debian/patches: Formally refresh for 2.10.0 release.

A few files needed straightforward manual intervention.

diff --git a/debian/changelog b/debian/changelog
index 2d6ceb4e3d1fc8ae3699b4aa25d6120dbc6aa6cf..2fe51e9a1ee0a2522cdf863c2aa96d6947addf1a 100644 (file)
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,10 @@
 ncbi-blast+ (2.10.0-1) UNRELEASED; urgency=medium
 
   * New upstream release.  (NOT RELEASED YET.)
+  * debian/patches: Formally refresh.  (A few files needed straightforward
+    manual intervention.)
 
- -- Aaron M. Ucko <ucko@debian.org>  Sat, 25 Apr 2020 21:44:42 -0400
+ -- Aaron M. Ucko <ucko@debian.org>  Sat, 25 Apr 2020 22:13:31 -0400
 
 ncbi-blast+ (2.9.0-4) unstable; urgency=high
 

diff --git a/debian/patches/enable_clean_after_failed_compile b/debian/patches/enable_clean_after_failed_compile
index 6222bf3e4ae854675c33e22fff3e1f8725d16c20..179768edbb6addf0ef63a78e52be6dbdb236c89f 100644 (file)
--- a/debian/patches/enable_clean_after_failed_compile
+++ b/debian/patches/enable_clean_after_failed_compile
@@ -5,7 +5,7 @@ Last-Updated: 2013-06-01
 Forwarded: no
 --- a/c++/src/build-system/new_module.sh.in
 +++ b/c++/src/build-system/new_module.sh.in
-@@ -198,7 +198,7 @@ if test -z "$datatool"; then # keep look
+@@ -198,7 +198,7 @@
          if test -n "$DYLD_LIBRARY_PATH"; then
              wrapper="DYLD_LIBRARY_PATH=$DYLD_LIBRARY_PATH"
          fi

diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps
index 89455233de90bc49ac7800e228cbca55f2806831..dc035f8961f6508605d4aa211eae5020df045df4 100644 (file)
--- a/debian/patches/fix_lib_deps
+++ b/debian/patches/fix_lib_deps
@@ -45,7 +45,7 @@ Last-Update: 2016-12-05
  
 +DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
 +
- ASN_DEP = seqset
+ ASN_DEP = seqset submit
  
  WATCHERS = morgulis
 --- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
@@ -94,7 +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
-@@ -1511,7 +1511,7 @@
+@@ -1543,7 +1543,7 @@
  xbiosample_util needs valid
  xbiosample_util needs xmlwrapp
  xbiosample_util needs xobjutil
@@ -359,16 +359,17 @@ Last-Update: 2016-12-05
  WATCHERS = camacho
 --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
 +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,6 +12,9 @@
+@@ -12,6 +12,10 @@
  # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
+ DLL_LIB = ncbi_xreader$(DLL) $(GENBANK_PSG_CLIENT_LDEP)
  
 +DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \
-+           id2 id1 ncbi_xreader xobjmgr seq xutil xncbi
++           id2 id1 ncbi_xreader $(GENBANK_PSG_CLIENT_LDEP) xobjmgr \
++           seq xutil xncbi
 +
- WATCHERS = vasilche
- 
+ LIBS = $(GENBANK_THIRD_PARTY_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS)
  
+ CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
 --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
 +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
 @@ -16,6 +16,9 @@
@@ -452,7 +453,7 @@ Last-Update: 2016-12-05
  
 --- a/c++/src/util/Makefile.util.lib
 +++ b/c++/src/util/Makefile.util.lib
-@@ -14,6 +14,7 @@
+@@ -15,6 +15,7 @@
  LIB = xutil
  PROJ_TAG = core
  
@@ -484,16 +485,14 @@ Last-Update: 2016-12-05
  USES_LIBRARIES =  \
 --- a/c++/src/objtools/readers/Makefile.xobjread.lib
 +++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -20,8 +20,7 @@
-       ucscregion_reader struct_cmt_reader \
+@@ -25,6 +25,6 @@
        message_listener line_error
  
--
--DLL_LIB = submit seqset $(SEQ_LIBS) general creaders xutil
-+DLL_LIB = submit seqset $(SEQ_LIBS) general creaders xutil pub xser xncbi
  
- USES_LIBRARIES =  \
-     creaders submit
+-DLL_LIB = submit seqset $(SEQ_LIBS) general xutil xlogging
++DLL_LIB = submit seqset $(SEQ_LIBS) general xutil xlogging pub xser xncbi
+ 
+ USES_LIBRARIES = submit xlogging
 --- a/c++/src/util/sequtil/Makefile.sequtil.lib
 +++ b/c++/src/util/sequtil/Makefile.sequtil.lib
 @@ -3,6 +3,8 @@
@@ -513,7 +512,7 @@ Last-Update: 2016-12-05
  
 +DLL_LIB = seq general xser xncbi
 +
- WATCHERS = dicuccio shchekot zherikov
+ WATCHERS = dicuccio smithrg zherikov
  
  
 --- a/c++/src/objects/medline/Makefile.medline.lib
@@ -692,19 +691,15 @@ Last-Update: 2016-12-05
      $(BLAST_LIBS) align_format blastxml blastxml2
 --- a/c++/src/objtools/cleanup/Makefile.cleanup.lib
 +++ b/c++/src/objtools/cleanup/Makefile.cleanup.lib
-@@ -10,11 +10,10 @@
+@@ -10,7 +10,7 @@
        cleanup_utils gene_qual_normalization cleanup_user_object cleanup_author \
        cleanup_pub newcleanupp capitalization_string fix_feature_id
  
