new upstream 2.2.28, include updates from T. Booth from Ubuntu to compile this release

diff --git a/debian/changelog b/debian/changelog
index 6bce91e9efecf4057f88af75cbb86e10054a4344..2b27ec06a7417bf92a09eabd8be3a07aea285ae7 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+ncbi-blast+ (2.2.28-1) unstable; urgency=low
+
+  * New upstream release
+    - Thanks to Tim Booth for package update help.
+
+ -- Olivier Sallou <osallou@debian.org>  Sat, 01 Jun 2013 08:40:51 +0200
+
 ncbi-blast+ (2.2.27-3) unstable; urgency=low
 
   * debian/series: active patch fix_arm_mips_build (Closes: #688661).

diff --git a/debian/compat b/debian/compat
index 7f8f011eb73d6043d2e6db9d2c101195ae2801f2..ec635144f60048986bc560c5576355344005e6e7 100644 (file)
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-7
+9

diff --git a/debian/control b/debian/control
index f192bffeba42086f5ba8d5c8b17811b1f3a9877f..fe13d9a25caee70c48c911df602f1dbbfa147968 100644 (file)
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,7 @@ Section: science
 Priority: optional
 Build-Depends: autotools-dev (>= 20100122),
                debhelper (>= 7.0.50~),
-              dpkg-dev (>= 1.16.1),
+               dpkg-dev (>= 1.16.1),
                libboost-test-dev,
                libbz2-dev,
                libc0.3-dev (>= 2.13-9~) [hurd-i386],

diff --git a/debian/patches/enable_clean_after_failed_compile b/debian/patches/enable_clean_after_failed_compile
new file mode 100644 (file)
index 0000000..bcc1bfa
--- /dev/null
+++ b/debian/patches/enable_clean_after_failed_compile
@@ -0,0 +1,11 @@
+--- a/c++/src/build-system/new_module.sh.in
++++ b/c++/src/build-system/new_module.sh.in
+@@ -178,7 +178,7 @@
+     if test -x "$bindir/datatool"; then
+         datatool=$bindir/datatool
+         COMMON_AddRunpath "$libdir"
+-    else
++    elif [ "$1" != "purge_sources" ] ; then
+         echo "Unable to find datatool." >&2
+         exit 2
+     fi

diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index df0d17eb9718adeb8abb0fb6ddae31a9ef52566d..fc310ca4d27e06d237e310fd5ff346c503b59593 100644 (file)
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -37,7 +37,7 @@ Last-Update: 2011-08-28
  
  CPPFLAGS = $(ORIG_CPPFLAGS)
  
--DLL_LIB = blastxml xhtml xcgi
+-DLL_LIB = align_format blastxml xhtml xcgi
 +DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
 +          seq general xser tables xncbi
  
@@ -79,7 +79,7 @@ Last-Update: 2011-08-28
 +DLL_LIB = xnetblast xser xconnect xutil xncbi
 --- a/c++/src/objtools/align_format/Makefile.align_format.lib
 +++ b/c++/src/objtools/align_format/Makefile.align_format.lib
-@@ -10,6 +10,10 @@
+@@ -13,6 +13,10 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS)
  
@@ -88,8 +88,8 @@ Last-Update: 2011-08-28
 +          xcgi xhtml tables xncbi
 +
  ###  EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
  # CFLAGS   = $(FAST_CFLAGS)
+ # CXXFLAGS = $(FAST_CXXFLAGS)
 --- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
 +++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
 @@ -12,3 +12,5 @@
@@ -109,7 +109,7 @@ Last-Update: 2011-08-28
  
 --- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
 +++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-@@ -11,6 +11,6 @@
+@@ -12,6 +12,6 @@
  mask_writer_blastdb_maskinfo
  
  ASN_DEP = seqset
@@ -169,7 +169,7 @@ Last-Update: 2011-08-28
 +DLL_LIB = xncbi
 --- a/c++/src/algo/blast/api/Makefile.xblast.lib
 +++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -74,11 +74,14 @@
+@@ -74,14 +74,15 @@
  deltablast_options \
  deltablast
  
@@ -178,11 +178,12 @@ Last-Update: 2011-08-28
  
  LIB = xblast
  
--DLL_LIB = xalgodustmask xobjutil $(OBJMGR_LIBS)
-+DLL_LIB = xalgoblastdbindex blast composition_adjustment xalgowinmask \
-+          xalgodustmask seqdb xobjread xobjutil xobjmgr \
-+          xnetblastcli xnetblast scoremat seqset seq general \
-+          xser xconnect sequtil tables xutil xncbi
+ DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \
+       xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \
+       blastdb xnetblastcli xnetblast scoremat xconnect tables \
+-      $(SOBJMGR_LIBS)
++        $(SOBJMGR_LIBS) blast seqdb seqset seq general \
++        xser xconnect sequtil tables xutil xncbi
  
  CFLAGS   = $(FAST_CFLAGS)
  # Strict gcc flags
@@ -192,10 +193,10 @@ Last-Update: 2011-08-28
  
  LIB = blastinput
  
--DLL_LIB = xblast $(OBJMGR_LIBS)
-+DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb \
-+          ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader seqdb xobjread \
-+          xobjmgr scoremat seqset seq xser xutil xncbi
+-DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread $(OBJMGR_LIBS) xutil
++    DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \
++              $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \
++              scoremat seqset seq xser xutil xncbi
  
  # should be redundant, given the above :-/
  ASN_DEP = seqset xnetblast
@@ -303,7 +304,7 @@ Last-Update: 2011-08-28
 +DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
  
