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update patches to new release
authorOlivier Sallou <osallou@debian.org>
Sun, 11 Feb 2018 09:21:27 +0000 (09:21 +0000)
committerOlivier Sallou <osallou@debian.org>
Sun, 11 Feb 2018 09:21:27 +0000 (09:21 +0000)
debian/patches/fix_lib_deps patch | blob | history
debian/patches/hurd_fixes patch | blob | history
debian/patches/no_multiarch_rpath patch | blob | history
debian/patches/suppress_gnutls_version_check patch | blob | history
debian/patches/use_pie_for_apps patch | blob | history

diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 0692cafef4e1d79b6ce38117ce3de554a50fa410..9182e5b8a48c553d267c2262fa63c1a524bf1937 100644 (file)
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -14,26 +14,6 @@ Subject: ensure that all libraries link against all direct dependencies
 Debian-Bug: 633567.
 Author: Aaron M. Ucko <ucko@debian.org>
 Last-Update: 2016-12-05
---- a/c++/src/algo/blast/api/Makefile.xblast.lib
-+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -76,14 +76,15 @@
- magicblast_options \
- magicblast
- 
--SRC  = $(SRC_C:%=.core_%) $(SRC_CXX)
-+SRC  = $(SRC_CXX) # $(SRC_C:%=.core_%)
- 
- LIB = xblast
- 
- 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) 
- CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
 --- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
 +++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
 @@ -27,7 +27,9 @@
@@ -114,7 +94,7 @@ Last-Update: 2016-12-05
      seqmasks_io
 --- a/c++/src/build-system/library_relations.txt
 +++ b/c++/src/build-system/library_relations.txt
-@@ -1287,7 +1287,7 @@
+@@ -1308,7 +1308,7 @@
  xbiosample_util needs $(XFORMAT_LIBS)
  xbiosample_util needs xalnmgr
  xbiosample_util needs xmlwrapp
@@ -134,17 +114,6 @@ Last-Update: 2016-12-05
  CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
  
  WATCHERS = vakatov
---- a/c++/src/connect/Makefile.xconnect.lib
-+++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -14,6 +14,8 @@
- LIB  = xconnect
- PROJ_TAG = core
- 
-+DLL_LIB = xncbi
-+
- LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
- 
- WATCHERS = lavr elisovdn
 --- a/c++/src/corelib/Makefile.test_boost.lib
 +++ b/c++/src/corelib/Makefile.test_boost.lib
 @@ -3,6 +3,8 @@
@@ -233,17 +202,6 @@ Last-Update: 2016-12-05
  WATCHERS = vasilche
  
  
---- a/c++/src/objects/seq/Makefile.seq.lib
-+++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -14,6 +14,8 @@
- 
- DLL_LIB = seqcode pub general xser sequtil
- 
-+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = vasilche grichenk
- 
- 
 --- a/c++/src/objects/seqcode/Makefile.seqcode.lib
 +++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
 @@ -1,6 +1,8 @@
@@ -266,17 +224,6 @@ Last-Update: 2016-12-05
  
  
  USES_LIBRARIES =  \
---- a/c++/src/objects/seqset/Makefile.seqset.lib
-+++ b/c++/src/objects/seqset/Makefile.seqset.lib
-@@ -1,6 +1,8 @@
- LIB = seqset
- SRC = seqset__ seqset___ gb_release_file
- 
-+DLL_LIB = seq general xser xncbi
-+
- 
- USES_LIBRARIES =  \
-     $(SEQ_LIBS) pub
 --- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
 +++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
 @@ -1,6 +1,8 @@
@@ -312,9 +259,9 @@ Last-Update: 2016-12-05
  
 --- a/c++/src/objmgr/util/Makefile.util.lib
 +++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -11,6 +11,8 @@
+@@ -14,6 +14,8 @@
  
- DLL_LIB = $(SOBJMGR_LIBS)
+ DLL_LIB = submit $(SOBJMGR_LIBS)
  
 +DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
 +
@@ -367,7 +314,7 @@ Last-Update: 2016-12-05
  CXXFLAGS = $(FAST_CXXFLAGS)
 --- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
 +++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-@@ -8,6 +8,9 @@
+@@ -11,6 +11,9 @@
  