--DLL_LIB = xregexp $(PCRE_LIB)      
+-DLL_LIB = $(OBJEDIT_LIBS) xregexp $(PCRE_LIB)
 +DLL_LIB = $(OBJEDIT_LIBS) xobjutil valid xregexp $(PCRE_LIB) $(SOBJMGR_LIBS)
  LIB = xcleanup
  
  LIBS = $(PCRE_LIBS)
- 
--
- USES_LIBRARIES =  \
-     submit valid xobjutil
 --- a/c++/src/objtools/format/Makefile.xformat.lib
 +++ b/c++/src/objtools/format/Makefile.xformat.lib
 @@ -22,6 +22,8 @@

diff --git a/debian/patches/fix_unit_tests b/debian/patches/fix_unit_tests
index e20a43c47fbc86037640061f19b237fb58f9283f..d75b78b1783861e44fd5204b7d2178d26d70f035 100644 (file)
--- a/debian/patches/fix_unit_tests
+++ b/debian/patches/fix_unit_tests
@@ -5,7 +5,7 @@ Author: Olivier Sallou <osallou@debian.org>
 Last-Updated: 2018-02-11
 --- a/c++/src/algo/blast/Makefile.blast_macros.mk
 +++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -21,7 +21,7 @@ BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) v
+@@ -21,7 +21,7 @@
  BLAST_LDEP = xalgoblastdbindex composition_adjustment \
               xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xalnmgr \
               xobjutil $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables $(LMDB_LIB)

diff --git a/debian/patches/hurd_fixes b/debian/patches/hurd_fixes
index fd29c84a1f2db2a68b7c7e6bd4f37023699cf685..adb1800d81432d94c2e495dfdffae76558019b6b 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
-@@ -9914,7 +9914,7 @@
+@@ -10017,7 +10017,7 @@
      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
-@@ -2136,7 +2136,7 @@
+@@ -2175,7 +2175,7 @@
      solaris* )
        CONF_f_runpath="-R"
        ;;

diff --git a/debian/patches/legacy_rename_rpsblast b/debian/patches/legacy_rename_rpsblast
index 5b23961373e047c6742e846a5962371c9aeafb57..f40204b183e760b48aa5c4d84c6d11d7219efaaf 100644 (file)
--- a/debian/patches/legacy_rename_rpsblast
+++ b/debian/patches/legacy_rename_rpsblast
@@ -3,7 +3,7 @@ Description: rename binary as blast+ for package coherency.
 Last-Updated: 2011-10-03
 --- a/c++/src/app/blast/legacy_blast.pl
 +++ b/c++/src/app/blast/legacy_blast.pl
-@@ -1064,7 +1064,7 @@ sub handle_rpsblast
+@@ -1064,7 +1064,7 @@
      if (defined $opt_p and $opt_p =~ /f/i) {
          $retval .= "/rpstblastn";
      } else {

diff --git a/debian/patches/no_multiarch_rpath b/debian/patches/no_multiarch_rpath
index 8b11eb4ab7c73f9b4f25a4a36a174593d4c2f21c..de626df003b807c1f7b4d7e8d8724c7701dd9d41 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
-@@ -10022,7 +10022,7 @@
+@@ -10126,7 +10126,7 @@
                 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
-@@ -2203,7 +2203,7 @@
+@@ -2243,7 +2243,7 @@
                 break
                 ;;
              /* )

diff --git a/debian/patches/optionally_keep_sequence b/debian/patches/optionally_keep_sequence
index 2c1c0a85082c74814e4e4d12485782707bbeaa62..311b06de328dbddc673ac902f1127e289b922740 100644 (file)
--- a/debian/patches/optionally_keep_sequence
+++ b/debian/patches/optionally_keep_sequence
@@ -6,7 +6,7 @@ Description: Hang on to sequence data even if -parse_deflines recognized a non-l
     "true" value (English-only, case-insensitive true, t, yes, y, or 1).
 --- a/c++/src/algo/blast/api/search_strategy.cpp
 +++ b/c++/src/algo/blast/api/search_strategy.cpp
-@@ -495,6 +495,11 @@ void CExportStrategy::x_Process_Pssm(CRe
+@@ -544,6 +544,11 @@
      m_QueueSearchRequest->SetService(new_service);
  }
  
@@ -18,7 +18,7 @@ Description: Hang on to sequence data even if -parse_deflines recognized a non-l
  void CExportStrategy::x_Process_Query(CRef<IQueryFactory> & query)
  {
      if (query.Empty())
-@@ -516,7 +521,7 @@ void CExportStrategy::x_Process_Query(CR
+@@ -565,7 +570,7 @@
      // Check if there are any range restrictions applied and if local IDs are
      // being used to determine how to specify the query sequence(s)
  

diff --git a/debian/patches/reprobuild b/debian/patches/reprobuild
index d485fdeb5947c610783c2a2e7c0dafbba81601e5..0e659e982c3b7969e076ed684358772c1a96a1d0 100644 (file)
--- a/debian/patches/reprobuild
+++ b/debian/patches/reprobuild
@@ -1,8 +1,8 @@
 Author: Michael R. Crusoe <michael.crusoe@gmail.com>
 Description: make the build more reproducible
---- ncbi-blastplus.orig/c++/src/build-system/configure.ac
-+++ ncbi-blastplus/c++/src/build-system/configure.ac
-@@ -2826,13 +2826,13 @@
+--- a/c++/src/build-system/configure.ac
++++ b/c++/src/build-system/configure.ac
+@@ -2866,13 +2866,13 @@
     linux*)
        kver=`uname -r | sed -e 's/-.*//'`
        libcver=`ldd --version | awk 'NR == 1 { print $NF }'`
@@ -18,8 +18,8 @@ Description: make the build more reproducible
      | sed 's/\..*//; s/-/_/g; 1q'`
  signature="${signature_compiler}_${signature_compiler_version}-${release_debug}${mt_sfx}${dll_sfx}${bit64_sfx}${prof_sfx}--${verbose_host}-${signature_hostname}"
  AC_DEFINE_UNQUOTED(NCBI_SIGNATURE, "$signature",
---- ncbi-blastplus.orig/c++/include/algo/blast/core/blast_message.h
-+++ ncbi-blastplus/c++/include/algo/blast/core/blast_message.h
+--- a/c++/include/algo/blast/core/blast_message.h
++++ b/c++/include/algo/blast/core/blast_message.h
 @@ -117,7 +117,7 @@
  
