[med-svn] r1210 - in trunk/packages/glam2/trunk/debian: . patches

[charles-guest at alioth.debian.org]

Author: charles-guest
Date: 2008-01-29 06:25:08 +0000 (Tue, 29 Jan 2008)
New Revision: 1210

Added:
   trunk/packages/glam2/trunk/debian/patches/
   trunk/packages/glam2/trunk/debian/patches/Makefiles
   trunk/packages/glam2/trunk/debian/patches/series
Modified:
   trunk/packages/glam2/trunk/debian/control
   trunk/packages/glam2/trunk/debian/rules
Log:
Patched makefiles to better use CDBS.

Modified: trunk/packages/glam2/trunk/debian/control
===================================================================
--- trunk/packages/glam2/trunk/debian/control	2008-01-28 15:49:40 UTC (rev 1209)
+++ trunk/packages/glam2/trunk/debian/control	2008-01-29 06:25:08 UTC (rev 1210)
@@ -4,7 +4,7 @@
 Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 XS-DM-Upload-Allowed: yes
 Uploaders: Steffen Moeller <moeller at debian.org>, Charles Plessy <charles-debian-nospam at plessy.org>
-Build-Depends: debhelper (>= 5), cdbs, libfftw3-dev
+Build-Depends: debhelper (>= 5), cdbs, quilt, libfftw3-dev
 Standards-Version: 3.7.3
 Homepage: http://bioinformatics.org.au/glam2/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/glam2/trunk/

Added: trunk/packages/glam2/trunk/debian/patches/Makefiles
===================================================================
--- trunk/packages/glam2/trunk/debian/patches/Makefiles	                        (rev 0)
+++ trunk/packages/glam2/trunk/debian/patches/Makefiles	2008-01-29 06:25:08 UTC (rev 1210)
@@ -0,0 +1,67 @@
+--- a/purge/Makefile
++++ b/purge/Makefile
+@@ -1,3 +1,5 @@
+ # Command for compiling purge:
+-purge: *.c *.h Makefile
+-	cc -Wall -O3 -o purge *.c -lm
++# Renamed glam2-purge in Debian
++CXXFLAGS = -g -Wall -O2
++glam2-purge: *.c *.h Makefile
++	cc $(CXXFLAGS) -o glam2-purge *.c -lm
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -6,6 +6,8 @@
+ # -Wall means turn on compiler warnings (optional)
+ # -O3 means optimization level 3 (the maximum for gcc)
+ # -lm means include the math library
++# In Debian, optimisation level can be overriden by build options.
++CXXFLAGS = -g -Wall -O2
+ 
+ # Source files for glam2:
+ GSRC = alphabet.c args.c column_sample.c dirichlet.c dna_prior.c	\
+@@ -27,26 +29,28 @@
+ all: glam2 glam2scan glam2format glam2mask
+ 
+ # Command for compiling glam2:
+-glam2: $(GSRC) *.h Makefile
+-	cc -Wall -O3 -o glam2 $(GSRC) -lm
++# The Debian package uses an fft-enabled version of glam2.
++glam2nofft: $(GSRC) *.h Makefile
++	cc $(CXXFLAGS) -o glam2nofft $(GSRC) -lm
+ 
+ # Command for compiling glam2scan:
+ glam2scan: $(SSRC) *.h Makefile
+-	cc -Wall -O3 -o glam2scan $(SSRC) -lm
++	cc $(CXXFLAGS) -o glam2scan $(SSRC) -lm
+ 
+ # Command for compiling glam2format:
+ glam2format: $(FSRC) *.h Makefile
+-	cc -Wall -O3 -o glam2format $(FSRC) -lm
++	cc $(CXXFLAGS) -o glam2format $(FSRC) -lm
+ 
+ # Command for compiling glam2mask:
+ glam2mask: $(MSRC) *.h Makefile
+-	cc -Wall -O3 -o glam2mask $(MSRC) -lm
++	cc $(CXXFLAGS) -o glam2mask $(MSRC) -lm
+ 
+ # Here follow commands for compiling special versions of the programs
+ 
+ # Compile glam2 including FFT algorithm (requires FFTW to be installed):
+-glam2fft: $(GSRC) convolve.c *.h Makefile
+-	cc -Wall -O3 -DFFT -o glam2fft $(GSRC) convolve.c -lm -lfftw3
++# glam2fft is simply renamed glam2 in Debian.
++glam2: $(GSRC) convolve.c *.h Makefile
++	cc $(CXXFLAGS) -DFFT -o glam2 $(GSRC) convolve.c -lm -lfftw3
+ 
+ # Compile for debugging with gdb or valgrind, with extra compiler warnings:
+ glam2_d: $(GSRC) *.h Makefile
+--- /dev/null
++++ b/Makefile
+@@ -0,0 +1,7 @@
++all:
++	make -C src all
++	make -C src glam2fft
++	make -C purge
++
++clean:
++	rm -f  purge/*.o purge/purge purge/glam2-purge src/*.o src/{glam2,glam2mask,glam2format,glam2scan,glam2fft}

Added: trunk/packages/glam2/trunk/debian/patches/series
===================================================================
--- trunk/packages/glam2/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/glam2/trunk/debian/patches/series	2008-01-29 06:25:08 UTC (rev 1210)
@@ -0,0 +1 @@
+Makefiles

Modified: trunk/packages/glam2/trunk/debian/rules
===================================================================
--- trunk/packages/glam2/trunk/debian/rules	2008-01-28 15:49:40 UTC (rev 1209)
+++ trunk/packages/glam2/trunk/debian/rules	2008-01-29 06:25:08 UTC (rev 1210)
@@ -2,15 +2,9 @@
 
 DEB_COMPRESS_EXCLUDE := .pdf
 
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
 include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/class/makefile.mk
 
-build/glam2:: 
-	$(MAKE) -C src
-	$(MAKE) -C src glam2fft
-	$(MAKE) -C purge
-	mv $(CURDIR)/src/glam2fft $(CURDIR)/src/glam
-	mv $(CURDIR)/purge/purge $(CURDIR)/purge/glam2-purge
-
-clean::
-	rm -f  purge/*.o purge/purge purge/glam2-purge src/*.o src/{glam2,glam2mask,glam2format,glam2scan,glam2-fft}
+DEB_MAKE_BUILD_TARGET   = all
+DEB_MAKE_CLEAN_TARGET	= clean