  LIB = writedb
  
@@ -449,7 +396,7 @@ Last-Update: 2016-12-05
 +++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
 @@ -12,6 +12,8 @@
  # Dependencies for shared library
- DLL_LIB = xconnect ncbi_xreader$(DLL)
+ DLL_LIB = ncbi_xreader$(DLL) $(GENBANK_READER_LDEP)
  
 +DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
 +
@@ -622,16 +569,6 @@ Last-Update: 2016-12-05
  
  USES_LIBRARIES =  \
      xser
---- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-+++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
-@@ -5,6 +5,7 @@
- LIB = entrez2cli
- SRC = entrez2_client entrez2_client_
- 
-+DLL_LIB = entrez2 xconnect xser xutil xncbi
- 
- USES_LIBRARIES =  \
-     entrez2 xconnect
 --- a/c++/src/objects/gbseq/Makefile.gbseq.lib
 +++ b/c++/src/objects/gbseq/Makefile.gbseq.lib
 @@ -1,6 +1,7 @@
@@ -704,7 +641,7 @@ Last-Update: 2016-12-05
      $(SEQ_LIBS) pub xconnect
 --- a/c++/src/objects/taxon3/Makefile.taxon3.lib
 +++ b/c++/src/objects/taxon3/Makefile.taxon3.lib
-@@ -7,6 +7,7 @@
+@@ -8,6 +8,7 @@
  
  WATCHERS = bollin holmesbr
  
@@ -795,14 +732,63 @@ Last-Update: 2016-12-05
  USES_LIBRARIES =  \
      xregexp $(PCRE_LIB) $(PCRE_LIBS) xncbi
  
---- a/c++/src/algo/blast/Makefile.blast_macros.mk
-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -18,7 +18,7 @@
- BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
- 
- # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
--BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
-+BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment blast \
-               xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xalnmgr \
-               xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables
- # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
+--- a/c++/src/algo/blast/api/Makefile.xblast.lib
++++ b/c++/src/algo/blast/api/Makefile.xblast.lib
+@@ -77,11 +77,11 @@
+ magicblast_options \
+ magicblast
+ 
+-SRC  = $(SRC_C:%=.core_%) $(SRC_CXX)
++SRC  = $(SRC_CXX)
+ 
+ LIB = xblast
+ 
+-DLL_LIB = $(BLAST_LDEP) $(SOBJMGR_LIBS)
++DLL_LIB = $(BLAST_LDEP) $(SOBJMGR_LIBS) blast seqdb seqset seq general xser xconnect sequtil tables xutil xncbi
+ 
+ CFLAGS   = $(FAST_CFLAGS) 
+ CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
+--- a/c++/src/connect/Makefile.xconnect.lib
++++ b/c++/src/connect/Makefile.xconnect.lib
+@@ -14,6 +14,8 @@
+ LIB      = xconnect
+ PROJ_TAG = core
+ 
++DLL_LIB = xncbi
++
+ LIBS     = $(NETWORK_LIBS) $(ORIG_LIBS)
+ 
+ WATCHERS = lavr mcelhany
+--- a/c++/src/objects/seq/Makefile.seq.lib
++++ b/c++/src/objects/seq/Makefile.seq.lib
+@@ -12,7 +12,7 @@
+       seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map so_map \
+       seq_loc_from_string seq_loc_reverse_complementer
+ 
+-DLL_LIB = seqcode pub general xser sequtil
++DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
+ 
+ WATCHERS = vasilche grichenk bollin ludwigf
+ 
+--- a/c++/src/objects/seqset/Makefile.seqset.lib
++++ b/c++/src/objects/seqset/Makefile.seqset.lib
+@@ -1,7 +1,7 @@
+ LIB = seqset
+ SRC = seqset__ seqset___ gb_release_file
+ 
+-DLL_LIB = $(SEQ_LIBS)
++DLL_LIB = $(SEQ_LIBS) xser xncbi
+ 
+ USES_LIBRARIES =  \
+     $(SEQ_LIBS) pub
+--- a/c++/src/objects/entrez2/Makefile.entrez2cli.lib
++++ b/c++/src/objects/entrez2/Makefile.entrez2cli.lib
+@@ -5,7 +5,7 @@
+ LIB = entrez2cli
+ SRC = entrez2_client entrez2_client_
+ 
+-DLL_LIB = entrez2 xconnect
++DLL_LIB = entrez2 xconnect xser xutil xncbi
+ 
+ USES_LIBRARIES =  \
+     entrez2 xconnect
diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes
index 13d20726e92b964ac3ef3e8c4b4bcae036dba1c4..c664ef2a7c47e7f0b9bbc8691ba432ad2891d377 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
-@@ -9157,7 +9157,7 @@
+@@ -9716,7 +9716,7 @@
      solaris* )
        CONF_f_runpath="-R"
        ;;
@@ -20,7 +20,7 @@ Last-Update: 2011-06-10
      irix*:* | linux*:KCC | *:Compaq )
 --- a/c++/src/build-system/configure.ac
 +++ b/c++/src/build-system/configure.ac
-@@ -1939,7 +1939,7 @@
+@@ -2081,7 +2081,7 @@
      solaris* )
        CONF_f_runpath="-R"
        ;;
diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath
index 15cd5e30425c40576716efea60bd37a32242ad79..a5601282694e626a0e3d7888af6fbde28f001bed 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
-@@ -9285,7 +9285,7 @@
+@@ -9823,7 +9823,7 @@
                 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
-@@ -2006,7 +2006,7 @@
+@@ -2148,7 +2148,7 @@
                 break
                 ;;
              /* )
diff --git a/debian/patches/suppress_gnutls_version_check b/debian/patches/suppress_gnutls_version_check
index 7dca5fc0db464bb59f66ed706681a19ff35f6eb6..3794f6c1c9ea4b4f314c5ce152d855c663e9eb56 100644 (file)
--- a/debian/patches/suppress_gnutls_version_check
+++ b/debian/patches/suppress_gnutls_version_check
@@ -1,6 +1,6 @@
 --- a/c++/src/connect/ncbi_gnutls.c
 +++ b/c++/src/connect/ncbi_gnutls.c
-@@ -585,6 +585,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
+@@ -661,6 +661,7 @@
  