  /** Convenient define to call the function Blast_PerrorEx. */
@@ -29,9 +29,9 @@ Description: make the build more reproducible
  
  /** Extended version of Blast_Perror which includes parameters for the file
   * name and line number where the error/warning occurred. This function should
---- ncbi-blastplus.orig/c++/include/connect/ncbi_util.h
-+++ ncbi-blastplus/c++/include/connect/ncbi_util.h
-@@ -113,7 +113,7 @@
+--- a/c++/include/connect/ncbi_util.h
++++ b/c++/include/connect/ncbi_util.h
+@@ -135,7 +135,7 @@
   */
  #define  LOG_WRITE(lg, code, subcode, level, message)                        \
      LOG_Write(lg, code, subcode, level, THIS_MODULE, CORE_CURRENT_FUNCTION,  \
@@ -40,7 +40,7 @@ Description: make the build more reproducible
  
  #ifdef   LOG_DATA
  /* AIX's <pthread.h> defines LOG_DATA to be an integer constant;
-@@ -122,7 +122,7 @@
+@@ -144,7 +144,7 @@
  #endif
  #define  LOG_DATA(lg, code, subcode, level, data, size, message)             \
      LOG_Write(lg, code, subcode, level, THIS_MODULE, CORE_CURRENT_FUNCTION,  \
@@ -49,8 +49,8 @@ Description: make the build more reproducible
  
  
  /** Default for THIS_MODULE.
---- ncbi-blastplus.orig/c++/include/corelib/impl/ncbi_java.h
-+++ ncbi-blastplus/c++/include/corelib/impl/ncbi_java.h
+--- a/c++/include/corelib/impl/ncbi_java.h
++++ b/c++/include/corelib/impl/ncbi_java.h
 @@ -63,7 +63,7 @@
  
  #define JAVA_ABORT(msg) \
@@ -60,9 +60,9 @@ Description: make the build more reproducible
          abort(); \
      }
  
---- ncbi-blastplus.orig/c++/include/corelib/ncbidiag.hpp
-+++ ncbi-blastplus/c++/include/corelib/ncbidiag.hpp
-@@ -167,7 +167,7 @@
+--- a/c++/include/corelib/ncbidiag.hpp
++++ b/c++/include/corelib/ncbidiag.hpp
+@@ -168,7 +168,7 @@
  /// @sa
  ///   CDiagCompileInfo
  #define DIAG_COMPILE_INFO                                           \
@@ -71,9 +71,9 @@ Description: make the build more reproducible
                                     __LINE__,                        \
                                     NCBI_CURRENT_FUNCTION,           \
                                     NCBI_MAKE_MODULE(NCBI_MODULE))
---- ncbi-blastplus.orig/c++/include/corelib/test_boost.hpp
-+++ ncbi-blastplus/c++/include/corelib/test_boost.hpp
-@@ -249,7 +249,7 @@
+--- a/c++/include/corelib/test_boost.hpp
++++ b/c++/include/corelib/test_boost.hpp
+@@ -275,7 +275,7 @@
  BOOST_JOIN( BOOST_JOIN( test_name, _registrar ), __LINE__ ) (           \
      boost::unit_test::make_test_case(                                   \
          &BOOST_AUTO_TC_INVOKER( test_name ), #test_name,                \
@@ -82,8 +82,8 @@ Description: make the build more reproducible
      ::NCBI_NS_NCBI::SNcbiTestTCTimeout<                                 \
          BOOST_AUTO_TC_UNIQUE_ID( test_name )>::instance()->value(),     \
      decorators );                                                       \
---- ncbi-blastplus.orig/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
-+++ ncbi-blastplus/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
+--- a/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
++++ b/c++/include/objtools/blast/seqdb_reader/impl/seqdbgeneral.hpp
 @@ -1124,7 +1124,7 @@
  #define SEQDB_FILE_ASSERT(YESNO)                                        \
      do {                                                                \
@@ -93,8 +93,8 @@ Description: make the build more reproducible
          }                                                               \
      } while(0)
  
---- ncbi-blastplus.orig/c++/include/util/ddump_viewer.hpp
-+++ ncbi-blastplus/c++/include/util/ddump_viewer.hpp
+--- a/c++/include/util/ddump_viewer.hpp
++++ b/c++/include/util/ddump_viewer.hpp
 @@ -49,7 +49,7 @@
  //
  
@@ -104,8 +104,8 @@ Description: make the build more reproducible
  
  
  //---------------------------------------------------------------------------
---- ncbi-blastplus.orig/c++/include/util/static_set.hpp
-+++ ncbi-blastplus/c++/include/util/static_set.hpp
+--- a/c++/include/util/static_set.hpp
++++ b/c++/include/util/static_set.hpp
 @@ -886,17 +886,17 @@
      static const Type Var
  
@@ -128,9 +128,9 @@ Description: make the build more reproducible
                       NCBI_NS_NCBI::NStaticArray::eCopyWarn_hide)
  
