From: Olivier Sallou <osallou@debian.org>
Date: Fri, 6 Jun 2014 20:53:24 +0000 (+0000)
Subject: update patches for new upstream release 2.2.29
X-Git-Tag: archive/raspbian/2.16.0+ds-7+rpi1~1^2~269
X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=64aec12adec92a097b18ab413ffe4957a6a3d306;p=ncbi-blast%2B.git

update patches for new upstream release 2.2.29
---

diff --git a/debian/changelog b/debian/changelog
index 5c405eab..69150c15 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+ncbi-blast+ (2.2.29-1) UNRELEASED; urgency=medium
+
+  * New upstream release 
+
+ -- Olivier Sallou <osallou@debian.org>  Fri, 06 Jun 2014 22:38:40 +0200
+
 ncbi-blast+ (2.2.28-2) unstable; urgency=low
 
   * debian/patches/use_pie_for_apps: Explicitly build all executables with
diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index fc310ca4..062a5980 100644
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -14,12 +14,12 @@ Last-Update: 2011-08-28
 --- a/c++/src/algo/blast/core/Makefile.blast.lib
 +++ b/c++/src/algo/blast/core/Makefile.blast.lib
 @@ -21,5 +21,6 @@
- CFLAGS  = $(FAST_CFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
+ CFLAGS  = $(FAST_CFLAGS)  
+ LDFLAGS = $(FAST_LDFLAGS) 
  
 +DLL_LIB = composition_adjustment xconnect tables
  
- WATCHERS = coulouri maning madden camacho
+ WATCHERS = maning madden camacho
 --- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
 +++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
 @@ -11,6 +11,8 @@
@@ -35,7 +35,7 @@ Last-Update: 2011-08-28
 +++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
 @@ -7,6 +7,7 @@
  
- CPPFLAGS = $(ORIG_CPPFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
  
 -DLL_LIB = align_format blastxml xhtml xcgi
 +DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
@@ -63,7 +63,7 @@ Last-Update: 2011-08-28
 --- a/c++/src/html/Makefile.html.lib
 +++ b/c++/src/html/Makefile.html.lib
 @@ -7,4 +7,6 @@
-       jsmenu commentdiag indentstream html_exception writer_htmlenc
+       commentdiag indentstream html_exception writer_htmlenc
  LIB = xhtml
  
 +DLL_LIB = xncbi
@@ -81,7 +81,7 @@ Last-Update: 2011-08-28
 +++ b/c++/src/objtools/align_format/Makefile.align_format.lib
 @@ -13,6 +13,10 @@
  
- CPPFLAGS = $(ORIG_CPPFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
  
 +DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
 +          xobjmgr xnetblast blastdb gene_info seqset seq general xser \
@@ -100,8 +100,8 @@ Last-Update: 2011-08-28
 +
 --- a/c++/src/objtools/readers/Makefile.xobjread.lib
 +++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -19,5 +19,5 @@
-       best_feat_finder source_mod_parser fasta_exception
+@@ -20,5 +20,5 @@
+       message_listener line_error
  
  
 -DLL_LIB = creaders
@@ -137,11 +137,11 @@ Last-Update: 2011-08-28
 +DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
 +
  CFLAGS   = $(FAST_CFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
  CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
 --- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
 +++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -5,4 +5,6 @@
+@@ -7,4 +7,6 @@
  
  ASN_DEP = blastdb seqset
  
@@ -150,9 +150,9 @@ Last-Update: 2011-08-28
  WATCHERS = camacho
 --- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
 +++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-@@ -3,6 +3,8 @@
- LIB = ncbi_xloader_blastdb_rmt
- SRC = bdbloader_rmt remote_blastdb_adapter
+@@ -5,6 +5,8 @@
+ 
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
  
 +DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
 +
@@ -161,8 +161,8 @@ Last-Update: 2011-08-28
  WATCHERS = camacho
 --- a/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
 +++ b/c++/src/objtools/blast/gene_info_reader/Makefile.gene_info.lib
-@@ -4,3 +4,5 @@
- 
+@@ -5,3 +5,5 @@
+ CPPFLAGS = -DNCBI_MODULE=GENEINFO $(ORIG_CPPFLAGS)
  LIB = gene_info
  SRC = gene_info gene_info_reader file_utils
 +
@@ -185,17 +185,17 @@ Last-Update: 2011-08-28
 +        $(SOBJMGR_LIBS) blast seqdb seqset seq general \
 +        xser xconnect sequtil tables xutil xncbi
  
- CFLAGS   = $(FAST_CFLAGS)
- # Strict gcc flags
+ CFLAGS   = $(FAST_CFLAGS) 
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
 --- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
 +++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
 @@ -24,7 +24,9 @@
  
  LIB = blastinput
  
--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 $(OBJREAD_LIBS) $(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 \
++              $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \
 +              scoremat seqset seq xser xutil xncbi
  
  # should be redundant, given the above :-/
@@ -288,18 +288,18 @@ Last-Update: 2011-08-28
 --- a/c++/src/objmgr/util/Makefile.util.lib
 +++ b/c++/src/objmgr/util/Makefile.util.lib
 @@ -8,5 +8,7 @@
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util
+ SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci
  LIB = xobjutil
  
 +DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
 +
- WATCHERS = ucko vasilche
+ WATCHERS = ucko vasilche kornbluh
  
 --- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
 +++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
 @@ -11,6 +11,7 @@
  
