[med-svn] r2763 - in trunk/packages/euler2/trunk/debian: . patches

[tille at alioth.debian.org]

Author: tille
Date: 2008-12-09 20:22:15 +0000 (Tue, 09 Dec 2008)
New Revision: 2763

Added:
   trunk/packages/euler2/trunk/debian/install
   trunk/packages/euler2/trunk/debian/patches/20_gcc4_static.patch
Modified:
   trunk/packages/euler2/trunk/debian/patches/20_warnings.patch
   trunk/packages/euler2/trunk/debian/patches/series
Log:
Commented the patches and make sure the source compiles.


Added: trunk/packages/euler2/trunk/debian/install
===================================================================
--- trunk/packages/euler2/trunk/debian/install	                        (rev 0)
+++ trunk/packages/euler2/trunk/debian/install	2008-12-09 20:22:15 UTC (rev 2763)
@@ -0,0 +1,22 @@
+euler_db           usr/bin
+euler_et           usr/bin
+euler_cons         usr/bin
+over-repeat-new    usr/bin
+over-repeat-end    usr/bin
+over-repeat-end-po usr/bin
+po-prod            usr/bin
+over-align-phrap   usr/bin
+overlapper-all     usr/bin
+over-align-all     usr/bin
+errcorr_pair_mem   usr/bin
+trans_qual         usr/bin
+trimseq_qual       usr/bin
+pairreads          usr/bin
+pairreads_file     usr/bin
+pairreads1         usr/bin
+pairreads2         usr/bin
+pairreads3         usr/bin
+errcorr_fin_mem    usr/bin
+makeintv           usr/bin
+makealn            usr/bin
+

Added: trunk/packages/euler2/trunk/debian/patches/20_gcc4_static.patch
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/20_gcc4_static.patch	                        (rev 0)
+++ trunk/packages/euler2/trunk/debian/patches/20_gcc4_static.patch	2008-12-09 20:22:15 UTC (rev 2763)
@@ -0,0 +1,21 @@
+The compilation fails with gcc 4.x with 
+  gcc -g -O2 -g -Wall -O2 -Iinc/ -c g_band.c
+  g_band.c:44: error: static declaration of ‘g’ follows non-static declaration
+  inc/extvab.h:20: error: previous declaration of ‘g’ was here
+  g_band.c:44: error: static declaration of ‘h’ follows non-static declaration
+  inc/extvab.h:20: error: previous declaration of ‘h’ was here
+and some googling revealed patches which simply removed static.
+So I tried the same which compiles fine - but some testing is
+needed whether it does the right things.
+--- euler-2.0.orig/g_band.c
++++ euler-2.0/g_band.c
+@@ -41,7 +41,8 @@
+ static char *FT;
+ 
+ static int (*w)[15];				/* w = W */
+-static int g, h, m;				/* g = G, h = H, m = g+h */
++int g, h;				        /* g = G, h = H */
++static int m;				        /* m = g+h */
+ 
+ #define gap(k)  ((k) <= 0 ? 0 : (g+h*(k)))	/* k-symbol indel cost */
+ 

Modified: trunk/packages/euler2/trunk/debian/patches/20_warnings.patch
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/20_warnings.patch	2008-12-09 19:22:49 UTC (rev 2762)
+++ trunk/packages/euler2/trunk/debian/patches/20_warnings.patch	2008-12-09 20:22:15 UTC (rev 2763)
@@ -1,3 +1,6 @@
+Compilation of Euler2 with -Wall switch as it is done by default in Debian
+packaging revealed a huge amount of warnings.  I had some time while
+traveling and tried to start fixing the warnings...
 --- euler-2.0.orig/readseq1by1.c
 +++ euler-2.0/readseq1by1.c
 @@ -63,8 +63,7 @@

Modified: trunk/packages/euler2/trunk/debian/patches/series
===================================================================
--- trunk/packages/euler2/trunk/debian/patches/series	2008-12-09 19:22:49 UTC (rev 2762)
+++ trunk/packages/euler2/trunk/debian/patches/series	2008-12-09 20:22:15 UTC (rev 2763)
@@ -1 +1,2 @@
 20_warnings.patch
+20_gcc4_static.patch