  
---- ncbi-blastplus.orig/c++/src/connect/mbedtls/mbedtls/debug.h
-+++ ncbi-blastplus/c++/src/connect/mbedtls/mbedtls/debug.h
-@@ -40,28 +40,28 @@
+--- a/c++/src/connect/mbedtls/mbedtls/debug.h
++++ b/c++/src/connect/mbedtls/mbedtls/debug.h
+@@ -41,28 +41,28 @@
  #define MBEDTLS_DEBUG_STRIP_PARENS( ... )   __VA_ARGS__
  
  #define MBEDTLS_SSL_DEBUG_MSG( level, args )                    \
@@ -165,8 +165,8 @@ Description: make the build more reproducible
  #endif
  
  #else /* MBEDTLS_DEBUG_C */
---- ncbi-blastplus.orig/c++/src/connect/ncbi_lbos_cxx.cpp
-+++ ncbi-blastplus/c++/src/connect/ncbi_lbos_cxx.cpp
+--- a/c++/src/connect/ncbi_lbos_cxx.cpp
++++ b/c++/src/connect/ncbi_lbos_cxx.cpp
 @@ -145,7 +145,7 @@
  {
      /* Hostname should not be empty in any case */
@@ -284,8 +284,8 @@ Description: make the build more reproducible
              CLBOSException::eInvalidArgs,
              "This convenience function throws on whitespace characters "
              "in \"extra\" meta parameter. If you know what you are doing, "
---- ncbi-blastplus.orig/c++/src/connect/ncbi_monkey.cpp
-+++ ncbi-blastplus/c++/src/connect/ncbi_monkey.cpp
+--- a/c++/src/connect/ncbi_monkey.cpp
++++ b/c++/src/connect/ncbi_monkey.cpp
 @@ -83,7 +83,7 @@
  const string             kSeedField      = "seed";
  
@@ -511,9 +511,9 @@ Description: make the build more reproducible
              NULL, CMonkeyException::e_MonkeyInvalidArgs,
              ss.str());
      }
---- ncbi-blastplus.orig/c++/src/connect/ncbi_priv.h
-+++ ncbi-blastplus/c++/src/connect/ncbi_priv.h
-@@ -223,7 +223,7 @@
+--- a/c++/src/connect/ncbi_priv.h
++++ b/c++/src/connect/ncbi_priv.h
+@@ -222,7 +222,7 @@
              _mess.level       = _xx_level;                              \
              _mess.module      = THIS_MODULE;                            \
              _mess.func        = CORE_CURRENT_FUNCTION;                  \
@@ -522,9 +522,9 @@ Description: make the build more reproducible
              _mess.line        = __LINE__;                               \
              _mess.raw_data    = (_raw_data);                            \
              _mess.raw_size    = (_raw_size);                            \
---- ncbi-blastplus.orig/c++/src/objects/seqfeat/BioSource.cpp
-+++ ncbi-blastplus/c++/src/objects/seqfeat/BioSource.cpp
-@@ -938,7 +938,7 @@
+--- a/c++/src/objects/seqfeat/BioSource.cpp
++++ b/c++/src/objects/seqfeat/BioSource.cpp
+@@ -941,7 +941,7 @@
  };
  
  typedef CStaticArraySet<const char*, PNocase_CStr> TCIgnoreCaseQualsSet;
@@ -532,8 +532,8 @@ Description: make the build more reproducible
 +static const TCIgnoreCaseQualsSet s_IgnoreCaseQualsSet(s_IgnoreCaseQuals, sizeof(s_IgnoreCaseQuals), "c++/src/objects/seqfeat/BioSource.cpp", __LINE__);
  
  bool s_MayIgnoreCase(const string& value)
- {   
-@@ -960,7 +960,7 @@
+ {
+@@ -963,7 +963,7 @@
  };
  
  typedef CStaticArraySet<const char*, PNocase_CStr> TCTaxNameElementQualsSet;
@@ -541,8 +541,8 @@ Description: make the build more reproducible
 +static const TCTaxNameElementQualsSet s_TaxNameElementQualsSet(s_TaxNameElementQuals, sizeof(s_TaxNameElementQuals), "c++/src/objects/seqfeat/BioSource.cpp", __LINE__);
  
  bool s_IsTaxNameElement(const string& value)
- {   
-@@ -1364,7 +1364,7 @@
+ {
+@@ -1367,7 +1367,7 @@
  };
  
  typedef CStaticArraySet<const char*, PNocase_CStr> TCStopWordStrSet;
@@ -551,9 +551,9 @@ Description: make the build more reproducible
  
  
  bool CBioSource::IsStopWord(const string& value)
---- ncbi-blastplus.orig/c++/src/objects/seqfeat/SubSource.cpp
-+++ ncbi-blastplus/c++/src/objects/seqfeat/SubSource.cpp
-@@ -3043,7 +3043,7 @@
+--- a/c++/src/objects/seqfeat/SubSource.cpp
++++ b/c++/src/objects/seqfeat/SubSource.cpp
+@@ -3080,7 +3080,7 @@
      "Zimbabwe"
  };
  typedef CStaticArraySet<const char*, PCase_CStr> TCStrSet;
@@ -562,7 +562,7 @@ Description: make the build more reproducible
  
