[med-svn] r14351 - in trunk/packages/soap/soapdenovo2/trunk/debian: . patches

[Olivier Sallou]

Author: osallou
Date: 2013-08-05 12:55:59 +0000 (Mon, 05 Aug 2013)
New Revision: 14351

Modified:
   trunk/packages/soap/soapdenovo2/trunk/debian/changelog
   trunk/packages/soap/soapdenovo2/trunk/debian/copyright
   trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening
   trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation
Log:
back to unreleased, some headers are copies of debian, but removing them create compil issues

Modified: trunk/packages/soap/soapdenovo2/trunk/debian/changelog
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/changelog	2013-08-05 12:18:03 UTC (rev 14350)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/changelog	2013-08-05 12:55:59 UTC (rev 14351)
@@ -1,6 +1,8 @@
-soapdenovo2 (240+dfsg-1) unstable; urgency=low
+soapdenovo2 (240+dfsg-1) UNRELEASED; urgency=low
 
   * New upstream release
+    Upstream embeds libz.so and various headers.
+    Removing headers raise compilation issues
 
  -- Olivier Sallou <osallou at debian.org>  Thu, 27 Jun 2013 16:23:26 +0200
 

Modified: trunk/packages/soap/soapdenovo2/trunk/debian/copyright
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/copyright	2013-08-05 12:18:03 UTC (rev 14350)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/copyright	2013-08-05 12:55:59 UTC (rev 14351)
@@ -4,6 +4,9 @@
 Files-Excluded:
     standardPregraph/*.a
     standardPregraph/inc/zlib.h
+    standardPregraph/inc/zconf.h
+    sparsePregraph/inc/zlib.h
+    sparsePregraph/inc/zconf.h
     standardPregraph/inc/*.so
     sparsePregraph/*.a
 

Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening	2013-08-05 12:18:03 UTC (rev 14350)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/add_hardening	2013-08-05 12:55:59 UTC (rev 14351)
@@ -69,7 +69,7 @@
 +
  SUBDIRS = sparsePregraph standardPregraph
  PROG=       SOAPdenovo-63mer SOAPdenovo-127mer
- INCLUDES=   -I./sparsePregraph/inc -I./standardPregraph/inc
+ INCLUDES=   -I./sparsePregraph/inc -I./standardPregraph/inc -I/usr/include/x86_64-linux-gnu
 @@ -64,11 +69,11 @@
  SOAPdenovo-63mer:
  	@cd sparsePregraph;make 63mer=1;cd ..;

Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation	2013-08-05 12:18:03 UTC (rev 14350)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/fix_compilation	2013-08-05 12:55:59 UTC (rev 14351)
@@ -27,3 +27,14 @@
  typedef struct parameter
  {
  	unsigned char threadID;
+--- a/Makefile
++++ b/Makefile
+@@ -7,7 +7,7 @@
+ 
+ SUBDIRS = sparsePregraph standardPregraph
+ PROG=       SOAPdenovo-63mer SOAPdenovo-127mer
+-INCLUDES=   -I./sparsePregraph/inc -I./standardPregraph/inc
++INCLUDES=   -I./sparsePregraph/inc -I./standardPregraph/inc -I/usr/include/x86_64-linux-gnu
+ 
+ LIBPATH=    -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc
+ LIBS=       -pthread -lz -lm