From ef898b4071b9b52c91692c9a434937c1c73041ca Mon Sep 17 00:00:00 2001 From: "Aaron M. Ucko" Date: Sat, 25 Apr 2020 22:13:32 -0400 Subject: [PATCH] debian/patches: Formally refresh for 2.10.0 release. A few files needed straightforward manual intervention. --- debian/changelog | 4 +- .../patches/enable_clean_after_failed_compile | 2 +- debian/patches/fix_lib_deps | 39 +++-- debian/patches/fix_unit_tests | 2 +- debian/patches/hurd_fixes | 4 +- debian/patches/legacy_rename_rpsblast | 2 +- debian/patches/no_multiarch_rpath | 4 +- debian/patches/optionally_keep_sequence | 4 +- debian/patches/reprobuild | 136 +++++++++--------- debian/patches/skip_services_unit_test | 2 +- debian/patches/spelling | 84 +++++------ debian/patches/suppress_gnutls_version_check | 4 +- debian/patches/system_mbedtls_only | 2 +- debian/patches/use_pie_for_apps | 6 +- 14 files changed, 146 insertions(+), 149 deletions(-) diff --git a/debian/changelog b/debian/changelog index 2d6ceb4e..2fe51e9a 100644 --- 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 Sat, 25 Apr 2020 21:44:42 -0400 + -- Aaron M. Ucko 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 6222bf3e..179768ed 100644 --- 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=$DYLD_LIBRARY_PATH" fi diff --git a/debian/patches/fix_lib_deps b/debian/patches/fix_lib_deps index 89455233..dc035f89 100644 --- a/debian/patches/fix_lib_deps +++ b/debian/patches/fix_lib_deps @@ -45,7 +45,7 @@ Last-Update: 2016-12-05 +DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi + - ASN_DEP = seqset + ASN_DEP = seqset submit WATCHERS = morgulis --- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app @@ -94,7 +94,7 @@ Last-Update: 2016-12-05 seqmasks_io --- a/c++/src/build-system/library_relations.txt +++ b/c++/src/build-system/library_relations.txt -@@ -1511,7 +1511,7 @@ +@@ -1543,7 +1543,7 @@ xbiosample_util needs valid xbiosample_util needs xmlwrapp xbiosample_util needs xobjutil @@ -359,16 +359,17 @@ Last-Update: 2016-12-05 WATCHERS = camacho --- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib +++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib -@@ -12,6 +12,9 @@ +@@ -12,6 +12,10 @@ # Dependencies for shared library - DLL_LIB = ncbi_xreader$(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 e20a43c4..d75b78b1 100644 --- a/debian/patches/fix_unit_tests +++ b/debian/patches/fix_unit_tests @@ -5,7 +5,7 @@ Author: Olivier Sallou 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 fd29c84a..adb1800d 100644 --- a/debian/patches/hurd_fixes +++ b/debian/patches/hurd_fixes @@ -9,7 +9,7 @@ Author: Aaron M. Ucko 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 5b239613..f40204b1 100644 --- 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 8b11eb4a..de626df0 100644 --- a/debian/patches/no_multiarch_rpath +++ b/debian/patches/no_multiarch_rpath @@ -10,7 +10,7 @@ Author: Aaron M. Ucko 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 2c1c0a85..311b06de 100644 --- 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 & 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 d485fdeb..0e659e98 100644 --- a/debian/patches/reprobuild +++ b/debian/patches/reprobuild @@ -1,8 +1,8 @@ Author: Michael R. Crusoe 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 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 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 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 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 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("< 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\ts\tBotanic Garden Meise\t\t\t", @@ -139,10 +139,10 @@ Subject: Spelling fixes +"BR\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 s Botanic Garden Meise @@ -150,9 +150,9 @@ Subject: Spelling fixes +BR 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 c6f7dc25..25ab480b 100644 --- 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 61c24e5a..68cccaeb 100644 --- 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 89bc7d7d..ab72b526 100644 --- a/debian/patches/use_pie_for_apps +++ b/debian/patches/use_pie_for_apps @@ -7,10 +7,10 @@ Author: Aaron M. Ucko 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) -- 2.30.2