      assert(!s_GnuTlsCredAnon);
  
@@ -8,11 +8,11 @@
      version = gnutls_check_version(0);
      if (strcasecmp(GNUTLS_VERSION, version) != 0) {
          CORE_LOGF(eLOG_Critical,
-@@ -592,6 +593,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
+@@ -668,6 +669,7 @@
                     GNUTLS_VERSION, version));
          assert(0);
      }
 +#endif
  
-     val = ConnNetInfo_GetValue(0, "GNUTLS_LOGLEVEL", buf, sizeof(buf), 0);
-     CORE_LOCK_READ;
+     if (!pull  ||  !push)
+         return eIO_InvalidArg;
diff --git a/debian/patches/use_pie_for_apps b/debian/patches/use_pie_for_apps
index b43c7b4f251435971daa1ca1c24811913dcbac53..89bc7d7df3a6ee5457c033ef8d635b04136fc5f7 100644 (file)
--- a/debian/patches/use_pie_for_apps
+++ b/debian/patches/use_pie_for_apps
@@ -7,7 +7,7 @@ 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 setup
  
@@ -18,12 +18,12 @@ Last-Update: 2012-05-10
  SOURCES      = @UNIX_SRC@ $(SRC)
  
  ### Standard application build rules
-@@ -53,7 +53,7 @@ ifneq "" "$(wildcard Makefile.$(TMPL).ap
-   endif
- endif
+@@ -56,7 +56,7 @@
+ include $(builddir)/Makefile.$(Rules)
  
--CMD_BASE = $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS)
-+CMD_BASE = $(LINK_WRAPPER) $(LINK) $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS)
+ CMD_BASE = $(LINK_WRAPPER) $(LINK)
+-CMD_BASEARGS = $(LDFLAGS) $(APP_LDFLAGS) $(XOBJ) $(XOBJ2) $(PRE_LIBS)
++CMD_BASEARGS = $(LDFLAGS) $(APP_LDFLAGS) -fPIE -pie $(XOBJ) $(XOBJ2) $(PRE_LIBS)
  CMD_TAIL = @f_outexe@$(XAPP) $(LINK_FILTER)
- CMD  = $(CMD_BASE) $(XLIB) $(XAPP_LIBS) $(CMD_TAIL)
- CMD2 = $(CMD_BASE) $(XLIB2) $(XAPP_LIBS2) $(CMD_TAIL)
+ CMD_ARGS  = $(CMD_BASEARGS) $(XLIB)  $(XAPP_LIBS)
+ CMD_ARGS2 = $(CMD_BASEARGS) $(XLIB2) $(XAPP_LIBS2)
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