[med-svn] r17541 - in trunk/packages/arb/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-07-29 09:56:30 +0000 (Tue, 29 Jul 2014)
New Revision: 17541

Added:
   trunk/packages/arb/trunk/debian/patches/72_add_math_lib_to_linker.patch
Modified:
   trunk/packages/arb/trunk/debian/changelog
   trunk/packages/arb/trunk/debian/control
   trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch
   trunk/packages/arb/trunk/debian/patches/series
Log:
Exclude fasttree, mafft, mrbayes, muscle, phyml and probcons from building in GDE and rather use the according Debian packages by adding these to the list of dependencies



Modified: trunk/packages/arb/trunk/debian/changelog
===================================================================
--- trunk/packages/arb/trunk/debian/changelog	2014-07-29 07:50:00 UTC (rev 17540)
+++ trunk/packages/arb/trunk/debian/changelog	2014-07-29 09:56:30 UTC (rev 17541)
@@ -5,6 +5,9 @@
   * Build-Depends: libglib2.0-dev
   * debian/patches/0_no_GL.patch: Switch of GL for the moment since it
     generates build errors (FIXME)
+  * Exclude fasttree, mafft, mrbayes, muscle, phyml and probcons from building
+    in GDE and rather use the according Debian packages by adding these to the
+    list of dependencies
   TODO: Run test suite
 
  -- Andreas Tille <tille at debian.org>  Mon, 28 Jul 2014 14:36:39 +0200

Modified: trunk/packages/arb/trunk/debian/control
===================================================================
--- trunk/packages/arb/trunk/debian/control	2014-07-29 07:50:00 UTC (rev 17540)
+++ trunk/packages/arb/trunk/debian/control	2014-07-29 09:56:30 UTC (rev 17541)
@@ -34,7 +34,10 @@
          fastdnaml,
          libarb (= ${binary:Version}),
          openssh-client,
+         mafft,
+         mrbayes,
          phylip,
+         phyml,
          raxml,
          readseq,
          transfig,

Modified: trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch	2014-07-29 07:50:00 UTC (rev 17540)
+++ trunk/packages/arb/trunk/debian/patches/60_use_debian_packaged_raxml.patch	2014-07-29 09:56:30 UTC (rev 17541)
@@ -3,19 +3,37 @@
 
 --- a/GDE/Makefile
 +++ b/GDE/Makefile
-@@ -3,7 +3,6 @@ ARCHS_COMMON = \
+@@ -3,16 +3,9 @@ ARCHS_COMMON = \
  	CLUSTAL/CLUSTAL.dummy  \
  	SUPPORT/SUPPORT.dummy \
  	AxML/AxML.dummy \
 -	RAxML/RAxML.dummy \
- 	PHYML/PHYML.dummy \
- 	MrBAYES/MrBAYES.dummy \
+-	PHYML/PHYML.dummy \
+-	MrBAYES/MrBAYES.dummy \
  
-@@ -23,6 +22,7 @@ ARCHS_NO_DEPENDS = \
+ ARCHS_NO_DEPENDS = \
+ 	PHYML20130708/PHYML20130708.dummy \
+-	MAFFT/MAFFT.dummy \
+-	MUSCLE/MUSCLE.dummy \
+-	PROBCONS/PROBCONS.dummy \
+-	FASTTREE/FASTTREE.dummy \
+ 
+ # --------------------------------------------------------------------------------
+ # If a package is available as debian package it should go here
+@@ -22,9 +15,16 @@ ARCHS_NO_DEPENDS = \
+ 
  ARCHS_NON_DEBIAN = \
  	CLUSTALW/CLUSTALW.dummy  \
++	FASTTREE/FASTTREE.dummy \
++	MAFFT/MAFFT.dummy \
++	MrBAYES/MrBAYES.dummy \
++	MUSCLE/MUSCLE.dummy \
  	PHYLIP/PHYLIP.dummy \
++	PROBCONS/PROBCONS.dummy \
 +	RAxML/RAxML.dummy \
  	TREEPUZZLE/TREEPUZZLE.dummy \
  	FASTDNAML/FASTDNAML.dummy \
++	PHYML/PHYML.dummy \
  
+ # --------------------------------------------------------------------------------
+ 

Added: trunk/packages/arb/trunk/debian/patches/72_add_math_lib_to_linker.patch
===================================================================
--- trunk/packages/arb/trunk/debian/patches/72_add_math_lib_to_linker.patch	                        (rev 0)
+++ trunk/packages/arb/trunk/debian/patches/72_add_math_lib_to_linker.patch	2014-07-29 09:56:30 UTC (rev 17541)
@@ -0,0 +1,11 @@
+--- a/GDE/AxML/Makefile
++++ b/GDE/AxML/Makefile
+@@ -31,7 +31,7 @@ endif
+ all : $(TARGET)
+ 
+ $(TARGET) : $(OBJECTS)
+-	$(CC) $(CFLAGS) -o $@ $< $(LDFLAGS)
++	$(CC) $(CFLAGS) -o $@ $< -lm $(LDFLAGS)
+ 
+ .c.o:
+ 	$(CC) $(CFLAGS) -c -o $@ $<

Modified: trunk/packages/arb/trunk/debian/patches/series
===================================================================
--- trunk/packages/arb/trunk/debian/patches/series	2014-07-29 07:50:00 UTC (rev 17540)
+++ trunk/packages/arb/trunk/debian/patches/series	2014-07-29 09:56:30 UTC (rev 17541)
@@ -7,3 +7,4 @@
 60_use_debian_packaged_raxml.patch
 70_hardening.patch
 80_no_GL.patch
+72_add_math_lib_to_linker.patch