  // former legal country names, must be in alphabetical order (case sensitive)
  static const char* const s_Former_Countries[] = {
-@@ -3061,7 +3061,7 @@
+@@ -3098,7 +3098,7 @@
      "Yugoslavia",
      "Zaire"
  };
@@ -571,8 +571,8 @@ Description: make the build more reproducible
  
  bool CCountries::IsValid(const string& country)
  {
---- ncbi-blastplus.orig/c++/src/serial/datatool/classstr.cpp
-+++ ncbi-blastplus/c++/src/serial/datatool/classstr.cpp
+--- a/c++/src/serial/datatool/classstr.cpp
++++ b/c++/src/serial/datatool/classstr.cpp
 @@ -850,7 +850,7 @@
                          "    if (!CanGet"<< mem_cName<<"()) {\n"
                          "        ThrowUnassigned("<<member_index;
@@ -582,8 +582,8 @@ Description: make the build more reproducible
  #endif
                      code.Methods(inl) << ");\n"
                          "    }\n";
---- ncbi-blastplus.orig/c++/src/serial/serialobject.cpp
-+++ ncbi-blastplus/c++/src/serial/serialobject.cpp
+--- a/c++/src/serial/serialobject.cpp
++++ b/c++/src/serial/serialobject.cpp
 @@ -295,7 +295,7 @@
  // set temporary diag compile info to use argument file name and line
  #undef DIAG_COMPILE_INFO
@@ -602,8 +602,8 @@ Description: make the build more reproducible
                                         __LINE__,                        \
                                         NCBI_CURRENT_FUNCTION,           \
                                         NCBI_MAKE_MODULE(NCBI_MODULE))
---- ncbi-blastplus.orig/c++/src/util/lmdb/mdb.c
-+++ ncbi-blastplus/c++/src/util/lmdb/mdb.c
+--- a/c++/src/util/lmdb/mdb.c
++++ b/c++/src/util/lmdb/mdb.c
 @@ -1523,7 +1523,7 @@
  
  #ifndef NDEBUG
@@ -613,8 +613,8 @@ Description: make the build more reproducible
  
  static void ESECT
  mdb_assert_fail(MDB_env *env, const char *expr_txt,
---- ncbi-blastplus.orig/c++/src/util/lmdb/mtest.c
-+++ ncbi-blastplus/c++/src/util/lmdb/mtest.c
+--- a/c++/src/util/lmdb/mtest.c
++++ b/c++/src/util/lmdb/mtest.c
 @@ -19,7 +19,7 @@
  #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
  #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
@@ -624,8 +624,8 @@ Description: make the build more reproducible
  
  int main(int argc,char * argv[])
  {
---- ncbi-blastplus.orig/c++/src/util/lmdb/mtest2.c
-+++ ncbi-blastplus/c++/src/util/lmdb/mtest2.c
+--- a/c++/src/util/lmdb/mtest2.c
++++ b/c++/src/util/lmdb/mtest2.c
 @@ -22,7 +22,7 @@
  #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
  #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
@@ -635,8 +635,8 @@ Description: make the build more reproducible
  
  int main(int argc,char * argv[])
  {
---- ncbi-blastplus.orig/c++/src/util/lmdb/mtest3.c
-+++ ncbi-blastplus/c++/src/util/lmdb/mtest3.c
+--- a/c++/src/util/lmdb/mtest3.c
++++ b/c++/src/util/lmdb/mtest3.c
 @@ -22,7 +22,7 @@
  #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
  #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
@@ -646,8 +646,8 @@ Description: make the build more reproducible
  
  int main(int argc,char * argv[])
  {
---- ncbi-blastplus.orig/c++/src/util/lmdb/mtest4.c
-+++ ncbi-blastplus/c++/src/util/lmdb/mtest4.c
+--- a/c++/src/util/lmdb/mtest4.c
++++ b/c++/src/util/lmdb/mtest4.c
 @@ -22,7 +22,7 @@
  #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
  #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
@@ -657,8 +657,8 @@ Description: make the build more reproducible
  
  int main(int argc,char * argv[])
  {
---- ncbi-blastplus.orig/c++/src/util/lmdb/mtest5.c
-+++ ncbi-blastplus/c++/src/util/lmdb/mtest5.c
+--- a/c++/src/util/lmdb/mtest5.c
++++ b/c++/src/util/lmdb/mtest5.c
 @@ -22,7 +22,7 @@
  #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
  #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
@@ -668,8 +668,8 @@ Description: make the build more reproducible
  
  int main(int argc,char * argv[])
  {
---- ncbi-blastplus.orig/c++/src/util/lmdb/mtest6.c
-+++ ncbi-blastplus/c++/src/util/lmdb/mtest6.c
+--- a/c++/src/util/lmdb/mtest6.c
++++ b/c++/src/util/lmdb/mtest6.c
 @@ -22,7 +22,7 @@
  #define E(expr) CHECK((rc = (expr)) == MDB_SUCCESS, #expr)
  #define RES(err, expr) ((rc = expr) == (err) || (CHECK(!rc, #expr), 0))
@@ -679,8 +679,8 @@ Description: make the build more reproducible
  
  char dkbuf[1024];
  
---- ncbi-blastplus.orig/c++/src/util/regexp/pcre_scanner_unittest.cc
-+++ ncbi-blastplus/c++/src/util/regexp/pcre_scanner_unittest.cc
+--- a/c++/src/util/regexp/pcre_scanner_unittest.cc
++++ b/c++/src/util/regexp/pcre_scanner_unittest.cc
 @@ -51,7 +51,7 @@
  #define CHECK_EQ(a, b)  do {                                    \
    if ( (a) != (b) ) {                                           \
@@ -690,8 +690,8 @@ Description: make the build more reproducible
      exit(1);                                                    \
    }                                                             \
  } while (0)
---- ncbi-blastplus.orig/c++/src/util/regexp/pcre_stringpiece_unittest.cc
-+++ ncbi-blastplus/c++/src/util/regexp/pcre_stringpiece_unittest.cc
+--- a/c++/src/util/regexp/pcre_stringpiece_unittest.cc
++++ b/c++/src/util/regexp/pcre_stringpiece_unittest.cc
 @@ -19,7 +19,7 @@
  #define CHECK(condition) do {                           \
    if (!(condition)) {                                   \
@@ -701,8 +701,8 @@ Description: make the build more reproducible
      exit(1);                                            \
    }                                                     \
  } while (0)
---- ncbi-blastplus.orig/c++/src/util/static_set.cpp
-+++ ncbi-blastplus/c++/src/util/static_set.cpp
+--- a/c++/src/util/static_set.cpp
++++ b/c++/src/util/static_set.cpp
 @@ -87,7 +87,7 @@
            TParamStaticArrayCopyWarning::GetDefault()) ) {
          // report incorrect usage