- CPPFLAGS = $(ORIG_CPPFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
  
 +DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
  
@@ -314,8 +314,8 @@ Last-Update: 2011-08-28
 +DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
 +
  CFLAGS   = $(FAST_CFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)
  CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
 --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
 +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
 @@ -12,4 +12,7 @@
@@ -373,13 +373,13 @@ Last-Update: 2011-08-28
  WATCHERS = vasilche
 --- a/c++/src/util/compress/api/Makefile.compress.lib
 +++ b/c++/src/util/compress/api/Makefile.compress.lib
-@@ -6,7 +6,7 @@
+@@ -7,7 +7,7 @@
  
  CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
  
 -DLL_LIB =  $(BZ2_LIB)  $(Z_LIB)  $(LZO_LIB)
 +DLL_LIB =  $(BZ2_LIB)  $(Z_LIB)  $(LZO_LIB) xutil xncbi
- LIBS    =  $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS)
+ LIBS    =  $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)
  
  WATCHERS = ivanov
 --- a/c++/src/util/sequtil/Makefile.sequtil.lib
@@ -422,11 +422,14 @@ Last-Update: 2011-08-28
 +DLL_LIB = general xser xncbi
 --- a/c++/src/objects/blastdb/Makefile.blastdb.lib
 +++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
-@@ -1,2 +1,4 @@
- LIB = blastdb
- SRC = blastdb__ blastdb___
+@@ -1,5 +1,7 @@
+ # $Id: Makefile.blastdb.lib 395653 2013-04-12 14:33:22Z vakatov $
+ 
 +
 +DLL_LIB = seq xser xncbi
+ LIB = blastdb
+ SRC = blastdb__ blastdb___
+ 
 --- a/c++/src/objects/general/Makefile.general.lib
 +++ b/c++/src/objects/general/Makefile.general.lib
 @@ -1,2 +1,4 @@
@@ -518,14 +521,14 @@ Last-Update: 2011-08-28
  WATCHERS = gouriano
 --- a/c++/src/util/Makefile.util.lib
 +++ b/c++/src/util/Makefile.util.lib
-@@ -11,6 +11,7 @@
+@@ -12,6 +12,7 @@
  LIB = xutil
  PROJ_TAG = core
  
 +DLL_LIB = xncbi
  LIBS = $(ORIG_LIBS)
  
- WATCHERS = vakatov
+ WATCHERS = vakatov kornbluh
 --- a/c++/src/util/xregexp/Makefile.xregexp.lib
 +++ b/c++/src/util/xregexp/Makefile.xregexp.lib
 @@ -6,7 +6,7 @@
@@ -568,8 +571,8 @@ Last-Update: 2011-08-28
 +          xser sequtil xutil xncbi
 +
  CFLAGS   = $(FAST_CFLAGS)
+ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
  CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS  = $(FAST_LDFLAGS)
 --- a/c++/src/algo/blast/Makefile.blast_macros.mk
 +++ b/c++/src/algo/blast/Makefile.blast_macros.mk
 @@ -18,7 +18,7 @@
@@ -579,7 +582,7 @@ Last-Update: 2011-08-28
 -BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
 +BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
  		xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
- 		xobjread creaders xnetblastcli xnetblast blastdb scoremat tables xalnmgr
+ 		$(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr
  # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
 --- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
 +++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
@@ -587,8 +590,8 @@ Last-Update: 2011-08-28
  SRC = main mkindex_app
  
  LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
--      xobjread creaders xobjutil tables connect $(SOBJMGR_LIBS)
-+      xobjread creaders xobjutil tables xconnect $(SOBJMGR_LIBS)
+-      $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS)
++      $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS)
  LIB = $(LIB_:%=%$(STATIC))
  
  CXXFLAGS = $(FAST_CXXFLAGS)
diff --git a/debian/patches/use_pie_for_apps b/debian/patches/use_pie_for_apps
index 30173324..7e0b2c0d 100644
--- a/debian/patches/use_pie_for_apps
+++ b/debian/patches/use_pie_for_apps
@@ -7,23 +7,23 @@ Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2012-05-10
 --- a/c++/src/build-system/Makefile.app.in
 +++ b/c++/src/build-system/Makefile.app.in
-@@ -24,8 +24,8 @@ default_rule: all
+@@ -24,8 +24,8 @@
  
- ### C/C++ source file compilation (and maybe auto-dependencies) build rules
+ ### C/C++ source file compilation setup
  
 -CXXFLAGS_ALL = @f_compile@ $(CXXFLAGS) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
 -CFLAGS_ALL   = @f_compile@ $(CFLAGS) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
 +CXXFLAGS_ALL = @f_compile@ $(CXXFLAGS:-fPIC=-fPIE) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
 +CFLAGS_ALL   = @f_compile@ $(CFLAGS:-fPIC=-fPIE) $(LOCAL_CPPFLAGS) $(CPPFLAGS)
  SOURCES      = @UNIX_SRC@ $(SRC)
- include $(builddir)/Makefile.$(Rules)
- 
-@@ -72,7 +72,7 @@ rebuild-libs:
  
+ ### Standard application build rules
+@@ -122,7 +122,7 @@
+ else
  $(XAPP): $(XOBJ) $(XLIBDEP)
  	@-$(RM) .$(XAPP).stamp
 -	$(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER)
 +	$(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS) $(XLIB) $(XAPP_LIBS) @f_outexe@$(XAPP) $(LINK_FILTER)
  	$(STRIP) $(XAPP)
  	$(POST_LINK) $(XAPP)
- ifneq "$(BINCOPY)" "@:"
+   ifneq "$(BINCOPY)" "@:"