Refresh patches; drop fix_kfreebsd_ftbs.patch (applied upstream).

diff --git a/debian/changelog b/debian/changelog
index 05d4746241d2ddcfb9cdb75814ee0bb39c18304f..e74d1fdf0a18511d058c88be5986b1ef4037b87d 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+ncbi-blast+ (2.4.0-1) UNRELEASED; urgency=medium
+
+  * New upstream release.  (NOT RELEASED YET.)
+  * Refresh patches; drop fix_kfreebsd_ftbs.patch (applied upstream).
+
+ -- Aaron M. Ucko <ucko@debian.org>  Wed, 03 Aug 2016 18:58:57 -0400
+
 ncbi-blast+ (2.3.0-2) unstable; urgency=medium
 
   * Team upload.

diff --git a/debian/patches/fix_kfreebsd_ftbs.patch b/debian/patches/fix_kfreebsd_ftbs.patch
deleted file mode 100644 (file)
index eadc9d2..0000000
--- a/debian/patches/fix_kfreebsd_ftbs.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-Subject: Fix missing colon
-Description: colon missing causing FTBS on some archs
-Author: Olivier Sallou <olivier.sallou@irisa.fr>
-Forwarded: yes
-Comment: updated upstream at revision 70194
---- a/c++/src/corelib/ncbifile.cpp
-+++ b/c++/src/corelib/ncbifile.cpp
-@@ -4427,7 +4427,7 @@ static const SFileSystem s_FileSystem[]
-     if (statvfs(path.c_str(), &st) != 0) {                     \
-         NCBI_THROW(CFileErrnoException, eFileSystemInfo, msg); \
-     }                                                          \
--    info->total_space  = (Uint8)st.f_bsize * st.f_blocks       \
-+    info->total_space  = (Uint8)st.f_bsize * st.f_blocks;      \
-     if (st.f_frsize) {                                         \
-         info->free_space = (Uint8)st.f_frsize * st.f_bavail;   \
-         info->block_size = (unsigned long)st.f_frsize;         \
-@@ -4435,7 +4435,7 @@ static const SFileSystem s_FileSystem[]
-         info->free_space = (Uint8)st.f_bsize * st.f_bavail;    \
-         info->block_size = (unsigned long)st.f_bsize;          \
-     }                                                          \
--    info->used_space   = info->total_space - info->free_space
-+    info->used_space   = info->total_space - info->free_space;
- 
- 
- #define GET_STATFS_INFO                                        \
-@@ -4447,7 +4447,7 @@ static const SFileSystem s_FileSystem[]
-     info->total_space  = (Uint8)st.f_bsize * st.f_blocks;      \
-     info->free_space   = (Uint8)st.f_bsize * st.f_bavail;      \
-     info->used_space   = info->total_space - info->free_space; \
--    info->block_size   = (unsigned long)st.f_bsize
-+    info->block_size   = (unsigned long)st.f_bsize;
- 
- 
- 

diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 7d6ad7c54a81271fce2356357ec217637eaf4d60..3b17332a500affcd8e9580156b40073add8527dd 100644 (file)
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -59,14 +59,14 @@ Last-Update: 2014-12-02
  ASN_DEP = seqset xnetblast
 --- a/c++/src/algo/blast/core/Makefile.blast.lib
 +++ b/c++/src/algo/blast/core/Makefile.blast.lib
-@@ -21,6 +21,7 @@ LIB = blast
- CFLAGS  = $(FAST_CFLAGS)  
- LDFLAGS = $(FAST_LDFLAGS) 
- 
-+DLL_LIB = composition_adjustment xconnect tables
+@@ -23,6 +23,7 @@ LDFLAGS = $(FAST_LDFLAGS)
  
  WATCHERS = madden camacho fongah2
  
++DLL_LIB = composition_adjustment xconnect tables
+ 
+ USES_LIBRARIES =  \
+     composition_adjustment connect tables
 --- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
 +++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
 @@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \
@@ -124,10 +124,10 @@ Last-Update: 2014-12-02
      seqmasks_io
 --- a/c++/src/build-system/library_relations.txt
 +++ b/c++/src/build-system/library_relations.txt
-@@ -1268,7 +1268,7 @@ xasmcompare needs $(SEQ_LIBS)
- xasmcompare needs pub
- xasn needs xhtml
- xasn needs3party $(NCBI_C_ncbi)
+@@ -1331,7 +1331,7 @@ xbiosample_util needs $(OBJEDIT_LIBS)
+ xbiosample_util needs $(XFORMAT_LIBS)
+ xbiosample_util needs xalnmgr
+ xbiosample_util needs xmlwrapp
 -xblast includes blast
 +xblast needs blast
  xblast needs xalgoblastdbindex
@@ -154,7 +154,7 @@ Last-Update: 2014-12-02
 +
  LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
  
- WATCHERS = lavr
+ WATCHERS = lavr elisovdn
 --- a/c++/src/corelib/Makefile.test_boost.lib
 +++ b/c++/src/corelib/Makefile.test_boost.lib
 @@ -3,6 +3,8 @@
@@ -576,7 +576,7 @@ Last-Update: 2014-12-02
  
 +DLL_LIB = seq general xser xncbi
 +
- WATCHERS = dicuccio shchekot
+ WATCHERS = dicuccio shchekot zherikov
  
  
 --- a/c++/src/objects/medline/Makefile.medline.lib

diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath
index 94c158ef786a88e1f6d5d1bf56b139a27d103276..70543bb91d1dd5f674bdc8b8e371370ae039a7a4 100644 (file)
--- a/debian/patches/no_multiarch_rpath
+++ b/debian/patches/no_multiarch_rpath
@@ -10,7 +10,7 @@ Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2011-08-28
 --- a/c++/src/build-system/configure
 +++ b/c++/src/build-system/configure
-@@ -7758,7 +7758,7 @@ echo "$as_me: WARNING: Unable to find st
+@@ -9107,7 +9107,7 @@ echo "$as_me: WARNING: Unable to find st
                 break
                 ;;
              /* )
@@ -21,7 +21,7 @@ Last-Update: 2011-08-28
          esac
 --- a/c++/src/build-system/configure.ac
 +++ b/c++/src/build-system/configure.ac
-@@ -1951,7 +1951,7 @@ case "$compiler:$compiler_version:$with_
+@@ -1961,7 +1961,7 @@ case "$compiler:$compiler_version:$with_
                 break
                 ;;
              /* )

diff --git a/debian/patches/series b/debian/patches/series
index 11e1ab388f6a2efa436f997b77e505b302f8579b..405518265c990cf04d62c9f8738c1bce3eafe737 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -6,4 +6,3 @@ no_multiarch_rpath
 use_pie_for_apps
 skip_services_unit_test
 fix_configure
-fix_kfreebsd_ftbs.patch

diff --git a/debian/patches/use_pie_for_apps b/debian/patches/use_pie_for_apps
index 15dc1906edcb4eadb5f7485f239374a41d2f9241..b43c7b4f251435971daa1ca1c24811913dcbac53 100644 (file)
--- a/debian/patches/use_pie_for_apps
+++ b/debian/patches/use_pie_for_apps
@@ -18,7 +18,7 @@ Last-Update: 2012-05-10
  SOURCES      = @UNIX_SRC@ $(SRC)
  
  ### Standard application build rules
-@@ -52,7 +52,7 @@ ifneq "" "$(wildcard Makefile.$(TMPL).ap
+@@ -53,7 +53,7 @@ ifneq "" "$(wildcard Makefile.$(TMPL).ap
    endif
  endif