  ###  EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CPPFLAGS = $(ORIG_CPPFLAGS) $(NCBI_C_INCLUDE)
+ # CFLAGS   = $(FAST_CFLAGS)
 --- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
 +++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
 @@ -8,6 +8,8 @@
@@ -327,9 +328,9 @@ Last-Update: 2011-08-28
  WATCHERS = vasilche
 --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
 +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -14,4 +14,7 @@
- # Dependencies for shared library
+@@ -15,4 +15,7 @@
  DLL_LIB = 
+ DLL_DLIB = $(GENBANK_READER_LDEP)
  
 +DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
 +           xser xconnect xcompress xutil xncbi

diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes
index 4486d4d749aa97fa996146bc4862a25eb6f5cfb5..6e8e8f6ba73120648cd87f31fe796bc0f6eb1a61 100644 (file)
--- a/debian/patches/hurd_fixes
+++ b/debian/patches/hurd_fixes
@@ -9,7 +9,7 @@ Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2011-06-10
 --- a/c++/src/build-system/configure
 +++ b/c++/src/build-system/configure
-@@ -5817,7 +5817,7 @@
+@@ -5860,7 +5860,7 @@
      solaris* )
        CONF_f_runpath="-R"
        ;;
@@ -20,7 +20,7 @@ Last-Update: 2011-06-10
      linux*:ICC )
 --- a/c++/src/build-system/configure.ac
 +++ b/c++/src/build-system/configure.ac
-@@ -1535,7 +1535,7 @@
+@@ -1558,7 +1558,7 @@
      solaris* )
        CONF_f_runpath="-R"
        ;;
@@ -42,12 +42,14 @@ Last-Update: 2011-06-10
  
 --- a/c++/src/connect/ext/ncbi_localnet.c
 +++ b/c++/src/connect/ext/ncbi_localnet.c
-@@ -64,6 +64,8 @@
- 
- #if defined(NCBI_OS_MSWIN) && !defined(PATH_MAX)
- #  define PATH_MAX _MAX_PATH
-+#elif !defined(PATH_MAX)
-+#  define PATH_MAX 4096
+@@ -62,6 +62,10 @@
+ #  endif /*_MAX_PATH*/
  #endif /*NCBI_OS_MSWIN && !PATH_MAX*/
  
++#if !defined(PATH_MAX)
++#  define PATH_MAX 4096
++#endif /*Patch added for Ubuntu build*/
++
  #if PATH_MAX < 256
+ #  define BUFSIZE  256
+ #else

diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath
index 6bf56aab042d2ec8c2de05d7069496396148e9e8..b9e30ad150fb98953aa9eabced70472a50476639 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
-@@ -5880,7 +5880,7 @@
+@@ -5923,7 +5923,7 @@
                 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
-@@ -1597,7 +1597,7 @@
+@@ -1620,7 +1620,7 @@
                 break
                 ;;
              /* )

diff --git a/debian/patches/series b/debian/patches/series
index 5a6a434d7a9e71dc2a3c86e2e78f0e89ee2082f1..4e45003426eb3aa1186b1945ab1ee574c5f63d9f 100644 (file)
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,6 +1,7 @@
+enable_clean_after_failed_compile
 hurd_fixes
 legacy_rename_rpsblast
 fix_lib_deps
 no_multiarch_rpath
 use_pie_for_apps
-fix_arm_mips_build
+skip_services_unit_test

diff --git a/debian/patches/skip_services_unit_test b/debian/patches/skip_services_unit_test
new file mode 100644 (file)
index 0000000..2d5249b
--- /dev/null
+++ b/debian/patches/skip_services_unit_test
@@ -0,0 +1,11 @@
+--- a/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
++++ b/c++/src/objtools/blast/services/unit_test/Makefile.blast_services_unit_test.app
+@@ -11,6 +11,7 @@
+ 
+ LIBS = $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS)
+ 
+-CHECK_CMD = blast_services_unit_test
++# This test requires an internet connection, shouldn't be run on a build server
++# CHECK_CMD = blast_services_unit_test
+ 
+ WATCHERS = madden camacho

diff --git a/debian/rules b/debian/rules
index e7b553b9291d3795d159df2f30e5641a77d543aa..99f222210176547229863dc169d874a397c3e52d 100755 (executable)
--- a/debian/rules
+++ b/debian/rules
@@ -69,14 +69,22 @@ override_dh_install:
 
 override_dh_clean:
        dh_clean
-       -for x in c++/src/objects/*/*.files; do \
-         if [ -d $$x ]; then \
-           (cd `dirname $$x`  &&  ../../../BUILD/build/new_module.sh \
-               `basename $$x .files`.module purge_sources); \
-         fi \
+       #Tricky - for each module directory there may be several module files
+       #or there may be none but then there is still a module named after the
+       #directory.  Clean everything!
+       -for x in c++/src/objects/* ; do \
+           (cd "$$x"  && ( \
+               mods="`echo *.module`" ; \
+               [ "$${mods#*\*}" = "$$mods" ] || mods="`basename $$x`" ; \
+               for mod in $$mods ; do \
+                           ../../../BUILD/build/new_module.sh $$mod purge_sources ; \
+               done ) ; \
+           ) ; \
        done
-       rm -rf c++/BUILD c++/compilers/dll c++/config.log c++/Makefile
+       rm -rf c++/compilers/dll c++/config.log c++/Makefile
        rm -f c++/configure.lineno c++/src/objects/blastxml/blastxml.module
+       find -name check_exec.pid -delete
+       rm -rf c++/BUILD
 
 %:
        dh $@ -Dc++ --with autotools_dev --with quilt