[med-svn] r19466 - in trunk/packages/ncbi-blast+/trunk/debian: . patches

[Aaron M. Ucko]

Author: ucko
Date: 2015-07-02 20:20:51 +0000 (Thu, 02 Jul 2015)
New Revision: 19466

Modified:
   trunk/packages/ncbi-blast+/trunk/debian/changelog
   trunk/packages/ncbi-blast+/trunk/debian/patches/fix_compilation
Log:
d/patches/fix_compilation: Add an upstream patch to
include/util/bitset/bmconst.h to fix builds with GCC 5 on platforms
such as arm64 on which char is unsigned.  (Closes: #790667.)


Modified: trunk/packages/ncbi-blast+/trunk/debian/changelog
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/changelog	2015-07-02 20:16:40 UTC (rev 19465)
+++ trunk/packages/ncbi-blast+/trunk/debian/changelog	2015-07-02 20:20:51 UTC (rev 19466)
@@ -1,8 +1,11 @@
 ncbi-blast+ (2.2.30-4) UNRELEASED; urgency=medium
 
   * NOT YET RELEASED.
+  * d/patches/fix_compilation: Add an upstream patch to
+    include/util/bitset/bmconst.h to fix builds with GCC 5 on platforms
+    such as arm64 on which char is unsigned.  (Closes: #790667.)
 
- -- Aaron M. Ucko <ucko at debian.org>  Thu, 02 Jul 2015 16:16:36 -0400
+ -- Aaron M. Ucko <ucko at debian.org>  Thu, 02 Jul 2015 16:20:49 -0400
 
 ncbi-blast+ (2.2.30-3) unstable; urgency=medium
 

Modified: trunk/packages/ncbi-blast+/trunk/debian/patches/fix_compilation
===================================================================
--- trunk/packages/ncbi-blast+/trunk/debian/patches/fix_compilation	2015-07-02 20:16:40 UTC (rev 19465)
+++ trunk/packages/ncbi-blast+/trunk/debian/patches/fix_compilation	2015-07-02 20:20:51 UTC (rev 19466)
@@ -5,7 +5,7 @@
 Last-Updated: 2014-12-14
 --- a/c++/src/util/regexp/pcretest.c
 +++ b/c++/src/util/regexp/pcretest.c
-@@ -250,7 +250,7 @@
+@@ -250,7 +250,7 @@ for (;;)
      /* Read the next line by normal means, prompting if the file is stdin. */
  
        {
@@ -14,3 +14,19 @@
        if (fgets((char *)here, rlen,  f) == NULL)
          return (here == start)? NULL : start;
        }
+--- a/c++/include/util/bitset/bmconst.h
++++ b/c++/include/util/bitset/bmconst.h
+@@ -147,11 +147,11 @@ const unsigned DeBruijn_bit_position<T>:
+ */
+ template<bool T> struct first_bit_table
+ {
+-    static const char _idx[256];
++    static const signed char _idx[256];
+ };
+ 
+ template<bool T>
+-const char first_bit_table<T>::_idx[256] = {
++const signed char first_bit_table<T>::_idx[256] = {
+   -1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
+     4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
+     5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5,