f \{\} \; ; \
+ done
ant clean
override_dh_auto_build:
@@ -32,10 +42,13 @@
cd native && /bin/sh compileNativeLinux.sh
#
# Build extra LaTeX documentation
+ #
cd doc/BookSection; pdflatex BookSection.tex; pdflatex BookSection.tex
cd doc/StarBEAST; pdflatex STARBEAST.tex; bibtex STARBEAST; pdflatex
STARBEAST.tex; pdflatex STARBEAST.tex
cd doc/Virus\ Practical\ Tex; pdflatex Practical_BEAST.tex; pdflatex
Practical_BEAST.tex
cd doc; pdflatex Yule.tex; pdflatex Yule.tex
+ cd doc; pdflatex SerialSampleCoalescent.tex; pdflatex
SerialSampleCoalescent.tex
+ cd doc; pdflatex BEAST14_Manual.tex; pdflatex BEAST14_Manual.tex
#
#####################################################################
## Run test suite ##
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