diff --git a/debian/patches/skip_services_unit_test b/debian/patches/skip_services_unit_test
index 87cc4460f885b3e2866e646de05786954874cb02..a97840fe95b1bc5a245fa8349e89bace06e3a097 100644 (file)
--- a/debian/patches/skip_services_unit_test
+++ b/debian/patches/skip_services_unit_test
@@ -5,7 +5,7 @@ Description: test require internet connection
 Last-Updated: 2013-06-01
 --- 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 @@ LIB = test_boost blast_services xnetblas
+@@ -11,6 +11,7 @@
  
  LIBS = $(NETWORK_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(BLAST_THIRD_PARTY_LIBS) $(ORIG_LIBS)
  

diff --git a/debian/patches/spelling b/debian/patches/spelling
index 5fc132664183a13262826f1a3c90a6c64737cb16..b6da0056b27ef6dc85f7ff72edd8236303624ce7 100644 (file)
--- a/debian/patches/spelling
+++ b/debian/patches/spelling
@@ -1,7 +1,7 @@
 From: Michael R. Crusoe <michael.crusoe@gmail.com>
 Subject: Spelling fixes
---- ncbi-blastplus.orig/c++/include/objtools/alnmgr/seqids_extractor.hpp
-+++ ncbi-blastplus/c++/include/objtools/alnmgr/seqids_extractor.hpp
+--- a/c++/include/objtools/alnmgr/seqids_extractor.hpp
++++ b/c++/include/objtools/alnmgr/seqids_extractor.hpp
 @@ -232,7 +232,7 @@
                          else if (*id_vec[i] != *id) {
                              string err("Inconsistent Seq-ids found in seg ");
@@ -11,8 +11,8 @@ Subject: Spelling fixes
                                  ", encountered " + id->AsString() + ".";
                              NCBI_THROW(CAlnException, eInvalidSeqId, err);
                          }
---- ncbi-blastplus.orig/c++/src/algo/blast/api/blast_setup_cxx.cpp
-+++ ncbi-blastplus/c++/src/algo/blast/api/blast_setup_cxx.cpp
+--- a/c++/src/algo/blast/api/blast_setup_cxx.cpp
++++ b/c++/src/algo/blast/api/blast_setup_cxx.cpp
 @@ -784,7 +784,7 @@
                        if(warning != kEmptyStr){
                                warning += ": ";
@@ -22,8 +22,8 @@ Subject: Spelling fixes
                        ERR_POST(Warning << warning);
                        continue;
                }
---- ncbi-blastplus.orig/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
-+++ ncbi-blastplus/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
+--- a/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
++++ b/c++/src/algo/winmask/seq_masker_ostat_factory.cpp
 @@ -75,7 +75,7 @@
          }
          else NCBI_THROW( CSeqMaskerOstatFactoryException,
@@ -42,8 +42,8 @@ Subject: Spelling fixes
      }
      catch( CException & e ) {
          NCBI_RETHROW( e, CSeqMaskerOstatFactoryException, eCreateFail,
---- ncbi-blastplus.orig/c++/src/app/blastdb/blastdbcheck.cpp
-+++ ncbi-blastplus/c++/src/app/blastdb/blastdbcheck.cpp
+--- a/c++/src/app/blastdb/blastdbcheck.cpp
++++ b/c++/src/app/blastdb/blastdbcheck.cpp
 @@ -232,7 +232,7 @@
           "Require that all sequences in the database have taxid set.");
  
@@ -53,8 +53,8 @@ Subject: Spelling fixes
  
      // Setup arg.descriptions for this application
      SetupArgDescriptions(arg_desc.release());
---- ncbi-blastplus.orig/c++/src/app/blastdb/makeprofiledb.cpp
-+++ ncbi-blastplus/c++/src/app/blastdb/makeprofiledb.cpp
+--- a/c++/src/app/blastdb/makeprofiledb.cpp
++++ b/c++/src/app/blastdb/makeprofiledb.cpp
 @@ -546,13 +546,13 @@
  
                if(!pssm.IsSetQuery() || (0 == pssm.GetQueryLength()))
@@ -96,8 +96,8 @@ Subject: Spelling fixes
        return false;
      }
  
---- ncbi-blastplus.orig/c++/src/connect/ncbi_lbos.c
-+++ ncbi-blastplus/c++/src/connect/ncbi_lbos.c
+--- a/c++/src/connect/ncbi_lbos.c
++++ b/c++/src/connect/ncbi_lbos.c
 @@ -951,7 +951,7 @@
                                             sizeof(char) * (strlen(buf) + 1))) ) 
      {
@@ -107,8 +107,8 @@ Subject: Spelling fixes
      }  else  {
          buf = realloc_result;
      }
---- ncbi-blastplus.orig/c++/src/objects/seqalign/Dense_seg.cpp
-+++ ncbi-blastplus/c++/src/objects/seqalign/Dense_seg.cpp
+--- a/c++/src/objects/seqalign/Dense_seg.cpp
++++ b/c++/src/objects/seqalign/Dense_seg.cpp
 @@ -988,7 +988,7 @@
              if (loc_plus != (seq_loc_i.GetStrand() != eNa_strand_minus)) {
                  NCBI_THROW(CSeqalignException, eInvalidInputData,
@@ -118,8 +118,8 @@ Subject: Spelling fixes
                             " the input seq-loc");
              }
          }
---- ncbi-blastplus.orig/c++/src/objects/seqalign/Seq_align.cpp
-+++ ncbi-blastplus/c++/src/objects/seqalign/Seq_align.cpp
+--- a/c++/src/objects/seqalign/Seq_align.cpp
++++ b/c++/src/objects/seqalign/Seq_align.cpp
 @@ -872,7 +872,7 @@
          if (dim != ss.GetDim()  ||  row != dim) {
              NCBI_THROW(CSeqalignException, eInvalidInputAlignment,
@@ -129,9 +129,9 @@ Subject: Spelling fixes
          }
  
          if (widths_determined[seg]) {
---- ncbi-blastplus.orig/c++/src/objects/seqfeat/institution_codes.inc
-+++ ncbi-blastplus/c++/src/objects/seqfeat/institution_codes.inc
-@@ -661,7 +661,7 @@
+--- a/c++/src/objects/seqfeat/institution_codes.inc
++++ b/c++/src/objects/seqfeat/institution_codes.inc
+@@ -687,7 +687,7 @@
  "BPS\ts\tCalifornia Department of Food and Agriculture\t\t\t",
  "BPU\ts\tEoetvoes Lorand University, Department of Plant Taxonomy and Ecology\t\t\t",
  "BR<BEL>\ts\tBotanic Garden Meise\t\t\t",
@@ -139,10 +139,10 @@ Subject: Spelling fixes
 +"BR<BRA>\tc\tJohanna Dobereiner Biological Resource Center (CRB-JD)\t\t\t",
  "BRA\ts\tSlovak National Museum, Botany Department\t\t\t",
  "BRAD\ts\tUniversity of Bradford, Biology Department\t\t\t",
- "BRC\ts\tBotanical Record Club\t\t\t",
---- ncbi-blastplus.orig/c++/src/objects/seqfeat/institution_codes.txt
-+++ ncbi-blastplus/c++/src/objects/seqfeat/institution_codes.txt
-@@ -628,7 +628,7 @@
+ "BRBA\ts\tUniversidade Federal do Oeste da Bahia\t\t\t",
+--- a/c++/src/objects/seqfeat/institution_codes.txt
++++ b/c++/src/objects/seqfeat/institution_codes.txt
+@@ -654,7 +654,7 @@
  BPS   s       California Department of Food and Agriculture                   
  BPU   s       Eoetvoes Lorand University, Department of Plant Taxonomy and Ecology                    
  BR<BEL>       s       Botanic Garden Meise                    
@@ -150,9 +150,9 @@ Subject: Spelling fixes
 +BR<BRA>       c       Johanna Dobereiner Biological Resource Center (CRB-JD)                  
  BRA   s       Slovak National Museum, Botany Department                       
  BRAD  s       University of Bradford, Biology Department                      
- BRC   s       Botanical Record Club                   
---- ncbi-blastplus.orig/c++/src/objmgr/util/sequence.cpp
-+++ ncbi-blastplus/c++/src/objmgr/util/sequence.cpp
+ BRBA  s       Universidade Federal do Oeste da Bahia                  
+--- a/c++/src/objmgr/util/sequence.cpp
++++ b/c++/src/objmgr/util/sequence.cpp
 @@ -274,7 +274,7 @@
      if ( best_feats.empty() ) {
          NCBI_THROW_FMT(CObjMgrException, eFindFailed,
@@ -162,9 +162,9 @@ Subject: Spelling fixes
      }
      if ( best_feats.size() > 1 ) {
          NCBI_THROW_FMT(CObjMgrException, eFindConflict,
---- ncbi-blastplus.orig/c++/src/objtools/align_format/taxFormat.cpp
-+++ ncbi-blastplus/c++/src/objtools/align_format/taxFormat.cpp
-@@ -587,7 +587,7 @@
+--- a/c++/src/objtools/align_format/taxFormat.cpp
++++ b/c++/src/objtools/align_format/taxFormat.cpp
+@@ -588,7 +588,7 @@
              }            
          }
          if (!tax_load_ok) {
@@ -173,9 +173,9 @@ Subject: Spelling fixes
          }
          m_TaxTreeLoaded = true;
              
---- ncbi-blastplus.orig/c++/src/objtools/format/flat_file_config.cpp
-+++ ncbi-blastplus/c++/src/objtools/format/flat_file_config.cpp
-@@ -614,7 +614,7 @@
+--- a/c++/src/objtools/format/flat_file_config.cpp
++++ b/c++/src/objtools/format/flat_file_config.cpp
+@@ -623,7 +623,7 @@
  
           // from
           arg_desc->AddOptionalKey("from", "From",
@@ -184,8 +184,8 @@ Subject: Spelling fixes
  
           // to
           arg_desc->AddOptionalKey("to", "To",
---- ncbi-blastplus.orig/c++/src/objtools/readers/agp_converter.cpp
-+++ ncbi-blastplus/c++/src/objtools/readers/agp_converter.cpp
+--- a/c++/src/objtools/readers/agp_converter.cpp
++++ b/c++/src/objtools/readers/agp_converter.cpp
 @@ -728,7 +728,7 @@
          submit_block_writer.WriteObject(m_pSubmitBlock.GetPointer(), m_pSubmitBlock->GetThisTypeInfo());
          submit_block_writer.Flush();
@@ -195,8 +195,8 @@ Subject: Spelling fixes
  
          out_sObjectOpeningString = seq_sub_header_strm.str();
          out_sObjectClosingString = "} }" + out_sObjectClosingString;
---- ncbi-blastplus.orig/c++/src/objtools/readers/agp_util.cpp
-+++ ncbi-blastplus/c++/src/objtools/readers/agp_util.cpp
+--- a/c++/src/objtools/readers/agp_util.cpp
++++ b/c++/src/objtools/readers/agp_util.cpp
 @@ -67,7 +67,7 @@
  
      "object_beg != previous object_end + 1",
@@ -206,7 +206,7 @@ Subject: Spelling fixes
      "in \"Scaffold from component\" file, invalid scaffold-breaking gap",
      "in \"Chromosome from scaffold\" file, invalid \"within-scaffold\" gap",
  
-@@ -88,7 +88,7 @@
+@@ -87,7 +87,7 @@
      // Content Warnings
      "gap at the end of object (OK if X is the circular chromosome/plasmid)",
      "gap at the beginning of object ",
@@ -215,9 +215,9 @@ Subject: Spelling fixes
          "a scaffold, two non scaffold-breaking gaps, ...)",
      "no components in object",
      "the span overlaps a previous span for this component",
---- ncbi-blastplus.orig/c++/src/objtools/readers/agp_validate_reader.cpp
-+++ ncbi-blastplus/c++/src/objtools/readers/agp_validate_reader.cpp
-@@ -295,7 +295,7 @@
+--- a/c++/src/objtools/readers/agp_validate_reader.cpp
++++ b/c++/src/objtools/readers/agp_validate_reader.cpp
+@@ -300,7 +300,7 @@
        int prev_comp_file=spans.rbegin()->file_num;
        int prev_comp_line=spans.rbegin()->line_num;
        if(prev_comp_file < m_last_scaf_start_file || prev_comp_line < m_last_scaf_start_line) {
@@ -226,8 +226,8 @@ Subject: Spelling fixes
          if(prev_comp_file && prev_comp_file!=m_AgpErr->GetFileNum()) {
            sameComId_otherScaf += m_AgpErr->GetFile(prev_comp_file);
            sameComId_otherScaf += ":";
---- ncbi-blastplus.orig/c++/src/util/compress/api/compress.cpp
-+++ ncbi-blastplus/c++/src/util/compress/api/compress.cpp
+--- a/c++/src/util/compress/api/compress.cpp
++++ b/c++/src/util/compress/api/compress.cpp
 @@ -160,7 +160,7 @@
      while ( (nread = src_file.Read(buf.get(), buf_size)) > 0 ) {
          os.write(buf.get(), nread);

diff --git a/debian/patches/suppress_gnutls_version_check b/debian/patches/suppress_gnutls_version_check
index c6f7dc253ae3e28fc7ab8e3ec226a21a4a7aae30..25ab480b796e8e2d74fb8b2939293e74e3f13526 100644 (file)
--- a/debian/patches/suppress_gnutls_version_check
+++ b/debian/patches/suppress_gnutls_version_check
@@ -7,7 +7,7 @@ Description: suppress gnutls version check
 
 --- a/c++/src/connect/ncbi_gnutls.c
 +++ b/c++/src/connect/ncbi_gnutls.c
-@@ -660,6 +660,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
+@@ -665,6 +665,7 @@
  
      assert(!s_GnuTlsCredAnon);
  
@@ -15,7 +15,7 @@ Description: suppress gnutls version check
      version = gnutls_check_version(0);
      if (strcasecmp(GNUTLS_VERSION, version) != 0) {
          CORE_LOGF(eLOG_Critical,
-@@ -667,6 +668,7 @@ static EIO_Status s_GnuTlsInit(FSSLPull
+@@ -672,6 +673,7 @@
                     GNUTLS_VERSION, version));
          assert(0);
      }

diff --git a/debian/patches/system_mbedtls_only b/debian/patches/system_mbedtls_only
index 61c24e5a057d38bf244e33f6b1e441f07298ab42..68cccaebde1bce60a652fcc3984e354f7988d038 100644 (file)
--- a/debian/patches/system_mbedtls_only
+++ b/debian/patches/system_mbedtls_only
@@ -11,6 +11,6 @@ Subject: Omit convenience mbed TLS copy
 +SRC_TLS  = ncbi_gnutls ncbi_mbedtls ncbi_tls
 +
 +SRC_MBEDTLS_UNUSED = \
-          mbedtls/aes mbedtls/aesni mbedtls/arc4 mbedtls/asn1parse \
+            mbedtls/aes mbedtls/aesni mbedtls/arc4 mbedtls/asn1parse \
             mbedtls/asn1write mbedtls/base64 mbedtls/bignum mbedtls/blowfish \
             mbedtls/camellia mbedtls/ccm mbedtls/cipher mbedtls/cipher_wrap \

diff --git a/debian/patches/use_pie_for_apps b/debian/patches/use_pie_for_apps
index 89bc7d7df3a6ee5457c033ef8d635b04136fc5f7..ab72b526f2d82a7a3868f316f333157a34e441a8 100644 (file)
--- a/debian/patches/use_pie_for_apps
+++ b/debian/patches/use_pie_for_apps
@@ -7,10 +7,10 @@ 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 @@
- 
+@@ -25,8 +25,8 @@
  ### C/C++ source file compilation setup
  
+ CPPFLAGS     += -DNCBI_APP_BUILT_AS=$(APP)
 -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)
@@ -18,7 +18,7 @@ Last-Update: 2012-05-10
  SOURCES      = @UNIX_SRC@ $(SRC)
  
  ### Standard application build rules
-@@ -56,7 +56,7 @@
+@@ -57,7 +57,7 @@
  include $(builddir)/Makefile.$(Rules)
  
  CMD_BASE = $(LINK_WRAPPER) $(LINK)